Single-Cell Profiling Reveals Immune Aberrations in Progressive Idiopathic Pulmonary Fibrosis
American Journal of Respiratory And Critical Care Medicine 210(4):484-496 [2024 Aug 15]
38 peripheral blood mononuclear cells (PBMCs) samples from 25 patients with IPF (12 patients with progressive disease and 13 patients with stable disease) and 13 matched control subjects were profiled using 10x Genomics Chromium 5’ single-cell RNA sequencing (scRNA-seq).
Immune responses in checkpoint myocarditis across heart, blood and tumour
Nature 636(8041):215-223 [2024 Dec]
Heart samples were taken through endomyocardial biopsies or autopsy from patients receiving an ICI for cancer. Additionally, patients had PBMCs collected at multiple timepoints through their course of treatment. Samples were then used for scRNA-seq.
Nature Immunology 25(11):2152-2165 [2024 Nov]
To be supplemented.
Nature Communications 15(1):8894 [2024 Oct 15]
overall_design too long too uplode
Single-cell CAR T atlas reveals type 2 function in 8-year leukaemia remission
Nature 634(8034):702-711 [2024 Oct]
Combining scRNA-seq and CITE-seq, we performed multi-omics profiling of both basal unstimulated CAR T cells and the activated CAR+ cells.
Single-cell multi-omics map of human fetal blood in Down syndrome
Nature 634(8032):104-112 [2024 Oct]
Here, we performed single cell RNA sequencing (scRNA-seq) of human fetal liver and bone marrow tissue samples from 15 trisomy 21 (Ts21) and 3 healthy foetuses (median age 14 post-conception weeks). The data set is composed of approximately 1.1 million cells from three different populations: CD235- (niche and haematopoietic cells depleted of erythrocytes), CD34+/Lin- (haematopoietic progenitors), and CD45+ (all haematopoietic cells).
Multi-omics Reveals Immune Response and Metabolic Profiles during High-Altitude Mountaineering
Single-cell RNA sequencing reveals immune responses of PBMCs during High-Altitude Mountaineering.
Immunity 56(12):2836-2854.e9 [2023 Dec]
Using single-cell RNA/TCR/BCR-seq, researchers profiled 2 million cells from 166 healthy individuals (ages 25-85), identifying 55 blood immune subpopulations, with 12 changing with age. Key findings include the accumulation of GZMK+CD8+ and HLA-DR+CD4+ T cells, and an age-associated shift towards IL-4-expressing memory T cell subpopulations.
Nature Medicine 26(4):618-629 [2020 Apr]
Researchers identified baseline blood transcriptional signatures that predict antibody responses to influenza and yellow fever vaccinations. These signatures, linked to a plasmacytoid dendritic cell–type I IFN–T/B lymphocyte network, also correlate with disease activity in systemic lupus erythematosus. Their findings suggest modulating these immune states could improve vaccine responses and mitigate autoimmune activity.
An immune-cell signature of bacterial sepsis
Nature Medicine 26(3):333-340 [2020 Mar]
Researchers used single-cell RNA-sequencing to profile blood from sepsis patients, identifying 16 immune cell states, including a unique CD14+ monocyte state expanded in sepsis. This monocyte state was validated across 18 cohorts and associated with distinct epigenomic and functional phenotypes. Their findings offer insights into immune dysregulation in bacterial sepsis and propose a model for its induction from bone marrow.
NA
Human bone marrow assessment by single-cell RNA sequencing, mass cytometry, and flow cytometry
To be supplemented.
Single-cell RNA-sequencing analysis of NK cells from bone marrow of six healthy donors, blood of two healthy donors and a blood sample from a donor with GATA2T354M mutation
Single cell RNA sequencing analysis of 3 different CD8 T cell populations present in a vaccine recpient 14 days post vaccine administration
Discovery of specialized NK cell populations infiltrating human melanoma metastases
Matching samples were collected from blood and tumor-infiltrating NK cells in 5 patients with melanoma metastasis.
Characterization of cell fate probabilities in single-cell data with Palantir
NA
Landscape and Dynamics of Single Immune Cells in Hepatocellular Carcinoma
NA
CIMA analyzed molecular variations and regulatory mechanisms in human peripheral blood by performing scRNA-seq and scATAC-seq on immune cells, measuring plasma lipidomics and metabolomics, and obtaining individual genotypes through WGS.
Immune system adaptation during gender-affirming testosterone treatment
Nature 633(8028):155-164 [2024 Sep]
To be supplemented.
Fc-engineered antibodies promote neutrophil-dependent control of Mycobacterium tuberculosis
Nature Microbiology 9(9):2369-2382 [2024 Sep]
Whole-blood Mtb infection with antibody was placed through a 10X Genomics NextGEM Single Cell 3’ kit and processed using CellRanger v6.1.2 to generate gene expression count matrices and deMULTIplex to generate LMO barcode count matrices.
Nature Immunology 25(9):1731-1741 [2024 Sep]
Examination of 56 single-cell RNA-seq samples from PBMC and lymph node taken at multiple time points post-vaccination across multiple participants. Peripheral blood and/or drainging lymph node immune cells were across time points for infected or vaccinated individuals underwent single-cell RNA and T cell receptor sequencing to analyze the adaptive immune response.
Cranioencephalic functional lymphoid units in glioblastoma
Nature Medicine 30(10):2947-2956 [2024 Oct]
overall_design too long too uplode
Blood Advances 8(14):3665-3678 [2024 Jul 23]
Single Cell Sequencing of Human PBMCs in Clonal Hematopoeisis of Indeterminant Potential
Nature Communications 15(1):5949 [2024 Jul 15]
The single cell sequencing of PBMC of eight bullous pemphigoid patients and blister of four bullous pemphigoid patients. The single cell sequencing of PBMC in five healthy controls.
Single-cell RNA sequencing (scRNA-seq.) was performed on PBMCs from controls (n=3) and HF patients (n=8).
Frontiers in Endocrinology 15:1397661 [2024 Jul 12]
PBMCs from Type 2 diabietes patients were subjected to scRNA-seq, scBCR-seq and scTCR-seq with 10x Genomics.
Blood 144(1):46-60 [2024 Jul 4]
Examination of scTCR-Seq and scRNA-Seq of T cells in patients receiving CAR-T Therapy
Single-cell RNA-seq libraries were generated for two triple-negative breast cancer samples, including pre- and post- chemotherapy treatment samples, using the 10X Genomics Chromium platform and sequenced on the Illumina NovaSeq 6000.
Human SARS-CoV-2 challenge uncovers local and systemic response dynamics
Nature 631(8019):189-198 [2024 Jul]
36 healthy volunteers aged 18-29 years, with no evidence of previous infection or vaccination, were inoculated with SARS-CoV-2 virus and quarantined for 14 days. Blood samples for RNA sequencing were collected into PAXgene tubes before virus challenge, 6 hours after challenge, daily thereafter for 14 days and on day 28. Libraries were sequenced on the Illumina NovaSeq 6000 platform using NovaSeq 6000 S4 Reagent Kits (200 cycles).
Advanced Science 11(30):e2308393 [2024 Aug]
To be supplemented.
The Space Omics and Medical Atlas (SOMA) and international astronaut biobank
Nature 632(8027):1145-1154 [2024 Aug]
To be supplemented.
Urine scRNAseq reveals new insights into the bladder tumor immune microenvironment
Journal of Experimental Medicine 221(8):e20240045 [2024 Aug 5]
We spun down urine-derived cells from urine, isolated PBMC using Ficoll-based separation, and dissociated cells from tumor. We analyzed each specimen individually using scRNAseq.
Multiomic analyses uncover immunological signatures in acute and chronic coronary syndromes
Nature Medicine 30(6):1696-1710 [2024 Jun]
To be supplemented.
Single-Cell Dissection of the Immune Response After Acute Myocardial Infarction
Circulation-genomic And Precision Medicine 17(3):e004374 [2024 Jun]
To be supplemented.
Coordinated immune dysregulation in juvenile dermatomyositis revealed by single-cell genomics
Jci Insight 9(12):e176963 [2024 May 14]
To be supplemented.
Communications Biology 7(1):524 2024 [May 3]
To be supplemented.
Epigenetic dysregulation in Alzheimer's disease peripheral immunity
Neuron 112(8):1235-1248.e5 [2024 Apr 17]
Peripheral blood mononuclear cells from healthy control and Alzheimer's disease patients, matched for age, sex, and APOE genotype. Samples were thawed, FACS sorted for live cells, and profiled using scRNA-seq and scV(D)J-seq (BCR and TCR). Peripheral blood mononuclear cells from healthy control and Alzheimer's disease patients, matched for age, sex, and APOE genotype. Samples were thawed, FACS sorted for live cells, lysed to isolate nuclei, and profiled using scATAC-seq.
HIV-1–infected T cell clones are shared across cerebrospinal fluid and blood during ART
Jci Insight 9(7):e176208 [2024 Apr 8]
overall_design too long too uplode
Comparative Analysis of Single-Cell RNA Sequencing Methods with and without Sample Multiplexing
International Journal of Molecular Sciences
overall_design too long too uplode
Genome Medicine 16(1):45 [2024 Mar 27]
Type 1 diabetes mellitus (T1DM) is a prototypic endocrine autoimmune disease resulting from an immune-mediated destruction of pancreatic insulin-secreting beta-cells. A comprehensive immune cell phenotype evaluation in T1DM has not been performed thus far at the single. In this cross-sectional analysis, we generated a single-cell transcriptomic dataset of peripheral blood mononuclear cells (PBMCs) from 46 manifest T1DM (Stage 3) cases and 31 matched controls.
The Innovation 5(3):100599 [2024 Mar 1]
Reestablishment of immune homeostasis under the tacrolimus-based immunosuppressive treatment after liver transplantation (LT) is essential for long-term graft survival. Herein, we mapped the dynamic immune cell compositions and functions alteration of the peripheral immune microenvironment at single-cell resolution in patients with and without acute cellular rejection (ACR) in the scenario with treatment of tacrolimus based immunosuppressive regimen after LT.
The gene regulatory basis of bystander activation in CD8+ T cells
CD8+ cells were magnetically enriched by positive selection (anti-human CD8 microbeads; Miltenyi Biotech) from rested PBMCs or CBMCs. Isolated cells were then treated with IL-2 with or without co-treatment with IL-12 and IL-18 and analyzed using scRNAseq.
Annals of The Rheumatic Diseases 83(3):300-311 [2024 Feb 15]
335 whole blood samples from 84 RA, SLE, and healthy controls before pregnancy, at each trimester, 6 weeks, 6 months, and 12 months postpartum were analysed. We ran bulk and single cell RNA analyses and then combined these for cell-type estimation, validated by flow cytometry. These results were then used in a cell-type adjusted analysis for an improved resolution of unrecognized gene expression changes associated with RA and SLE pregnancies.
Single-Cell Sequencing Reveals Functional Alterations in Tuberculosis
Advanced Science 11(11):e2305592 [2024 Mar]
To be supplemented.
Single-Cell RNA sequencing data of 28774 circulating immune cells from 8 pregnant women diagnosed with preeclampsia (PE group, included one early-onset PE and seven late-onset PE) and 15 normal pregnant women (NP group)
Current Issues in Molecular Biology
To be supplemented.
Biorxiv : The Preprint Server For Biology [Preprint] 2023.12.26.573390 [2023 Dec 27]
To be supplemented.
Science Translational Medicine 15(725):eadg3451 [2023 Dec 6]
To be supplemented.
Iscience 26(12):108572 [2023 Nov 24]
We profiled crculating immune cells from five adults with acute COVID-19 infection and nine healthy adults, seven of whom received theBNT162b2 vaccine. For three of the vaccine recipients, samples were also collected before and after receiving a booster. Samples were taken at multiple time points, resulting in a total of 42 post-vaccination and 9 post-infection samples
Advanced Science (Weinheim, Baden-Wurttemberg, Germany) 10(36):e2303913 [2023 Dec]
We performed single-cell RNA sequencing on patients with NKTCL and obtained 137,304 cells from 10 tumor-blood pairs. Raw data will be uploaded to China Genomic Sequence Archive (GSA), according to the Regulations on the Management of Human Genetic Resources in China, and we will provide the accession number once the paper is accepted.
Determining a multimodal aging clock in a cohort of Chinese women
Medicine 2.0 4(11):825-848.e13 [2023 Nov 10]
Single-cell RNA-seq for peripheral blood monocyte cells of 3 young and 3 old healthy females.
Nature Communications 14(1):7387 [2023 Nov 15]
Peripheral blood mononuclear cells (PBMCs) from 6 individuals (age 6-24) with P. falciparum infection and 2 healthy adult endemic controls (ages 20 and 27) were collected before drug treatment (day 0) and at 7 and 28 days after treatment. PBMCs were isolated by Fluorescence-activated cell sorting (FACS) according to the presence or absence of XX signal, and analysed using droplet-based scRNAseq.”
Arteriosclerosis, Thrombosis, and Vascular Biology 43(12):2312-2332 [2023 Oct]
To be supplemented.
Iscience 26(10):107943 [2023 Sep 16]
Primary Sjogren's syndrome (pSS) is a heterogeneous systemic autoimmune disease characterized by lymphocytic infiltration and exocrine, especially salivary gland (SG), dysfunction. Here, we investigated cellular and immune heterogeneity in pSS by single-cell RNA sequencing of the SG in 11 pSS patients and 5 non-SS controls.
Single-cell chromatin accessibility and transcriptomic characterization of Behcet's disease
Communications Biology 6(1):1048 [2023 Oct 17]
Single-cell analysis of Behcet disease
Nature Immunology 24(11):1947-1959 [2023 Nov]
scRNAseq was performed on 48 samples. In addition, TEA-seq (a novel method for simulaneous single-cell profiling of transcripts, epitopes, and chromatin accessiblity) was performed on 16 of those samples, as well as on 3 control samples (IMM19_435, IMM19_438, and IMM19_445). As part of TEA-seq testing we prepared CITE-seq, scATAC-seq, single-cell and single-nuclei 10x Multiome ATAC + Gene Expression, and TEA-seq libraries from the same PBMC sample in parallel.
Nature Communications 14(1):5789 [2023 Oct 11]
To be supplemented.
Nature Immunology 24(10):1725-1734 [2023 Oct]
To be supplemented.
Tumor-associated monocytes promote mesenchymal transformation through EGFR signaling in glioma
Cell Reports Medicine 4(9):101177 [2023 Sep 19]
The GB or peripheral blood cell suspension was loaded into Chromium microfluidic chips with 3’ (v3) chemistry and barcoded with a 10× Chromium Controller (10X Genomics). RNA from the barcoded cells was subsequently reverse-transcribed and sequencing libraries constructed with reagents from a Chromium Single Cell 3’ (v3) reagent kit (10X Genomics) according to the manufacturer’s recommendations. Sequencing was performed with Illumina (NovaSeq) according to the manufacturer’s recommendations (Illumina).
A pan-cancer single-cell panorama of human natural killer cells
Cell 186(19):4235-4251.e20 [2023 Sep 14]
We generated scRNA-seq data from 47 cancer patients to investigate tumor-infiltrating NK cells across multiple cancer types, including tumor and normal tissue. The raw sequencing data were provided at China Genomic Sequence Archive (GSA): HRA000321.
Clinical Cancer Research 30(17):3919-3936 [2024 Sep 3]
Our study examined the transcriptional dynamics of plasma cells (PCs) from diagnosis through to post-treatment. We collected and sequenced a total of 38 paired bone marrow (BM) samples.
Epigenetic memory of coronavirus infection in innate immune cells and their progenitors
Cell 186(18):3882-3902.e24 [2023 Aug 31]
To discover changes in chromatin post-SARS-CoV-2 infection, ATAC-seq and RNA-seq were performed on CD34+ HSPCs and CD14+ monocytes sorted from PBMC of healthy, non-COVID-19 post-ICU pateitns, mild convalescent, and severe convalescent COVID-19 patients.
Cell Reports 42(8):112991 [2023 Aug 29]
This data includes scRNA-seq, scTCR-seq and scBCR-seq of 21 individuals post Covid'19 vaccination. Individuals range from the ages 52 to 75. Samples were genotype multiplexed in an overlapping mixture design, pooled, and sequenced on 16 lanes (10X, 5' GEM).
Multimodal Single-Cell Sequencing of B Cells in Primary Sjögren's Syndrome
Arthritis & Rheumatology 76(2):255-267 [2024 Feb]
B cells from the peripheral blood from 24 patients with primary Sjögren's syndrome (pSS), from three patient groups based on auto-antibody stratification (SSA-: pSS patients where auto-antibodies to SSA or SSB were not detected (n = 6). SSA+: pSS patients where SSA but not SSB auto-antibodies were detected (n = 8). SSAB: pSS patients where SSA and SSB auto-antibodies were detected (n = 10)), and B cells from the peripheral blood of four healthy controls.
Cell Reports Medicine 4(8):101158 [2023 Aug 15]
Single cell gene expression profiles for 22 bone marrow samples from patients treated with CAR T-cell product, chemotherapy, and healthy donors. Due to patient privacy concerns the raw data is available through the European Genome-Phenome Archive.
Evolution of immune and stromal cell states and ecotypes during gastric adenocarcinoma progression
Cancer Cell 41(8):1407-1426.e9 [2023 Aug 14]
overall_design too long too uplode
Dissecting human population variation in single-cell responses to SARS-CoV-2
Nature 621(7977):120-128 [2023 Sep]
Transcriptional profiles at the single cell level (scRNA-seq) of human PBMCs stimulated for 6h with Influenza A and SARS-CoV-2 viruses in 222 healthy, SARS-CoV-2-naïve individuals of African, European, and East Asian ancestries. For 8 individuals, data is also available at T0 and 24h post stimulation (experimental run 1). For 16 samples (run 16), extracellular protein markers were labelled with the CITE-seq technology in addition to scRNA-seq.
Single-cell transcriptomics identifies prothymosin α restriction of HIV-1 in vivo
Science Translational Medicine 15(707):eadg0873 [2023 Aug 2]
Single cell gene expression profiles of immune cells during acute HIV-1 infection
Frontiers in Immunology 14:1091237 [2023 Aug 1]
Single-cell RNA sequencing was performed on peripheral blood mononuclear cells (PBMC) from 6 volunteers without any disease, including 3 volunteers with high immune response (HR) to hepatitis B vaccine (HBsAb >1000 mIU /ml) and 3 volunteers with no immune response (NR) to hepatitis B vaccine (HBsAb<10mIU/ml). HBsAb testing and sample collection were performed 1 month after hepatitis B vaccination according to the 0 , 1 , and 6 month schedule.
Mapping disease regulatory circuits at cell-type resolution from single-cell multiomics data
Nature Computational Science 3(7):644-657 [2023 Jul]
scATAC sequencing of PBMCs from 10 samples with MRSAs, 11 samples with MSSAs and 23 healthy controls. scRNA sequencing of PBMCs from 10 samples with MRSAs, 11 samples with MSSAs and 23 healthy controls. scATAC sequencing of PBMCs from 6 samples with mild SARS-CoV-2 infection and 3 healthy controls
Annals of The Rheumatic Diseases 82(10):1348-1358 [2023 Oct]
Single-cell transcriptional landscape of submandibular glands and peripheral blood mononuclear cells in IgG4-RD patients and controls
A Th1-like CD4(+) T-cell Cluster That Predicts Disease-free Survival in Early-stage Lung Cancer
Cancer Research Communications
Investigating how differences in gene expression and TCR repatoires of T cells in PBMCs and TILs affect the postoperative disease-free survival. Please note that the processed data generated from both scRNAseq and Feature Barcoding(ADT) samples are linked to the corresponding scRNA-seq sample records.
Genome Medicine 15(1):53 [2023 Jul 18]
To be supplemented.
Medicine 2.0 4(7):432-456.e6 [2023 Jul 14]
PBMC from 11 post-OHCA patients and 3 healthy subjects were used for 10X single-cell RNA-sequencing. Sorted PBMC were processed for bulk RNA sequencing.
Scientific Data 10(1):433 [2023 Jul 6]
We performed single-cell gene expression profiling on 6 different samples for resting, stimulated, fresh and frozen PBMC samples.
Science Advances 9(26):eabq7599 [2023 Jun 28]
All volunteers were evaluated as generally healthy at the time of blood collection based on evaluation of their medical history and assessment of their vital signs. In our present study, 17 healthy volunteers were enrolled in the single-cell RNA sequencing.
Immunity 56(6):1410-1428.e8 [2023 Jun]
Here, we systematically profiled clinical phenomes, transcriptomes, proteomes, metabolomes, and immune repertoire of blood cells or plasma in over 1000 specimens from SARS-CoV-2 Omicron patients across multiple disease phases.
Emerging microbes & infections 12(1):e2187245 [2023 May]
this study intends to characterize cellular and molecular variabilities of peripheral immune cells in healthy inactivated SARS-CoV-2 vaccine recipients by single-cell RNA sequencing
A single-cell view on host immune transcriptional response to in vivo BCG-induced trained immunity
Cell Reports 42(5):112487 [2023 May 30]
We have paired 39 individuals in 4 conditions: T0_RPMI (baseline, before BCG and without LPS); T0_LPS (before BCG and with LPS); T3m_RPMI (3 months after BCG, without LPS); T3m_LPS (3 months after BCG, with LPS).
Nature Immunology 24(5):767-779 [2023 May]
overall_design too long too uplode
Nature Genetics 55(5):753-767 [2023 Apr]
Researchers analyzed single-cell transcriptomes and B/T cell receptors from 73 COVID-19 patients and 75 healthy controls, identifying reduced nonclassical monocytes (ncMono) and decreased transitions from classical monocytes in COVID-19. Severe cases showed lower CXCL10 expression and reduced cellular interactions involving ncMono. Clonal B cell expansions were observed in plasmablasts, and genetic risk variants, including at the IFNAR2 locus, were linked to monocyte-specific effects. This study highlights
Nature Biotechnology 42(1):40-51 [2024 Jan]
To test the impact of nonsense-mediated decay (NMD) on BCR/TCR RNA sequences, we treated peripheral blood mononuclear cells (PBMCs) with cycloheximide to block NMD and analyzed treated and untreated cells by scRNA-seq with scVDJ-seq.
Single-cell transcriptomics to characterize the monocytes characters in the peripheral blood mononuclear cells (PBMCs) of 7 High-Altitude pulmonary Hypertension cases,5controls and 6 pulmonary Hypertension cases.
To be supplemented.
Journal Of Infection 86(5):421-438 [2023 Mar]
To be supplemented.
Spatial multiomics map of trophoblast development in early pregnancy
Nature 616(7955):143-151 [2023 Apr]
To be supplemented.
Single-cell expression profiling of the liver metastases of CRC in treatment patients and untreated patients.
Experimental & Molecular Medicine 55(3):653-664 [2023 Mar]
overall design too long too uplode
Science Immunology 8(81):eabn6429 [2023 Mar 17]
To be supplemented.
Jci Insight 8(8):e167490 [2023 Apr 24]
This project mainly focous on the change of CD8+ T cells in pSS patients.
Dynamic blood single-cell immune responses in patients with COVID-19
Signal Transduction and Targeted Therapy 6(1):110 [2023 Mar]
To be supplemented.
Science Advances 9(8):eade5090 [2023 Feb 24]
To be supplemented.
We unveiled the characteristics of pTh17s, which are polyfunctional IL-17A and IFN-γ-producing memory CD4+ T cells. scRNA-seq and cytometry analysis found that the co-expression of OX40 and GITR is increased in pTh17 cells. We performed transcriptome and cytometric analysis to understand pTh17.
Single-Cell Discovery and Multiomic Characterization of Therapeutic Targets in Multiple Myeloma
Cancer Research 83(8):1214-1233 [2023 Apr 14]
We used scRNA-seq to perform an unbiased search for genes with specific expression in plasma cells and/or B cells (relative to other detected cell types) on 53 bone marrow mononuclear cell (BMMC) samples taken from 41 patients.
European Respiratory Journa l61(2):2201465 [2023 Feb 9]
overall_design too long too uplode
Cell Genomics 3(2):100232 [2023 Feb 8]
Single-cell RNA-seq, single-cell ATAC-seq, and genotypes used in the analysis for the study "Altered and allele-specific open chromatin landscape reveal epigenetic and genetic regulators of innate immunity in COVID-19". The RNA-seq and ATAC-seq are raw data in FASTQ format while the genotypes are in the VCF format which was filtered and imputed (more details are available in the main text of the study).
Multimodal single‑cell analyses of peripheral blood mononuclear cells of COVID‑19 patients in Japan
To be supplemented.
Innovation (Cambridge (Mass.)),2023 Jan 30;4(1):100359
To be supplemented.
Jci Insight 8(2):e163859 [2023 Jan 24]
To be supplemented.
Cell Reports Medicine 4(1):100868 [2023 Jan 17]
T cells were isolated from PBMCs harvested from cancer patients before and after immunoptherapy.
Influenza vaccination reveals sex dimorphic imprints of prior mild COVID-19
Nature 614(7949):752-761 [2023 Feb]
Peripheral blood mononuclear cells from days 0, 1, and 28 among a selected group of 24 COVID19 patients and 16 healthy controls were profiled using multi-modal single cell CITE-seq, including surface protein staining (Biolegend TotalSeq-C lyophilized panel) and mRNA, on the 10x Genomics Chromium system. Samples from different donors were pooled and different timepoints from the same donor were pooled separately so that each pool contains only one timepoint from one donor.
Nature Cancer 4(1):27-42 [2023 Jan]
Single-cell RNAseq, CITEseq and TCRseq
Iscience 25(12):105509 [2022 Nov 4]
We collected blood from 3 pSS patients and 3 HCs recruited at the Rheumatology Department of Chongqing Traditional Chinese Medicine Hospital between October 2020 and March 2021. PBMCs were isolated from three patients with pSS and three healthy controls, and then a 10x Genomics Chromium Single Cell 5 ' Gene Expression workflow was used to perform single-cell RNA sequencing.
Mapping single-cell transcriptomes in the intra-tumoral and associated territories of kidney cancer
Cancer Cell 40(12):1583-1599.e10 [2022 Dec 12]
The dataset comprises of 5' single cell RNA sequencing with TCR enrichment with 10x Genomics' Chromium technology of multiregional biopsies of human renal cell carcinomas. Biopsies from different tumour regions, the tumour-normal interface, normal kidney, normal adrenal, metastatic regions, peri-nephric fat, and peripheral blood were sequenced from 12 patients with kidney tumours.
Frontiers in Immunology 2022 Dec 2:13:1034159
PBMCs were isolated from Healthy (n = 4), COVID-19 (n = 16) and recovered (n = 13) individuals, using BD vaccutainers cell prepataion tubes. PBMCs were isolated as per manufacturer's recommendation, and stored for future use. Samples were multiplexed using BD single cell multiplexing kit (Human), followed by tagging with a pool of 40 oligo-attached antibody for surface markers (Ab-Seq).
Nature Communications 13(1):6894 [2022 Nov 12]
For the single cell transcriptome analysis, PBMCs isolated from whole blood samples were used. Analysis compares the effect of vaccination among two groups classified as vaccine responders ( R ) and vaccine non responders (NR) after 7 days post vaccination. Each group is represented by three donors ( NR: I-0845, I-4236, I-4964; R: I-4229, I-5127,I-5402 )
Immune cell profiling of preeclamptic pregnant and postpartum women by single-cell RNA sequencing
International Reviews of Immunology 43(1):1-12 [2024]
Single-cell RNA sequencing of 80,429 cells in PE patients and health controls, including T cells, B cells, natural killer (NK) cells, myeloid cells in peripheral blood mononuclear cells to characterize the immune cell subgroups at the pregnant and postpartum stages of PE.
Cell Reports 41(6):111606 [2022 Nov 8]
Chromatin accessibility and single-cell transcriptome reveal novel subsets of CD4+ T cell associated with therapeutic process in systemic lupus erythematosus patients
Nature Communications 13(1):6458 [2022 Oct]
We performed single cell RNA-seq (scRNA-seq) on 4 healthy donors, 5 IIM disease controls, 7 active MDA5+ DM patients, 3 paired MDA5+ DM patients in remission and 1 end-stage MDA5+ DM patient who underwent lung transplantation. For scRNA-seq, after stringent computational quality control, 111,200 high-quality B and T cells from peripheral blood were obtained. This study reveals key immune-pathogenic features of MDA5+ DM and provides a potential basis for future tailored therapies.
Clonal expansion and epigenetic inheritance of long-lasting NK cell memory
Nature Immunology 23(11):1551-1563 [2022 Nov]
scATACseq with detection of surface proteins and mitochondrial DNA (ASAP-seq/mtscATAC-seq) of ex vivo isolated human Natural Killer cells. scATACseq with detection of surface proteins (ASAP-seq) of in vitro stimulated (via NKG2C and/or IL-12+IL-18) human Natural Killer cells. scRNA-seq with detection of surface proteins (CITE-seq) of ex vivo isolated human Natural Killer cells
Mostly natural sequencing-by-synthesis for scRNA-seq using Ultima sequencing
Nature Biotechnology 41(2):204-211 [2023 Feb]
We generated and analysed single cell RNA-seq (10x Chromium) data for 4 samples. 1) PBMC sample with 3' technology, 2) PBMC sample (same as 1) with 5' single cell technology, 3) a mixture of PBMCs from 8 individuals with 5' technology, and 4) a mixture of 8 Perturb-seq samples (mixed using cell hashing) with 3' technology. For each we sequenced with both Illumina and Ultima sequencing.
To be supplemented.
Distinct cellular dynamics associated with response to CAR-T therapy for refractory B cell lymphoma
Nature Medicine 28(9):1848-1859 [2022 Sep]
Single-cell RNA sequencing of PBMCs and infusion products from 32 patients treated with CD19 CAR-T therapy. NOTE FROM SUBMITTER: Raw sequencing data will be available at controlled access, dbGAP.
Npj Precision Oncology 6(1):58 [2022 Aug 18]
Five patients diagnosed with cholangiocarcinoma in the Eastern Hepatobiliary Surgery Hospital were incorporated into the current study, including two intrahepatic cholangiocarcinoma (iCCA), two gallbladder carcinoma (GBC) and one dCCA patients. Of note, none of the patients have undergone any preoperative treatments prior to tumor resection. Meanwhile, peripheral blood samples were collected prior to surgical procedures using anticoagulant tubes.
To be supplemented.
Journal of Immunology 209(2):238-249 [2022 Jul 15]
We used 10X single-cell RNA sequencing technology to sequence the peripheral blood mononuclear cells (PBMC) of 6 patients with Primary Sjogren's syndrome and 6 healthy controls, and analyzed the single-cell expression map of patients with Primary Sjogren's syndrome.
Nature Immunology 23(8):1273-1283 [2022 Aug]
8 patient PBMCs (4 with high IFN-I response capacity (IRC) and 4 with low IRC) and 2 healthy donor PBMCs were sequenced through multiome (scRNA + scATAC) sequencing. Briefly, cryopreseved PBMCs were thawed and 10X multiome seuqencing workflow was performed following DNAse treatment according to the manufacturer's protocol. Processing and sequencing was performed by the Princess Margaret Cancer Center Genomics Core.
Nature Communications 13(1):4046 [2022 Jul 13]
To be supplemented.
Integrated multi-omic characterization of congenital heart disease
Nature 608(7921):181-191 [2022 Aug]
Single nuclei RNA-seq was performed on cardiac tissue from patients and donore, and single cell rna-seq was performed on isolated PBMCs.
Frontiers in Immunology 2022 Jun 21:13:902232
This study includes single-cell RNA and ADT (protein) measurements of PBMCs from 4 treatment-naïve JDM (TN-JDM) subjects at baseline, 2, 4, and 6 months and 4 subjects with inactive disease. Samples were multiplexed across four 10X reactions. Provided in GEO are the filtered RNA and ADT matrices we used for clustering and differential gene expression analysis. We have also included a metadata file with cell annotations and file with UMAP coordinates to re-create our cell clusters.
Single-cell multiomics reveals persistence of HIV-1 in expanded cytotoxic T cell clones
Immunity 55(6):1013-1031.e7 [2022 Jun 14]
overall_design too long too uplode
Biochemical and Biophysical Research Communications 608:14-22 [2022 Jun 11]
PBMC single cell sequencing data from healthy neonatal cord blood and healthy adult
Blood 2022 Jun 9;139(23):3387-3401.
overall_design too long too uplode
Nature Communications 13(1):3267 [2022 Jun]
overall design too long too uplode
Immune disease risk variants regulate gene expression dynamics during CD4+ T cell activation
Nature Genetics 54(6):817-826 [2022 May]
Researchers used single-cell transcriptomics to map genetic effects on gene expression (eQTLs) in 655,349 CD4+ T cells, spanning unstimulated and activated states in 119 individuals. They identified 38 cell clusters and found 6,407 genes whose expression correlated with genetic variation, 35% of which were dynamically regulated during activation. Additionally, 127 genes were linked to immune disease-associated variants, highlighting the importance of context-specific gene regulation in understanding genetic
iScience 25(6):104473 [2022 Jun 17]
scRNA-seq were performed with peripheral blood mononuclear cells (PBMCs) from individuals who had received the 2 doses of ChAdOx1 (N=2), 2 doses of BNT162b2 (N=2), and heterologous ChAdOx1 and BNT162b2 vaccination (N=2).
Cross-tissue immune cell analysis reveals tissue-specific features in humans
Science 376(6594):eabl5197 [2022 May 13]
The goal of this project is to perform a systematic comparison of immune cell lineages across human tissues. To this end, we collected up to 16 tissues from twelve adult deceased organ donors, isolated immune cells and profiled them using single-cell RNA sequencing and VDJ sequencing generating a dataset of around 360,000 cells.
The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans
Science 376(6594):eabl4896 [2022 May 13]
Tabula Sapiens is a single cell transcriptomic atlas of 24 human tissues and organs.
To be supplemented.
Single-cell atlas of peripheral blood mononuclear cells from pregnant women
Clinical and Translational Medicine 12(5):e821 [2022 May]
To be supplemented.
Nature Aging 2(4):348-364 [2022 Apr]
Three cord blood samples, PBMC samples from 3 healthy young, 6 healthy old and 5 frail donors were used for single-cell RNA, TCR and cell surface protein (CCR7, CD45RA, CD4 and CD8) antibody barcoded sequencing to create a single-cell transcriptome and TCR atlas from newborns to frailty.
Immune phenotypic linkage between colorectal cancer and liver metastasis
Cancer Cell 40(4):424-437.e5 [2022 Apr 11]
We performed single-cell RNA sequencing on colorectal cancer patients with liver metastasis and obtained CD45+ cells from 101 samples including blood, mesenteric lymph nodes, matched primary and metastasis tumors and adjacent tissues.
Nature Communications 13(1):1981 [2022 Apr 11]
overall_design too long too uplode
Single-cell RNA sequencing coupled to TCR profiling of large granular lymphocyte leukemia T cells
Nature Communications 13(1):1982 [2022 Apr]
We applied scTCR-seq coupled with scRNA-seq to CD3+ T cells obtained from a relatively large cohort of T-LGLL patients and 7 healthy donors
Single-cell RNA-seq reveals cell type–specific molecular and genetic associations to lupus
Science 376(6589):eabf1970 [2022 Apr 8]
Examination of 1.2 million PBMCs in 162 SLE donors and 99 healthy individuals to find cellular and genetic correlates of SLE.
Single-cell eQTL mapping identifies cell type–specific genetic control of autoimmune disease
Science 376(6589):eabf3041 [2022 Apr 8]
Human PBMC mRNA profiles at single cell resolution
Blood 139(14):2198-2211 [2022 Apr 7]
To be supplemented.
Intensive Single Cell Analysis Reveals Immune Cell Diversity among Healthy Individuals
Life Science Alliance 5(7):e202201398 [2022 Apr 5]
To be supplemented.
Experimental And Molecular Medicine 54(4):483-492 [2022 Apr]
To be supplemented.
Nature Communications 13(1):1779 [2022 Apr 1]
Common variable immunodeficiency (CVID) is the most prevalent primary immunodeficiency. Here the authors perform single cell omics analyses in CVID discordant monozygotic twins and show epigenetic and transcriptional alterations associated with activation in memory B cells.
To be supplemented.
Blood 139(11):1670-1683 [2022 Mar 17]
1 sample: control and memory-like NK cell generated from the same normal donor are hashtagged into the same files
Frontiers in Immunology 13:809414 [2022 Mar 10]
Paired Single-cell RNA sequencing and T-cell receptor sequencing on 5 BPDCN bone marrow samples and 5 healthy controls
Multiple early factors anticipate post-acute COVID-19 sequelae
Cell 185(5):881-895.e20 [2022 Mar 3]
To be supplemented.
A blood atlas of COVID-19 defines hallmarks of disease severity and specificity
Cell 185(5):916-938.e58 [2022 Mar 3]
To be supplemented.
Frontiers in Immunology 13:835760 [2022 Mar 2]
overall_design too long too uplode
Single-cell transcriptomics of blood reveals a natural killer cell subset depletion in tuberculosis
To be supplemented.
Science Immunology 7(68):eabm2508 [2022 Feb]
To be supplemented.
Frontiers in Immunology 13:812514 [2022 Feb]
53 peripheral blood mono-nuclear cell (PBMC) samples including 42 COVID-19 patients derived samples and 11 healthy controls (HCs) derived samples
Nature Medicine 28(5):1050-1062 [2022 May]
To be supplemented.
Cell specific peripheral immune responses predict survival in critical COVID-19 patients
Nature Communications 13(1):882 [2022 Feb]
PBMCs were isolated at the stated days into COVID-19 study enrollment and hospitalizaiton for single-cell RNA sequencing
Journal of Clinical Investigation 132(7):e147719 [2022 Apr 1]
scRNAseq of monocytes from in vitro Trained immunity experiments stimulated by β-glucan (BG), uric acid (UA), muramyl dipeptide (MDP), oxidized low-density lipoprotein (oxLDL), or RPMI-Control, and respective samples restimulated with Lipopolysaccharide (LPS).
Complement activation induces excessive T cell cytotoxicity in severe COVID-19
Cell 185(3):493-512.e25 [2022 Feb 3]
Blood from 19 COVID-19 patients at acute and convalescent (for 13 patients) phases for mild-moderate (9 patients) and severe (10 patients), from 6 healthy controls as well as from 8 patients with flu-like disease and 4 patients with chronic HBV infection was collected and PBMC prepared.
Ebiomedicine 76:103860 [2022 Feb]
We longitudinally single-cell ATAC sequenced circulating mononuclear cells in 4 trauma patients (<4hrs, 24hrs and 72hrs post injury) along with paired healthy controls, total 16 samples.
Frontiers in Immunology 11:594658 [2021 Feb 2]
We applied single cell RNA sequencing (scRNA-seq) to 57, 288 peripheral blood mononuclear cells (PBMCs) from 5 patients with pSS and 5 healthy controls. The immune cell subsets and susceptibility genes involved in the pathogenesis of pSS were analyzed.
Cell Insight 1(1):100005 [2022 Jan 21]
To be supplemented.
Clinical And Translational Medicine
To be supplemented.
overall design too long too uplode
The immune-suppressive landscape in lepromatous leprosy revealed by single-cell RNA sequencing
To be supplemented.
Single cell transcriptomic landscape of diabetic foot ulcers
Nature Communications 13(1):181 [2022 Jan 10]
Single-cell RNA sequencing of foot and forearm skin cells, as well as peripheral blood mononuclear cells (PBMCs), from 10 samples from non-diabetic subjects, and 17 diabetic patients, 11 with, and 6 without DFU.
HLF expression defines the human hematopoietic stem cell state
Blood 138(25):2642-2654 [2021 Dec 23]
Single cell analysis (10X Chromium) to identify blood stem cell specific transcripts. 10X Chromium 3' v2
Single-cell profiling of T and B cell repertoires following SARS-CoV-2 mRNA vaccine
To be supplemented.
Local and systemic responses to SARS-CoV-2 infection in children and adults
Nature 602(7896):321-327[2022 Feb]
Single-cell data gene expression data set (5’Chromium 10X) of healthy paediatric volunteers, and paediatric and adult COVID-19 patients. Gene expression was determined from samples of nasal, tracheal and bronchial brushings and blood (PBMCs). In addition to gene expression, PBMC’s were assayed by CITE-seq. A subset of samples have VDJ sequencing data for T cell receptors (TCR) and B cell receptors (BCR).
overall design too long too uplode
Clinical And Translational Medicine 11(12):e621 [2021 Dec]
To be supplemented.
Nature Communications 2021 Dec 17;12(1):7338
PBL, CD45+ and CD45- samples from 18 treatment naïve patients were analyzed in this study
Cancer Cell 39(12):1578-1593.e8 [2021 Dec]
The mechanism underlying combination therapy of paclitaxel plus atezolizumab in advanced TNBC is poorly understood. Using single-cell RNA-seq and ATAC-seq technologies, we generated transcriptomes and chromatin accessibility profiles of CD45+ immune cells from primary or metastatic tumor tissues and peripheral blood of 22 advanced TNBC patients treated with paclitaxel or its combination with atezolizumab.
To be supplemented.
Single-cell RNA sequencing reveals B cell–related molecular biomarkers for Alzheimer’s disease
Experimental & Molecular Medicine 2021 Dec;53(12):1888-1901
Single-cell RNA sequencing analysis of PBMCs from 4 AD patients (2 at early stage, 2 at late stage) and 2 normal controls was performed to explore the differential cell subpopulations in PBMCs of AD patients.
Signature of long-lived memory CD8+ T cells in acute SARS-CoV-2 infection
Nature 602(7895):148-155 [2022 Feb]
To be supplemented.
Nature Communications 12(1):6960 [2021 Nov 29]
Single cell RNA-seq of tumor cells and bone marrow microenvironment in relapsed/refractory multiple myeloma, **The submitter declares that the raw data were deposited to EGA (EGAS00001004805) due to data protection regulations.**
Clinical And Translational Medicine 2021 Nov;11(11):e582
overall_design too long too uplode
Genetic ancestry effects on the response to viral infection are pervasive but cell type specific
Science 374(6571):1127-1133 [2021 Nov 26]
Multiplexed single-cell RNA expression profiles of control (mock-infected) and influenza A virus (IAV)-infected peripheral blood mononuclear cells (PBMCs) collected from African and European American individuals
Single-cell landscape of peripheral immune responses to fatal SFTS
Cell Reports 37(8):11003 [2021 Nov]
We performed scRNA-seq on 27 PBMC samples from 15 SFTS patients (including four deceased and 11 surviving) and four healthy controls. A cohort study was used to identify the role of peripheral immune responses in SFTS infection. A total of 15 SFTS patients, including 11 with the CT values of RT-qPCR ranging from 25 to 30 and four with the CT values of RT-qPCR less than 25, were prospectively sampled for scRNA-seq and flow cytometry analysis.
Nature immunology 22(12):1577-1589 [2021 Dec]
We have generated high content single-cell proteo-genomic reference maps of human blood and bone marrow that quantitatively link the expression of up to 197 surface markers to cellular identities and biological processes across all major hematopoietic cell types in healthy aging and leukemia.
Differential dynamics of peripheral immune responses to acute SARS-CoV-2 infection in older adults
Nature Aging 1(11):1038-1052 [2021 Nov]
To be supplemented.
Cell Discovery 26;7(1):99 [ 2021 Oct]
Single-cell mRNA sequencing (scRNA-seq) of peripheral blood mononuclear cells (PBMC) before and 28 days after the vaccination.
Untimely TGFβ responses in COVID-19 limit antiviral functions of NK cells
Nature 600(7888):295-301 [2021 Dec]
RNA Sequencing of flow cytometry-sorted peripheral blood NK cells (live CD3-CD14-CD19-CD45+CD56+ lymphocytes) from blood samples longitudinally obtained from 13 severe COVID-19 patients, 11 ambulant COVID-19 patients and 5 healthy controls. For in vitro stimulation, sorted NK cells from healthy donors were cultured in RPMI containing rh-IL12 and rh-IL15 with or without additional rh-TGF-beta. The 10X Genomics platform with the Single Cell 5’ Library & Gel Bead Kit was used for single cell RNA sequencing.
Dynamic transcriptional reprogramming leads to immunotherapeutic vulnerabilities in myeloma
Single cell expression profiles of 9 patients with relapsed/refractory multiple myeloma and two normal donors.
Immunity 54(10):2417-2432.e5 [2021 Oct 12]
To be supplemented.
Resolving the intertwining of inflammation and fibrosis in human heart failure at single-cell level
Basic Research in Cardiology 116(1):55 [2021 Oct 3]
we performed single cell RNA sequencing (scRNA-seq) in both normal and failed human heart. CD45- cells in the myocardium and immune cells (CD45+ cells) were isolated from myocardium and corresponding peripheral blood were sorted for scRNA-seq. Our findings were also validated with bulk RNAseq.
overall design too long too uplode
Immune signatures underlying post-acute COVID-19 lung sequelae
Science Immunology 6(65):eabk1741 [2021 Nov 12]
single-cell RNA-seq / TCR-seq assay of PBMC or BAL T cells from aged COVID-19 convalescents or healthy donors
Blood and immune development in human fetal bone marrow and Down syndrome
Nature 598(7880):327-331 [2021 Oct]
To be supplemented.
Dynamic changes in human single-cell transcriptional signatures during fatal sepsis
Single-cell RNA-sequencing of human peripheral blood mononuclear cells from heathy controls, survivor and non-survivor of gram-negative sepsis patients.
Nature Communications 2021 Sep 14;12(1):5444
PBMCs from KDs before and after IVIG therapy, and healthy controls were subjected to scRNA-seq, scBCR-seq and scTCR-seq with 10x Genomics.
Med (New York, N.Y.) 2021 Sep 10;2(9):1050-1071.e7
Total of 12 human samples, T cell samples from 3 controls and 3 patients were analyzed for the study. 3 Control and 3 patient samples were treated with SARS-CoV-2 antigens and 3 samples from patients were treated with MMR and 3 samples were treated with Tdap antigens.
Nature Biotechnology 40(1):110-120 [2021 Sep]
This study utilizes multi-omic biological data to perform deep immunophenotyping on the major immune cell classes in COVID-19 patients. 10X Genomics Chromium Single Cell Kits were used with Biolegend TotalSeq-C human antibodies to gather single-cell transcriptomic, surface protein, and TCR/BCR sequence information from 254 COVID-19 blood draws (a draw near diagnosis (-BL) and a draw a few days later (-AC)) and 16 healthy donors.
Annals Of The Rheumatic Diseases 81(3):379-385 [2022 Mar]
Single cell RNA-seq of peripheral blood mononuclear cells in autoimmune diseases.
Science Translational Medicine 13(612):eabh2624 [2021 Sep 22]
To be supplemented.
Nature Communications 12(1):4977 [2021 Augwo]
In the present study, we applied 3 single-cell RNA sequencing technologies to define the transcriptomes and status of CD45+ immune cells in the peripheral blood and synovial tissue of four healthy controls, seven ACPA-positive and seven ACPA negative RA patients.
PANS 118(33):e2023216118 [2021 Aug]
overall_design too long too uplode
Integrated single-cell analysis revealed immune dynamics during Ad5-nCoV immunization
Cell Discovery 2021 Aug 10;7(1):64
In this study, we performed scRNA/TCR-seq on peripheral blood mononuclear cells from four Ad5-nCoV(a adenovirus type 5 vectored vaccine candidate) recipients longitudinally during immunisation to provid an insightful knowledge and framework for assessing vaccine safety and immune dynamics of recipients.
Single-Cell RNA Sequencing of Peripheral Blood Reveals Immune Cell Signatures in Alzheimer's Disease
Frontiers in Immunology 2021 Aug 9:12:645666
Three patients with AD and two cognitively normal controls (NC)
Advanced Science (Weinheim, Baden-Wurttemberg, Germany) 2021 Oct;8(19):e2101447
Single cell RNA-seq with 28,812 T cells sorted from the peripheral blood of healthy individuals and patients with B cell-acute lymphoblastic leukemia, as well as T-cell receptor repertoire sequencing from one of the healthy individuals and the same patients.
The single-cell epigenomic and transcriptional landscape of immunity to influenza vaccination
Cell 184(15):3915-3935.e21 [2021 Jul 22]
H5N1_scRNA-seq; H5N1_scATAC-seq; TIV_scRNA-seq; TIV_scATAC-seq, overall_design too long too uplode
Clinical And Translational Medicine 2021 Jul;11(7):e489
To be supplemented.
Systems vaccinology of the BNT162b2 mRNA vaccine in humans
Nature 596(7872):410-416 [2021 Jul]
Methods: peripheral blood was isolated from 6 volunteers before, 24 or 48 hours, and 7 days after the primary and secondary immunization
Blood 138(1):23-33 [2021 Jul 8]
Full length mRNA profiles of hematopoietic stem and progenitor cells (HSPCs) under aplastic anemia (AA) and healthy conditions were generated by deep sequencing at single cell resolution, using Illumina Hiseq. 3' end mRNA profiles of hematopoietic stem and progenitor cells (HSPCs) and T cells under aplastic anemia (AA) and healthy conditions were generated by deep sequencing at single cell resolution, using Illumina Hiseq
Integrated analysis of multimodal single-cell data
Cell 184(13):3573-3587.e29 [2021 Jun 24]
Human PBMCs were profiled using CITE-seq and cell hashing
Nature Communications 12(1):3895 [2021 Jun 23]
Examination of single-cell transcriptomics from tumor-associated HSPCs and canonical HSPC
Science Translational Medicine 13(598):eabe9599 [2021 Jun 16]
To be supplemented.
Engineering 17:161-169 [2022 Oct]
To be supplemented.
Clinical and Translational Medicine 11(5):e430 [2021 May]
To be supplemented.
Adaptive Natural Killer Cells Facilitate Effector Functions of Daratumumab in Multiple Myeloma
Clinical Cancer Research 27(10):2947-2958 [2021 May 15]
NK cells sorted from 3 MM patients' bone marrow, no replicates
Cancer Cell 39(5):662-677.e6 [2021 May 10]
To be supplemented.
overall_design too long too uplode
Here, we exposed naïve bone-marrow derived MSCs, which had been harvested for bone-marrow transplantation treatments, to matrices with controlled elasticities and to a bipotential induction cocktail that permits differentiation towards fat or bone.
CD27hiCD38hi plasmablasts are activated B cells of mixed origin with distinct function
Iscience 24(5):102482 [2021 Apr 29]
DEG analysis from single-cell sorted Plasmablasts (CD19+IgD-CD27hiCD38hi) from 7 patients with primary or secondary dengue infection. Gene expression in plasmablasts from 2 dengue-infected patients (1 primary and 1 secondary).
Mucosal-associated invariant T cell responses differ by sex in COVID-19
Clinical and Translational Medicine 2(6):755-772.e5 [2021 Apr]
We collected 48 PBMC samples from 24 participants in this study. In exposed and infected cohorts, 13 subjects were sampled longitudinally with 2 or 3 samples per individual. Each sample is associated with 3 files of processed data and 12 files of raw data.
Single-cell multi-omics analysis of the immune response in COVID-19
Nature Medicine 27(5):904-916 [2021 May]
Multi-omics single-cell profiling of surface proteins, gene expression and lymphocyte immune receptors from hospitalised COVID-19 patient peripheral blood immune cells and healthy controls donors. Identification of the coordinated immune cell compositional and state changes in response to SARS-CoV-2 infection or LPS challenge, compared to healthy control immune cells.
Immunity 54(5):1083-1095.e7 [2021 Apr]
Single-cell RNA sequencing of PBMCs from 7 patients with MIS-C (severe and moderate, with 2 samples from recovered patients) and 6 pediatric healthy donors.
Immunity 54(4):797-814.e6 [2021 Apr 13]
To be supplemented.
Nature Immunology 22(5):607-619 [2021 May]
Human CD4+T cells from IPEX, HD and mothers were isolated from frozen peripheral blood mononuclear cells by flow cytometry as DAPI–CD3+CD4+ cells. In cohort 1, cells from separate donor were encapsulated in separate channel following 10x Genomics Single Cell 3′ Reagent Kit (V2 chemistry). In cohort 2, samples were tagged using a different Hashtags, pooled and encapsulared following 10x Genomics Single Cell 3′ Reagent Kit (V3 chemistry).
COVID-19 immune features revealed by a large-scale single-cell transcriptome atlas
Cell 184(7):1895-1913.e19 [2021 Apr 1]
Multiple types of tissues from healthy individuals and COVID-19 patients were collected to obtain single cells and were subjected to sequencing.
Heterogeneous bone-marrow stromal progenitors drive myelofibrosis via a druggable alarmin axis
Cell Stem Cell 28(4):637-652.e8 [2021 Apr 1]
We used scRNA 3' RNA sequencing product from 10x Genomics to profile human non-fibrotic bone marrow as well as bone marrow with diagnosed myelofibrosis
Time-resolved systems immunology reveals a late juncture linked to fatal COVID-19
Cell 184(7):1836-1857.e22 [2021 Apr 1]
overall_design too long too uplode
Frontiers in Immunology 12:636720 [2021 Mar 17]
overall_design too long too uplode
Integrative Single-Cell RNA-Seq and ATAC-Seq Analysis of Human Developmental Hematopoiesis
Cell Stem Cell 28(3):472-487.e7 [2021 Mar 4]
This is plate-based (SmartSeq2-Seq) single-cell transcriptome data set from 15 human foetal livers and bone marrow (17-22 PCW). It includes 5,867 cells with an average of 3,074 genes per cell before QC and 4,504 cells with an average of 3,642 genes per cell after QC.This is plate-based chromatin accessibility data set from 3 human foetal livers and bone marrow (18-21 PCW). It includes 4,001 cells before QC and 3,611 cells after QC.
Metabolic programs define dysfunctional immune responses in severe COVID-19 patients
3 Healthy Control PBMC and 6 COVID-19 patient's PBMC
Nature Medicine 27(3):491-503 [2021 Mar]
overall_design too long too uplode
Mbio 12(1):e02583-20 [2021 Feb 16]
PBMC from Control, Infection, Recovery and Fatal SFTS patients were collected in hospitals throughout South Korea. PBMC from each individual were processed separately through the ChromiumTM Single Cell Platform with the 10X Genomics ChromiumTM Single Cell 3’ Library and Gel Bead Kit v2 and the Chromium Single Cell A Chip Kit using the standard manufacturer’s protocol.
Nature Communications 12(1):865 [2021 Feb 8]
overall_design too long too uplode
Nature Communications 12(1):868 [2021 Feb 8]
A single cell cell RNA sequencing has been done for 8 longititunal samples collected from the same patient.
Molecular Therapy 29(2):645-657 [2021 Feb 3]
Single-cell RNA sequencing samples were collected at three phases: CAR-T products before infusion, CAR-T on day 8 after infusion, and CAR-T on day 15 after infusion. After obtaining the PBMCs for each phase, CAR-T and endogenous T cells were collected by fluorescence-activated cell sorting with anti-Mouse IgG Biotin, FITC Streptavidin, and anti-human CD3 APC.
We profile 176,447 cells from 10 NPC tumour-blood pairs, using single-cell transcriptome coupled with T cell receptor sequencing.
Mapping the immune environment in clear cell renal carcinoma by single-cell genomics
Communications Biology 4(1):122 [2021 Jan 27]
5' single-cell RNA sequencing performed on peripheral blood and tumor-infiltrating immune cells. Single-cell RNA sequencing was performed on immune cells from three patients using the 10x genomics 5-prime expression profiling kits and TCR seauences for T cells.
Immunity 54(1):99-115.e12 [2021 Jan 12]
To be supplemented.
overall_design too long too uplode
Science Immunology 6(55):eabd5778 [2021 Jan 29]
To be supplemented.
Single-Cell Mapping of Progressive Fetal-to-Adult Transition in Human Naive T Cells
Cell Reports 34(1):108573 [ 2021 Jan 5]
Single-cell RNAseq of FACSorted naïve CD4 (CD4+CD45RA+CD27+CD25-) and CD8 (+CD45RA+CD27+CCR7+CD95-) T cells from human samples: Fetal (18-23 gestational weeks) spleen, full-term newborn (37+ gestational weeks at birth) umbilical cord blood, and adult (ages 23 to 53) peripheral blood. CD34+ HSPCs were also sorted from these same donors for single-cell RNAseq.
Single-Cell Transcriptomics Reveal Immune Mechanisms of the Onset and Progression of IgA Nephropathy
Cell Reports 33(12):108525 [2020 Dec 22]
overall_design too long too uplode
Immunity 53(6):1296-1314.e9 [2020 Dec 15]
To be supplemented.
JCI Insight 6(2):e145108 [2021]
We longitudinally single-cell RNA sequenced circulating and bone marrow mononuclear cells in injured mice (3hrs, 6hrs and 24hrs representing escalating, peak and recovery phase of inflammation) and circulating mononuclear cells in trauma patients (<4hrs, 24hrs and 72hrs mainly representing the early changes after systematic injury) along with paired healthy controls.
Single-cell transcriptome profiling of an adult human cell atlas of 15 major organs
Genome Biology 21(1):294 [2020 Dec 7]
We performed single-cell transcriptomes of 84,363 cells derived from 15 tissue organs of one adult donor and generated an adult human cell atlas (AHCA).
Characterization and generation of human definitive multipotent hematopoietic stem/progenitor cells
Cell Discovery 6(1):89 [2020 Dec 1]
10X Single-cell RNASeq of FACS-sorted CD43+ hematopoietic cells differentiated from H1 hESCs at day 8 (hESCs-HPCs), as well as FACS-sorted Lin-CD34+CD38- HSPCs mobilized in human peripheral blood (PB-HSPCs).
Blood 137(18):2463-2480 [2021 May 6]
Single cell expression profiles of five patients with relapsed/refractory ETP-ALL and five normal donors. Single cell expression profiles of seven ETP-ALL PDX models and five T-ALL PDX models.
Genome Medicine 12(1):99 [2020 Nov 20]
Primary patient samples from diagnosis (N=6 BM samples, subtype ETV6-RUNX1, 4000-8000 cells per donor) with day 15 post-treatment sample collected from two cases. Cell line experiment in REH comparing two drugs targeting ETS-factors (TK216 ERG/FLI1 and XRP44X ELK3) at 72 h (N=1, 900-2500 cells per treatment).
A molecular cell atlas of the human lung from single-cell RNA sequencing
Nature 587(7835):619-625 [2020 Nov]
To be supplemented.
Journal of Clinical Investigation 131(2):e138519 [2021 Jan 19]
overall_design too long too uplode
Emerging Microbes & Infections
PBMCs from 6 HIV patients and 1 Healthy donor were subjected to scRNA seq.
Multi-Omics Resolves a Sharp Disease-State Shift between Mild and Moderate COVID-19
Cell 183(6):1479-1495.e20 [2020 Oct]
This study utilizes multi-omic biological data to perform deep immunophenotyping on the major immune cell classes in COVID-19 patients. 10X Genomics Chromium Single Cell Kits were used with Biolegend TotalSeq-C human antibodies to gather single-cell transcriptomic, surface protein, and TCR/BCR sequence information from 254 COVID-19 blood draws (a draw near diagnosis (-BL) and a draw a few days later (-AC)) and 16 healthy donors.
Multimodal mapping of the tumor and peripheral blood immune landscape in human pancreatic cancer
Nature Cancer 2020 Nov;1(11):1097-1112
overall_design too long too uplode
Cell Discovery 6:73 [2020 Oct]
To be supplemented.
Two subsets of stem-like CD8+ memory T cell progenitors with distinct fate commitments in humans
Heterogeneity of the bulk CD95+ CD8+ memory T cells sorted from four human healthy donors' peripheral blood.
A human circulating immune cell landscape in aging and COVID-19
Protein & Cell 11(10):740-770 [2020 Oct]
Researchers combined scRNA-seq, mass cytometry, and scATAC-seq to compare immune cells from young, old, and COVID-19 patients. They found age reprogrammed the immune landscape, with T cell polarization towards effector, cytotoxic, and exhausted states, along with increases in late NK cells, age-associated B cells, and inflammatory monocytes. Age-specific gene expression linked to coronavirus susceptibility was also upregulated. COVID-19 further promoted these age-related immune changes, suggesting that immu
Journal Of Autoimmunity 116:102547 [2021 Jan]
To be supplemented.
Science Immunology 5(52):eaba9953 [2020 Oct 23]
5 scRNAseq datasets were analyzed.
MYC Promotes Bone Marrow Stem Cell Dysfunction in Fanconi Anemia
Cell Stem Cell 28(1):33-47.e8 [2021 Jan 7]
Expression profiles of single cells from seven Fanconi Anemia patients and five healthy donors.
Genetic landscape and autoimmunity of monocytes in developing Vogt-Koyanagi-Harada disease
10X single cell RNA-seq from 3 normal people and 3 VHK patient
A single-cell survey of cellular hierarchy in acute myeloid leukemia
Journal of Hematology & Oncology 13(1):128 [2020 Sep 25]
We applied Micro-well seq, a high-throughput and low-costing single-cell RNA platform, to 40 patients with 3 healthy donors. We identified a key subgroup and characterized its gene expression pattern from diagnosis to relapse, revealing its features in refractory patients. In addition, we combined next generation and SMRT sequencing to track the clonal evolution.
Severe COVID-19 Is Marked by a Dysregulated Myeloid Cell Compartment
Cell 182(6):1419-1440.e23 [2020 Sep]
In a dual-center, two-cohort study, we performed single-cell RNA-sequencing of whole blood and peripheral blood mononuclear cells to determine changes in immune cell composition and activation in mild vs. severe COVID-19 over time. This study provides detailed insights into the systemic immune response to SARS-CoV-2 infection and reveals profound alterations in the myeloid cell compartment associated with severe COVID-19.
Immunity 53(3):685-696.e3 [2020 Sep 15]
The single-cell transcriptional landscape of longitudinally collected PBMCs in both COVID-19 and influenza A virus (IAV)-infected patients
Immunogenomic Landscape of Hematological Malignancies
Cancer Cell 38(3):380-399.e13 [2020 Sep 14]
We integrated over 8,000 transcriptomes and over 2,000 samples with multilevel genomic data of hematological cancers to investigate how immunological features are linked to cancer subtypes, genetic and epigenetic alterations, and patient survival. For more detailed follow-up analyses in acute myeloid leukemia (AML), single-cell RNA sequencing was performed on 8 AML bone marrow samples at diagnosis to profile the phenotypes of blasts and infiltrating immune cells in different disease subtypes.
Human germinal centres engage memory and naïve B cells after influenza vaccination
Nature 586(7827):127-132 [2020 Oct]
Examination of 21 single-cell RNA-seq samples from PBMC and lymph node taken at multiple time points pre- and post-vaccination.
Single-cell transcriptomic landscape of human blood cells
National Science Review 8(3):nwaa180 [2020 Aug 24]
Single cell RNAseq for BM/PB-derived 32 blood cells, involving in the samples from GSE137864(Single cell RNAseq for BM-derived HSPCs from 3 healthy donors)
Clinical Cancer Research 26(21):5668-5681 [2020 Nov 1]
To be supplemented.
Immunity 53(2):353-370.e8 [2020 Aug 18]
overall_design too long too uplode
Science Immunology 5(50):eabb4432 [2020 Aug 21]
Single-cell RNA-seq and BCR/TCR repertoire analyses of immune cell from 15 patients
Pathogen-induced tissue-resident memory TH17 (TRM17) cells amplify autoimmune kidney disease
Science Immunology 5(50):eaba4163 [2020 Aug 7]
To be supplemented.
Single-cell landscape of immunological responses in patients with COVID-19
Nature immunology 21(9):1107-1118 [2020 Aug]
To be supplemented.
Systems biological assessment of immunity to mild versus severe COVID-19 infection in humans
CITE-seq of 7 patients with COVID-19 and 5 healthy controls
overall_design too long too uplode
Elevated Calprotectin and Abnormal Myeloid Cell Subsets Discriminate Severe from Mild COVID-19
Red blood cells (RBC) depleted whole blood from COVID-19 patients and controls was harvested and processed in order to performed 10X single cell RNA-seq. For COVID-19 patients 2 samples 10 days a part were analyzed.
Mapping systemic lupus erythematosus heterogeneity at the single-cell level
Nature Immunology 21(9):1094-1106 [2020 Sep]
To be supplemented.
Risk-associated alterations in marrow T cells in pediatric leukemia
Jci Insight 5(16):e140179 [2020 Aug 20]
Examination of bone marrow immune cell transcriptomes in pediatric B-cell acute lymphoblastic leukemia patients (B-ALL: n=7), acute myeloid leukemia patients (AML: n=8), and healthy donors (n=4)
Single-cell analyses identify dysfunctional CD16+ CD8 T cells in smokers
Cell Reports Medicine 1(4):100054 [2020 Jul 21]
Peripheral blood cells from smoking and nonsmoking adults were extracted and libraries were prepared using Chromium™ Single Cell 3' Library & Gel Bead Kit v2 (10X Genomics) according to the manufacturer’s guidelines.
Cell 182(1):73-84.e16 [2020 Jul 9]
The COVID-19 pandemic urgently needs therapeutic and prophylactic interventions. Here we report the rapid identification of SARS-CoV-2 neutralizing antibodies by high-throughput single-cell RNA and VDJ sequencing of antigen-enriched B cells from 60 convalescent patients.
Science Immunology 5(49):eabd1554 [2020 Jul 10]
Single-cell RNA sequencing performed with PBMC of 5 flu, 11 COVID-19 patients and 4 healthy controls.
Nature Medicine 26(9):1459-1467 [2020 Sep]
Single cell sequencing profile of CD34+ stem/progenitor cells from two newly diagnosed AML patients (C8 and C10) at diagnosis (day -14) and after cusatuzumab monotherapy (C1D1)
Blood Advances 4(12):2656-2670 [2020 Jun 23]
mRNA profiles of single bone marrow CD34+ cells of eight GATA2 deficiency patients and four healthy donors were generated by deep sequencing using Illumina HiSeq 3000
Jci Insight 5(13):e135678 [2020 Jul 9]
7 Frozen PBMC samples, 4 with sepsis only, 3 with sepsis and ARDS
A single-cell atlas of the peripheral immune response in patients with severe COVID-19
Nature Medicine 26(7):1070-1076 [2020 Jul]
Single-cell RNA sequencing of peripheral blood mononuclear cells (PBMCs) from 8 samples from COVID-19 patients and 6 healthy controls.
Extensive Remodeling of the Immune Microenvironment in B Cell Acute Lymphoblastic Leukemia
Cancer Cell 37(6):867-882.e12 [2020 Jun 8]
Single-cell RNA-sequencing libraries of primary human peripheral blood immune populations. B-ALL patient bone marrow samples were separated into CD19+ B cell and CD19-CD45+ non-B cell fractions by flow-based sorting and then mixed at a ratio of 1:5 CD19+:CD19-CD45+ followed by scRNA-Seq. Total CD45+ peripheral blood cells were sequenced from healthy donors.
Evolution and structure of clinically relevant gene fusions in multiple myeloma
Nature Communications 11(1):2666 [2020 May 29]
To be supplemented.
Science Signaling 13(633):eaay8203 [2020 May 26]
To be supplemented.
CD235a+ cells were isolated from 3 adult bone marrow and 3 umbilical cord blood samples and further sequenced by 10x Genomics platform to obtain transcriptomic profiles.UMI Count matrices were generated by cellranger.
Deciphering human macrophage development at single-cell resolution
Nature 582(7813):571-576 [2020 Jun]
We sorted CD45+CD235a- hematopoietic cells using flow cytometry from human embryos at multiple Carnegie stages (CS11, CS12, CS13, CS15, CS17, CS20 and CS23) and sites (yolk sac, head, liver, blood, lung and skin), and then performed a modified single cell tagged reverse transcription (STRT) protocol.
Scientific Reports 10(1):8079 [2020 May 15]
10X Genomics 3’ single cell RNA-seq: Pre-B t(12;21) [ETV6-RUNX1] acute lymphoblastic leukemia, Pre-B High hyper diploid [HHD] acute lymphoblastic leukemia, Pre-T acute lymphoblastic leukemia, Healthy pediatric bone marrow mononuclear cells. Annotations.tsv contains sample, cell cycle phase, tSNE/UMAP coordinates, and assigned cell type.
Cancer Cell 37(5):690-704.e8 [ 2020 May 11]
The design for the 10x sort was: 8700 Lin-CD71+CD235a+ and 8700 Lin-CD71-CD235a- single cells were sorted from two human AEL samples and 15000 Lin-CD45. 1-GFP- single cells were sorted from two KLG-E mice. Libraries were preparing using the chromium single cell 3’ reagent kits v2 (10x Genomics, California USA) according to manufacturer’s protocol.
High systemic and tumor-associated IL-8 correlates with reduced clinical benefit of PD-L1 blockade
Nature Medicine 26(5):693-698 [2020 May]
Single-cell RNA-seq of baseline pretreatment PBMC samples from 10 cancer patients with 5 responders and 5 nonresponders.
Molecular Cell 78(3):477-492.e8 [2020 May 7]
We used 10x genomics platform to profile single-cell transcriptome of CD34+Lineage- hematopoietic stem/progenitor cells (HSPCs) derived from 15 human myelofibrosis tissue samples and 6 healthy donors
Single-cell RNA-seq analysis of human CSF microglia and myeloid cells in neuroinflammation
Neurology-neuroimmunology & Neuroinflammation 7(4):e732 [2020 May 5]
single cell made for 2 MS patients and 1 MOG patient (PBMC and CSF samples)
Immune cell profiling of COVID-19 patients in the recovery stage by single-cell sequencing.
Cell Discovery 6:41 [2020 May]
To be supplemented.
Immune cell profiling of COVID-19 patients in the recovery stage by single-cell sequencing
Cell Discovery 2020 May 4:6:31
To be supplemented.
Single-cell RNA sequencing reveals the heterogeneity of liver-resident immune cells in human
Cell Discovery 2020 Apr 28:6:22
Using 10x genomics to measure CD45+ immune cells in healthy human liver and paired spleen and PBMCs from the same donors access to liver transplantation.
Nature Cancer 1(5):493-506 [2020 May]
We employed single-cell RNA sequencing on 40.8K immune microenvironmental cells using 32 bone marrow samples from a cohort of 22 patients with varying stages of Multiple Myeloma progression and 9 healthy donors.
Nature Communications 11(1):1801 [2020 Apr 14]
Cytokines affect T cell responses by polarising them to different phenotypes. We isolated T cells from healthy platelet donors and cultured them in resting and stimulated condition, as well as in the presence of Th2, iTreg and Th17 polarizing cocktail. To characterize the efficacy of cytokine induced porization and subpopulation specific response, we profiled single cell transcriptome five days following polarization using 10x platform (3' v2).
Single-Cell Analyses Inform Mechanisms of Myeloid-Targeted Therapies in Colon Cancer
overall_design too long too uplode
Diversity of peripheral blood human NK cells identified by single-cell RNA sequencing
Blood Advances 4(7):1388-1406 [2020 Apr 14]
Single cell transriptional profiling of NK cells isolated from two CMV-negative healthy donors. scRNAseq of sorted NK cells from one healthy individual
Construction of a human cell landscape at single-cell level
Nature 581(7808):303-309 [2020 May]
Microwell-seq analyses of 60 types of human tissues and supplementary datasets for the Mouse Cell Atlas data.
Integrated single-cell analysis of multicellular immune dynamics during hyperacute HIV-1 infection
To be supplemented.
DNA methylation disruption reshapes the hematopoietic differentiation landscape
Nature Genetics 52(4):378-387 [2020 Apr]
overall_design too long too uplode
Blood 135(11):826-833 [2020 Mar 12]
Single cell RNA sequencing (scRNA-seq) was performed with peripheral blood cells before (Day 0, T0), during nivolumab treatment (Day 7, T1; Day 21, T2), and when plasma EBV turned negative (Day 76, T3) in 1 patient (patient 7). scRNA-seq libraries were generated following the recommended protocol of the 3’ scRNA-seq 10X genomics platform and using v2 chemistry, and sequenced data was collected by illumina NovaSeq 6000 sequencing.
Clinical Cancer Research 26(4):935-944 [ 2020 Feb 15]
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Clinical Cancer Research 26(11):2640-2653 [2020 Jun 1]
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Nature Communications 11(1):577 [2020 Jan 29]
12 scRNA-seq samples of peripheral blood mononuclear cells from chronic lymphocytic leukemia patients
Cell Reports 30(3):905-913.e6 [2020 Jan 21]
To be supplemented.
Integrated single cell analysis of blood and cerebrospinal fluid leukocytes in multiple sclerosis
Nature Communications 11(1):247 [2020 Jan]
We used a 5 v.s. 5 Case-Control design for the single cell RNAseq experiment. Each donor provided 2 samples from the cerebrospinal fluid and PBMC.
Immune Landscape of Viral- and Carcinogen-Driven Head and Neck Cancer
Total of 63 samples were analyzed by scRNAseq. Of these, 26 samples were paired peripheral blood mononuclear cells and tumor infiltrating immune cells from HNSCC patients (18 HPV- and 8 HPV+), 6 were peripheral blood mononuclear cells from healthy donors, and 5 were tissue resident immune cells from healthy donor tonsils.
Nature Communications 11(1):219 [2020 Jan 10]
We performed scRNA-seq on CD8+ CAR-T cells isolated from the IP and blood at the early, late, and very late time points from four patients who received CD19-specific CAR-T cells for refractory B cell malignancies. Single CD8+ CAR-T cells were sorted as CD8+/CD4-/EGFRt+ events and scRNA-seq was performed using the Chromium Single Cell 5’ library and V(D)J enrichment kit (10x Genomics). Libraries were sequenced on HiSeq2500.
Re-evaluation of human BDCA-2+ DC during acute sterile skin inflammation
Journal of Experimental Medicine 217(3):jem.20190811 [2020 Mar 2]
An unexpected BDCA-2+CD123+CD1a+ dendritic cell (DC) subset comprised a major DC population in acute human sterile skin inflammation. Single-cell RNAseq showed these to be activated DC able to express markers normally associated with plasmacytoid DC, prompting a re-evaluation of previous studies.
Blood 134(23):2111-2115 [2019 Dec 5]
4 normal, 3 thalassemia major and 5 sickle cell donors' bone marrow CD34+ cells were analyzed
Single-cell multiomic analysis identifies regulatory programs in mixed-phenotype acute leukemia
Nature Biotechnology 37(12):1458-1465 [2019 Dec]
scATAC-seq and CITE-seq performed on healthy bone marrow, CD34+ bone marrow, peripheral blood, and MPAL donors
Single-cell transcriptomics reveals expansion of cytotoxic CD4 T cells in supercentenarians
To be supplemented.
Nature Communications 10(1):4706[2019 Oct 17]
Single-cell RNA-sequencing of control and and anti-CD3/anti-CD28 stimulated T cells from bone marrow and blood.
Resolving the fibrotic niche of human liver cirrhosis at single-cell level
Nature 575(7783):512-518 [2019 Nov]
Single-cell transcriptomic data are presented from 5 healthy livers, 5 cirrhotic livers and 4 PBMC samples from cirrhotic patients. We also present single-cell transcriptomic data on hepatic macrophages from healthy mice or mice following chronic carbon tetrachloride administration.
Leukemia 34(2):589-603 [2020 Feb]
We used index sorting single-cell RNA sequencing (Precise Assay, Becton Dickinson) to identify genes and cell clusters related to disease dissemination by comparing the molecular profile of CTCs with patient-matched BM clonal PCs.
Single-cell immune landscape of human atherosclerotic plaques
Nature Medicine 25(10):1576-1588 [2019 Oct]
To be supplemented.
Immunity 51(3):573-589.e8 [2019 Sep 17]
Indexed single cell RNAseq (scRNAseq) of human peripheral blood dendritic cells and monocytes
A general approach for detecting expressed mutations in AML cells using single cell RNA-sequencing
Nature Communications 10(1):3660 [2019 Aug 14]
To be supplemented.
Cancer Discovery 9(8):1080-1101 [2019 Aug]
We profiled the human HSCe (Lineage-, CD34+, CD38-) transcriptome with aging at the single cell level. Single-cell RNAseq was performed on FACS isolated human bone marrow derived HSCe from 5 young (24-37 yo) and 4 aged donor (64-71 yo). Donors had no known hematological malignancy.
Nature Communications 10(1):3266 [2019 Jul 22]
Frozen PBMCs from healthy individual were defrosted and infected ex vivo with Salmonella enterica serovar Typhimurium.
Single cell RNA-Seq reveals pre-cDCs fate determined by transcription factor combinatorial dose
Bmc Molecular And Cell Biology 20(1):20 [2019 Jun 28]
mRNA profiles of pre-DCs, DC1 and DC2 in single cell and CDP, pre-DC, DC1 and DC2 in bulk from blood of human healthy donors
A comprehensive single cell transcriptional landscape of human hematopoietic progenitors
Nature Communications 10(1):2395 [2019 Jun 3]
overall_design too long too uplode
6 samples of purified human gd T cells from 3 donors (CMV+ and CMV-). Cell-sorted TCRVdelta1 and TCRVdelta2 T lymphocytes from each donor PBMC.
Single cell RNA sequencing (scRNAseq) of RBC-depleted cells from non-small cell lung tumor and from blood of 7 patients. ScRNAseq of CD45-positive cells from lungs of 2 healthy mice and 2 lung tumor-bearing mice.
Clinical Cancer Research 25(10):2996-3005 [2019 May 15]
Single-cell RNA sequencing was performed on CD4+ T cells isolated from the blood of a patient with Sezary Syndrome using the 10x genomics 5-prime expression profiling kits. The peripheral blood sample was separated into malignant (P4, CD3+CD4+CD5brightSSChi) and nonmalignant (P5, (CD3+CD4+CD5intSSCint).
Peripheral blood mononuclear cells (PBMC) from healthy donors, skin cells from the dorsal mid-forearm of healthy donors, and lung cells from streptococcus pneumonia (SP) infected and naïve mice
Molecular Cell 73(6):1292-1305.e8 [2019 Mar 21]
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Single-Cell RNA-Seq Reveals AML Hierarchies Relevant to Disease Progression and Immunity
Cell 176(6):1265-1281.e24 [2019 Mar 7]
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Leukemia 33(7):1783-1796 [2019 Jul]
Bone marrow-derived MSCs from healthy donors were cultured for 24 h in presence/absence of IFN-γ (10 ng/ml) and TNF-α (15 ng/ml). Subsequently, cells were subjected to droplet single-cell RNA-sequencing.
Molecular signatures of multiple myeloma progression through single cell RNA-Seq
Blood Cancer Journal 9(1):2 [2019 Jan 3]
597 single cell libraries passed QC and were included in the downstream analysis
Molecular and functional heterogeneity of IL-10-producing CD4+ T cells
Nature Communications 9(1):5457 [2018 Dec 21]
We performed scRNA-seq analysis of IL-10-producing CD4+ T cells isolated from the blood (PBMCs) of two healthy donors
Single cell dissection of plasma cell heterogeneity in symptomatic and asymptomatic myeloma
Nature Medicine 24(12):1867-1876 [2018 Dec]
The study includes 29 newly diagnosed patients with plasma cell neoplasms and 11 control donors, for which bone marrow plasma cells were single cell sorted by FACS, and their mRNA sequenced. For 11 patients, targeted genomic DNA panel analysis for myeloma was performed.
Immunity 49(5):971-986.e5 [2018 Nov 20]
Spleen and Blood paired NK cells from 3 individual human brain dead donors (CD45+ CD3– CD14– CD19– CD56+) and 3*5 pooled mice (CD45+ CD3– CD19– NKp46+ NK1.1+) were sorted.
Cell Reports 25(8):2083-2093.e4 [2018 Nov 20]
overall_design too long too uplode
Single-cell reconstruction of the early maternal–fetal interface in humans
Nature 563(7731):347-353 [ 2018 Nov]
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Blood cells from dengue virus infected human patients were subjected to virus-inclusive single cell RNA-Seq.
Targeting individual cells by barcode in pooled sequence libraries
Nucleic Acids Research 47(1):e4 [2019 Jan 10]
10X libraries were prepared from two FACs sorted populations (HLA-DR and CD19) followed by enrichment for targeted single cells in triplicate. Enrichment was achieved with multiplex PCR with primers targeting the single cell barcodes that are added through library preparation.
Acquired cancer resistance to combination immunotherapy from transcriptional loss of class I HLA
Nature Communications 9(1):3868 [2018 Sep 24]
Serial blood draws from four time points, serial tumor biopsies from two time points - single cell digests were viably preserved, comparisons were performed on a within tissue basis, discovery patient for associated manuscript
Cell Reports 24(9):2329-2341.e8 [2018 Aug 28]
Neutrophil progenitor isolated from mouse and human fresh bone marrow without treatment were sequeced to explore heterogeneities; 3' Transcriptome sequencing (10X genomics)
Single-Cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment
Cell 174(5):1293-1308.e36 [2018 Aug 23]
Single-cell RNA sequencing was performed on eight donors using the InDrop v2 protocol. For each donor populations of CD45+ immune cells were assayed for trancriptome-wide RNA-sequence. At least one replicate was taken for each donor.
Nature Communications 9(1):3317 [2018 Aug 20]
Examination of the transcriptional profiles from single human plasmacytoid dendritic cells that were stimulated with CpG-C
PBMC fixation and processing for Chromium single-cell RNA sequencing
Journal of Translational Medicine 16(1):198 [ 2018 Jul 17]
single cell RNA sequencing of PBMC, CD8+ T cell or KLM1 cell line after fixation with methonal and resuspension in SSC buffer
Cell 173(6):1535-1548.e16 [2018 May 31]
Profiles of single cell epigenomes, assayed using scATAC-seq, across sorted cell types from CD34+ bone marrow.
Cell Reports 23(4):942-950 [2018 Apr 24]
overall_design too long too uplode
Single-cell RNA sequencing identifies celltype-specific cis-eQTLs and co-expression QTLs
Nature Genetics 50(4):493-497 [2018 Apr]
overall_design too long too uplode
Genome Biology 19(1):10 [2018 Jan 29]
Single-cell RNA-seq profiling of HIV-1-exposed cDCs and media controls from 3 elite controllers used to identify reproducible gene expression programs associated with cell-intrinsic HIV-1 immune recognition.
Precursors of human CD4+ cytotoxic T lymphocytes identified by single-cell transcriptome analysis
Science Immunology 3(19):eaan8664 [2018 Jan 19]
Transcriptome analysis of purified populations of human CD4 memory cell subsets by single-cell RNA-sequencing.
Multiplexed droplet single-cell RNA-sequencing using natural genetic variation
Nature Biotechnology 36(1):89-94 [2018 Jan]
HiSeq 2500 data for sequencing of PBMCs from SLE patients and 2 controls. We collected 1M cells each from frozen PBMC samples that were Ficoll isolated and prepared using the 10x Single Cell instrument according to standard protocol. Samples A, B, and C were prepared on the instrument directly following thaw, while samples 2.1 and 2.2 were cultured for 6 hours with (B) or without (A) IFN-beta stimulation prior to loading on the 10x Single Cell instrument.
Nucleic Acids Research 45(16):e148 [2017 Sep 19]
overall_design too long too uplode
Journal of Immunology 199(1):323-335 [2017 Jul 1]
This project contains RNA-seq files from four cell types: 1) T cell clone (N=149 single cell profiles); 2) T cell clone (N=9 bulk cell profiles); 3) CD8+ influenza-reactive T cells (N=45 single cell profiles); and 4) CD4+ pooled islet antigen-reactive T cells (N=246 single cell profiles).
Landscape of Infiltrating T Cells in Liver Cancer Revealed by Single-Cell Sequencing
Cell 169(7):1342-1356.e16 [2017 Jun 15]
overall_design too long too uplode
Nature Medicine 23(6):692-702 [2017 Jun]
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Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors
overall_design too long too uplode
Human haematopoietic stem cell lineage commitment is a continuous process
Nature Cell Biology 19(4):271-281 [2017 Apr]
overall_design too long too uplode
Journal of Experimental Medicine 213(13):2861-2870 [2016 Dec 12]
RNA seq libraries from 957 single cells were prepared using the SMART-Seq 2 protocol (Picelli et al., 2013); 341 Blood pre-cDC (Blood pre-cDC_S* data columns in the expMatrix.txt); 452 CB pre-cDC (CB pre-cDC_S* data columns in the expMatrix.txt); 87 CD141+ cDC (blood_bdca3_S* data columns in the expMatrix.txt); 77 CD1c+ cDC (blood_bdca1_S* data columns in the expMatrix.txt)