Studying tissue composition and function in non-human primates (NHP) is crucial to understand the nature of our own species. Here, we presen…

Late prenatal development of the human neocortex encompasses a critical period of gliogenesis and cortical expansion. However, systematic si…

Over 320 million years of evolution, amniotes have developed complex brains and cognition through largely unexplored genetic and gene expres…

To determine whether sarcomas 鈥?tumors of mesenchymal origin 鈥?are subject to the same technical artifacts, we profiled patient-derived tumo…

we use single-cell mRNA sequencing to determine the cell-type composition of all major human organs and construct a scheme for the human cel…

COVID-19 exhibits extensive clinical heterogeneity ranging from asymptomatic infection to death. Unraveling the basis of immune response dif…

Novel single cell technologies have paved the way for the characterization and improved biological understanding of prostate cancer, here we…

Although melanoma is notorious for its high degree of heterogeneity and plasticity, the origin and magnitude of cell state diversity remains…

The TREM2-DAP12 receptor complex sustains microglia functions. Heterozygous TREM2 variants subtly impair microglia, facilitating manifestati…

Background: Acute kidney injury (AKI) occurs frequently in critically ill patients and is associated with adverse outcomes. Cellular mechani…

Acute myeloid leukemia (AML) is a hematopoietic malignancy with poor prognosis and limited treatment options. Here we provide a comprehensiv…

Studies of ascidian (sea squirt) embryos have highlighted the importance of cell lineages in animal development for over 100 years. As simp…

Due to commonalities in pathophysiology, age-related macular degeneration represents a uniquely accessible model to investigate therapies fo…

We have sequenced ovarian tumors in several different ways: 1) poly-A captured scRNA-seq, 2) poly-A captured pooled scRNA-seq in pools of 4 …

Comparison of neonate- vs. child-derived cardiac c-kit+ stromal cell (CSC) from congenital heart disease patients

SARS-CoV-2 infection in children is generally milder than in adults, yet a proportion of cases result in hyperinflammatory conditions often …

The immunopathogenesis of psoriasis, a common chronic inflammatory disease of the skin, is still incompletely understood. Here we demonstrat…

Titintruncating variants(TTNtv) have been identified as the single largestgenetic cause of dilated cardiomyopathy(DCM). In this studywe mode…

Cancer metastasis in the bone represents an incurable disease. About one-third of patients with advanced renal cell carcinoma (ccRCC) have b…

Single-cell RNA sequencing of PBMCs and infusion products from 32 patients treated with CD19 CAR-T therapy

We constructed the first single cell atlas of the human, porcine and zebrafish ocular compartments and compared inter-species transcriptomic…

Single-cell transcriptomic profiling of human liver tissues collected from hepatocellular carcinoma and intrahepatic聽cholangiocarcinoma pati…

Limb regeneration, while observed lifelong in salamanders, is restricted to pre-metamorphic stages in Xenopus laevis frogs. After amputation…

Pathophysiological pregnancies amy result from gene-environmental interactions. In this study, investigation of the placental cell developme…

Non-human primates provide a unique way to study the only model in which both developmental and pathological features of the brain in a spec…

We carried out sex-balanced sampling of peripheral blood mononuclear cells (PBMCs) from confirmed COVID-19 inpatients (hospitalized) and out…

This SuperSeries is composed of the SubSeries listed below.; For metadata files please visit https://livercellatlas.org

Development of the human intestine is not well understood. Here we link single-cell RNA sequencing and spatial transcriptomics to characteri…

Development of the human intestine is not well understood. Here we link single-cell RNA sequencing and spatial transcriptomics to characteri…

We performed single cell RNA sequencing on bronchial cells from human bronchoalveolar lavage fluid from 4 independent study participants who…

Introduction Our previous study demonstrated that myc, mitochondrial oxidative phosphorylation, mTOR, and stemness were independently respo…

SARS-CoV-2 infection triggers profound and variable immune responses in human hosts. Chromatin remodeling has been observed in individuals s…

Over 16,000 nuclei were isolated from human postmartum brain frozen prefrontal cortex samples of alcoholic and control individuals. Librari…

While SARS-CoV-2 infection has pleiotropic and systemic effects in some patients, many others experience milder symptoms. We sought a holist…

Both single cell and bulk RNA sequencing was performed on expanding or differentiating snake venom gland organoids (from Aspidelaps Lubricus…

Single-cell RNAseq (10x Genomics) analysis of human CD4+ T cells in IPEX patients, healthy donors and heterozygous mothers (blood). Human CD…

Non -obstructive azoospermia (NOA) affects 1% of men. However, the unknowns of NOA pathogenesis and even normal spermatogenic microenvironme…

Bulk RNA-Seq and snRNA-Seq of human orbital aft

Brain malignancies encompass gliomas and brain metastases originating from extracranial tumors. To reveal the specific characteristics of gl…

We profiled transcriptomes of >370,000 individual cells from endometriomas (n=8), endometriosis (n=28), eutopic endometrium (n=10), unaffect…

Pancreatic islet (dys)function is central to glucose homeostasis and type 2 diabetes (patho)physiology. Human islets consist of multiple end…

Longitudinally sampled peripheral blood samples of 9 CLL patients were subjected to single cell RNA sequencing before and at relapse after c…

Mutations in the lysosomal enzyme 尾-glucocerebrosidase (GCase), which cause Gaucher麓s disease, are the most frequent genetic risk factor for…

We developed Microwell-seq, a high-throughput and low-cost scRNA-seq platform using simple, inexpensive devices. Using Microwell-seq, we con…

This SuperSeries is composed of the SubSeries listed below.

To investigate the cell composition and cell-cell interaction in RA and PsA patient inflamed joints

We sought a comprehensive understanding of myeloid cell types driving fibrosis in diffuse cutaneous systemic sclerosis (dcSSc) skin. T-sto…

Background: Airway epithelium in patients with allergic airway disease actively releases and is subjected to the influence of type-2 cytokin…

Several next-generation cancer immunotherapies are designed to target LAG3 and TIM3 checkpoints, though the molecular and cellular mechanism…

Cell types in the human retina are highly heterogeneous with their abundance varies by several orders of magnitude. To decipher the complexi…

Human telencephalon is an evolutionary advanced brain structure associated with many uniquely human behaviors and disorders. However, cell l…

10x single-cell RNA-sequencing to profile human cerebrovascular cells in health and disease

The heterogeneous nature of tumour microenvironment (TME) underlying diverse treatment responses remains unclear in nasopharyngeal carcinoma…

We conducted a comparison of scRNA-seq on four paired fresh and cryopreserved atheroma samples, two from coronary arteries and two from caro…

Purpose: Chracterization of cell populations and biological functions in CSF during the development of BM.; Method: Cells in each CSF sample…

Lupus, a server and complex autoimmune disease, is clinically divided into cutaneous lupus erythematosus (CLE) which featured in skin damage…

Seven hemophilia B gene therapy participants were taken blood for single cell sequencing at four timepoints, and then compared the immune st…

Purpose: The goal of the study is to determine the phenotypic and functional states of glioma cells induce in response to a standard gliobla…

Hepatocellular carcinoma (HCC), the fourth leading cause of cancer mortality, develops almost exclusively in patients with chronic liver dis…

Osteoarthritis (OA) affects all tissues in the knee joint but therapeutic targets have often been selected for their role in cartilage damag…

Small Cell Lung Cancer (SCLC) is often a heterogeneous tumor, where dynamic regulation of key transcription factors can drive multiple popul…

The pathogenic determinants of chronic periodontitis leading to extra-oral comorbidity are unclear. This study was conducted to investigate …

We present a single-cell perspective of healthy human kidney from 19 living donors, with equal contribution from males and females, profilin…

We did single cell RNA sequencing on three lean and three obese donors. For each donor, we sorted CD45 positive and CD45 negative cells and …

Chi3l1 (Chitinase 3-like 1) is a secreted protein highly expressed in glioblastoma. Here, we show that exposure of glioma stem cells (GSCs) …

Hepatocellular carcinoma (HCC) develops almost exclusively in patients with chronic liver disease (CLD) and advanced fibrosis. Here we inter…

Background: As core units of organ tissues, cells of various types play their harmonious rhythms to maintain the homeostasis of the human bo…

De novomutations and copy number variations (CNVs) inNRXN1(2p16.3) pose a significant risk for schizophrenia (SCZ). HowNRXN1CNVs impact cort…

Age-associated B cells are considered a homogenoeus B cell sub-population whose accumulation has been linked to a altered immune response. W…

This SuperSeries is composed of the SubSeries listed below.

Vascular cell types are under-represented in standard single-nucleus RNA-Seq studies of human frozen post-mortem brain tissue. Using a novel…

An snRNAseq analysis of the Atlantic salmon gill to characterise its cellular complexity and development.

Systemic juvenile idiopathic arthritis (SJIA) is a clinically heterogenous systemic inflammatory disorder sometimes complicated by macrophag…

Chronic myeloproliferative neoplasms (MPNs) exhibit a propensity for transformation to secondary acute myeloid leukemia (sAML), for which th…

Chronic infection with HCV is manifested by dysregulation of innate immune responses and impaired T cell function at multiple levels. These…

Single-cell RNA-seq analysis of PBMCs during COVID-19

Creating in vitro models of diseases of the pancreatic ductal compartment requires a comprehensive understanding of the dev…

PD-1 is an essential inhibitory receptor in T cells, and antibodies that block its interaction with its ligands can augment anti-tumor immun…

In this work, we address the impact of CAR density on the in vitro and in vivo functionality of BCMA-CAR T cells. Phenotypic, functional, tr…

Paired single-cell RNA and T cell receptor sequencing (scRNA/TCR-seq) has allowed for enhanced resolution of clonal T cell dynamics in cance…

Most clinical trials for glioblastoma (GBM) enroll patients at recurrence. However, most pre-clinical animal models are of primary disease. …

Development of T lymphocytes in the thymus has been widely studied in mice, but our insights into human T cell development are scarce. Using…

We collected bursal tissue from the control and antibiotic groups at 1, 9, 49 and 140 days. Single cell suspensions were prepared from isola…

Canonical (H3.1/H3.2) and noncanonical (H3.3) histone 3 K27M-mutant gliomas have unique spatiotemporal distributions, partner alterations, a…

Obesity, characterized by chronic low-grade inflammation of the adipose tissue, is associated with adverse coronavirus disease 2019 (COVID-1…

Hematopoietic Stem/Progenitor cells (HSPCs) are endowed with the role of maintaining a diverse pool of blood cells throughout the human life…

The mechanisms by which DNA alleles contribute to disease risk, drug response, and other human phenotypes are highly context-specific, varyi…

Multiple myeloma (MM) is a highly refractory hematological cancer. Targeted immunotherapy has shown promise in MM but remains hindered by th…

Controlled dengue human challenge studies present a unique opportunity to address many longstanding questions in the field of flavivirus bio…

Significant efforts are ongoing to develop refined differentiation protocols to generate midbrain DA neurons from pluripotent stem cells (PS…

<p>Glioblastoma are an important type of central nerve tumors that affect human life and health. Even after surgical incision, radiotherapy …

Myelomatous effusion (ME) is a rare manifestion of extramedullary multiple myeloma (MM) with limited therapeutic options and poor outcomes. …

Single-cell transcriptomes of corpus cavernosum from three males with normal erections and five organic erectile dysfunction (ED) patients.

Cutaneous squamous cell carcinoma (cSCC) is the second most frequent of the keratinocyte-derived malignancies with actinic keratosis (AK) as…

Myeloblast expansion is a hallmark of disease progression in leukemias and comprises of CD34+ hematopoeitic stem and progeneitor cells. We u…

Immune checkpoint inhibitors (ICI) represent the cornerstone for treatment of patients with metastatic clear-cell renal cell carcinoma (ccRC…

Cerebrospinal fluid (CSF) protects the central nervous system (CNS) and analyzing CSF aids the diagnosis of CNS diseases, but our understand…

We performed single-cell/nuclei RNA-sequencing (sc/snRNA-seq) of 22 treatment-naïve melanoma brain metastases (MBM; 5 samples using scRNA-se…

The oral mucosa remains an understudied barrier tissue rich in exposure to antigens, commensals and pathogens. Moreover, it is the tissue wh…

Schinzel-Giedion syndrome (SGS) is a developmental syndrome, due to SETBP1 gene mutations inducing the accumulation of the relative protein,…

Studying tissue composition and function in non-human primates (NHP) is crucial to understand the nature of our own species. Here, we presen…

Late prenatal development of the human neocortex encompasses a critical period of gliogenesis and cortical expansion. However, systematic si…

Over 320 million years of evolution, amniotes have developed complex brains and cognition through largely unexplored genetic and gene expres…

To determine whether sarcomas 鈥?tumors of mesenchymal origin 鈥?are subject to the same technical artifacts, we profiled patient-derived tumo…

we use single-cell mRNA sequencing to determine the cell-type composition of all major human organs and construct a scheme for the human cel…

COVID-19 exhibits extensive clinical heterogeneity ranging from asymptomatic infection to death. Unraveling the basis of immune response dif…

Novel single cell technologies have paved the way for the characterization and improved biological understanding of prostate cancer, here we…

Although melanoma is notorious for its high degree of heterogeneity and plasticity, the origin and magnitude of cell state diversity remains…

The TREM2-DAP12 receptor complex sustains microglia functions. Heterozygous TREM2 variants subtly impair microglia, facilitating manifestati…

Background: Acute kidney injury (AKI) occurs frequently in critically ill patients and is associated with adverse outcomes. Cellular mechani…

Acute myeloid leukemia (AML) is a hematopoietic malignancy with poor prognosis and limited treatment options. Here we provide a comprehensiv…

Studies of ascidian (sea squirt) embryos have highlighted the importance of cell lineages in animal development for over 100 years. As simp…

Due to commonalities in pathophysiology, age-related macular degeneration represents a uniquely accessible model to investigate therapies fo…

We have sequenced ovarian tumors in several different ways: 1) poly-A captured scRNA-seq, 2) poly-A captured pooled scRNA-seq in pools of 4 …

Comparison of neonate- vs. child-derived cardiac c-kit+ stromal cell (CSC) from congenital heart disease patients

SARS-CoV-2 infection in children is generally milder than in adults, yet a proportion of cases result in hyperinflammatory conditions often …

The immunopathogenesis of psoriasis, a common chronic inflammatory disease of the skin, is still incompletely understood. Here we demonstrat…

Titintruncating variants(TTNtv) have been identified as the single largestgenetic cause of dilated cardiomyopathy(DCM). In this studywe mode…

Cancer metastasis in the bone represents an incurable disease. About one-third of patients with advanced renal cell carcinoma (ccRCC) have b…

Single-cell RNA sequencing of PBMCs and infusion products from 32 patients treated with CD19 CAR-T therapy

We constructed the first single cell atlas of the human, porcine and zebrafish ocular compartments and compared inter-species transcriptomic…

Single-cell transcriptomic profiling of human liver tissues collected from hepatocellular carcinoma and intrahepatic聽cholangiocarcinoma pati…

Limb regeneration, while observed lifelong in salamanders, is restricted to pre-metamorphic stages in Xenopus laevis frogs. After amputation…

Pathophysiological pregnancies amy result from gene-environmental interactions. In this study, investigation of the placental cell developme…

Non-human primates provide a unique way to study the only model in which both developmental and pathological features of the brain in a spec…

We carried out sex-balanced sampling of peripheral blood mononuclear cells (PBMCs) from confirmed COVID-19 inpatients (hospitalized) and out…

This SuperSeries is composed of the SubSeries listed below.; For metadata files please visit https://livercellatlas.org

Development of the human intestine is not well understood. Here we link single-cell RNA sequencing and spatial transcriptomics to characteri…

Development of the human intestine is not well understood. Here we link single-cell RNA sequencing and spatial transcriptomics to characteri…

We performed single cell RNA sequencing on bronchial cells from human bronchoalveolar lavage fluid from 4 independent study participants who…

Introduction Our previous study demonstrated that myc, mitochondrial oxidative phosphorylation, mTOR, and stemness were independently respo…

SARS-CoV-2 infection triggers profound and variable immune responses in human hosts. Chromatin remodeling has been observed in individuals s…

Over 16,000 nuclei were isolated from human postmartum brain frozen prefrontal cortex samples of alcoholic and control individuals. Librari…

While SARS-CoV-2 infection has pleiotropic and systemic effects in some patients, many others experience milder symptoms. We sought a holist…

Both single cell and bulk RNA sequencing was performed on expanding or differentiating snake venom gland organoids (from Aspidelaps Lubricus…

Single-cell RNAseq (10x Genomics) analysis of human CD4+ T cells in IPEX patients, healthy donors and heterozygous mothers (blood). Human CD…

Non -obstructive azoospermia (NOA) affects 1% of men. However, the unknowns of NOA pathogenesis and even normal spermatogenic microenvironme…

Bulk RNA-Seq and snRNA-Seq of human orbital aft

Brain malignancies encompass gliomas and brain metastases originating from extracranial tumors. To reveal the specific characteristics of gl…

We profiled transcriptomes of >370,000 individual cells from endometriomas (n=8), endometriosis (n=28), eutopic endometrium (n=10), unaffect…

Pancreatic islet (dys)function is central to glucose homeostasis and type 2 diabetes (patho)physiology. Human islets consist of multiple end…

Longitudinally sampled peripheral blood samples of 9 CLL patients were subjected to single cell RNA sequencing before and at relapse after c…

Mutations in the lysosomal enzyme 尾-glucocerebrosidase (GCase), which cause Gaucher麓s disease, are the most frequent genetic risk factor for…

We developed Microwell-seq, a high-throughput and low-cost scRNA-seq platform using simple, inexpensive devices. Using Microwell-seq, we con…

This SuperSeries is composed of the SubSeries listed below.

To investigate the cell composition and cell-cell interaction in RA and PsA patient inflamed joints

We sought a comprehensive understanding of myeloid cell types driving fibrosis in diffuse cutaneous systemic sclerosis (dcSSc) skin. T-sto…

Background: Airway epithelium in patients with allergic airway disease actively releases and is subjected to the influence of type-2 cytokin…

Several next-generation cancer immunotherapies are designed to target LAG3 and TIM3 checkpoints, though the molecular and cellular mechanism…

Cell types in the human retina are highly heterogeneous with their abundance varies by several orders of magnitude. To decipher the complexi…

Human telencephalon is an evolutionary advanced brain structure associated with many uniquely human behaviors and disorders. However, cell l…

10x single-cell RNA-sequencing to profile human cerebrovascular cells in health and disease

The heterogeneous nature of tumour microenvironment (TME) underlying diverse treatment responses remains unclear in nasopharyngeal carcinoma…

We conducted a comparison of scRNA-seq on four paired fresh and cryopreserved atheroma samples, two from coronary arteries and two from caro…

Purpose: Chracterization of cell populations and biological functions in CSF during the development of BM.; Method: Cells in each CSF sample…

Lupus, a server and complex autoimmune disease, is clinically divided into cutaneous lupus erythematosus (CLE) which featured in skin damage…

Seven hemophilia B gene therapy participants were taken blood for single cell sequencing at four timepoints, and then compared the immune st…

Purpose: The goal of the study is to determine the phenotypic and functional states of glioma cells induce in response to a standard gliobla…

Hepatocellular carcinoma (HCC), the fourth leading cause of cancer mortality, develops almost exclusively in patients with chronic liver dis…

Osteoarthritis (OA) affects all tissues in the knee joint but therapeutic targets have often been selected for their role in cartilage damag…

Small Cell Lung Cancer (SCLC) is often a heterogeneous tumor, where dynamic regulation of key transcription factors can drive multiple popul…

The pathogenic determinants of chronic periodontitis leading to extra-oral comorbidity are unclear. This study was conducted to investigate …

We present a single-cell perspective of healthy human kidney from 19 living donors, with equal contribution from males and females, profilin…

We did single cell RNA sequencing on three lean and three obese donors. For each donor, we sorted CD45 positive and CD45 negative cells and …

Chi3l1 (Chitinase 3-like 1) is a secreted protein highly expressed in glioblastoma. Here, we show that exposure of glioma stem cells (GSCs) …

Hepatocellular carcinoma (HCC) develops almost exclusively in patients with chronic liver disease (CLD) and advanced fibrosis. Here we inter…

Background: As core units of organ tissues, cells of various types play their harmonious rhythms to maintain the homeostasis of the human bo…

De novomutations and copy number variations (CNVs) inNRXN1(2p16.3) pose a significant risk for schizophrenia (SCZ). HowNRXN1CNVs impact cort…

Age-associated B cells are considered a homogenoeus B cell sub-population whose accumulation has been linked to a altered immune response. W…

This SuperSeries is composed of the SubSeries listed below.

Vascular cell types are under-represented in standard single-nucleus RNA-Seq studies of human frozen post-mortem brain tissue. Using a novel…

An snRNAseq analysis of the Atlantic salmon gill to characterise its cellular complexity and development.

Systemic juvenile idiopathic arthritis (SJIA) is a clinically heterogenous systemic inflammatory disorder sometimes complicated by macrophag…

Chronic myeloproliferative neoplasms (MPNs) exhibit a propensity for transformation to secondary acute myeloid leukemia (sAML), for which th…

Chronic infection with HCV is manifested by dysregulation of innate immune responses and impaired T cell function at multiple levels. These…

Single-cell RNA-seq analysis of PBMCs during COVID-19

Creating in vitro models of diseases of the pancreatic ductal compartment requires a comprehensive understanding of the dev…

PD-1 is an essential inhibitory receptor in T cells, and antibodies that block its interaction with its ligands can augment anti-tumor immun…

In this work, we address the impact of CAR density on the in vitro and in vivo functionality of BCMA-CAR T cells. Phenotypic, functional, tr…

Paired single-cell RNA and T cell receptor sequencing (scRNA/TCR-seq) has allowed for enhanced resolution of clonal T cell dynamics in cance…

Most clinical trials for glioblastoma (GBM) enroll patients at recurrence. However, most pre-clinical animal models are of primary disease. …

Development of T lymphocytes in the thymus has been widely studied in mice, but our insights into human T cell development are scarce. Using…

We collected bursal tissue from the control and antibiotic groups at 1, 9, 49 and 140 days. Single cell suspensions were prepared from isola…

Canonical (H3.1/H3.2) and noncanonical (H3.3) histone 3 K27M-mutant gliomas have unique spatiotemporal distributions, partner alterations, a…

Obesity, characterized by chronic low-grade inflammation of the adipose tissue, is associated with adverse coronavirus disease 2019 (COVID-1…

Hematopoietic Stem/Progenitor cells (HSPCs) are endowed with the role of maintaining a diverse pool of blood cells throughout the human life…

The mechanisms by which DNA alleles contribute to disease risk, drug response, and other human phenotypes are highly context-specific, varyi…

Multiple myeloma (MM) is a highly refractory hematological cancer. Targeted immunotherapy has shown promise in MM but remains hindered by th…

Controlled dengue human challenge studies present a unique opportunity to address many longstanding questions in the field of flavivirus bio…

Significant efforts are ongoing to develop refined differentiation protocols to generate midbrain DA neurons from pluripotent stem cells (PS…

<p>Glioblastoma are an important type of central nerve tumors that affect human life and health. Even after surgical incision, radiotherapy …

Myelomatous effusion (ME) is a rare manifestion of extramedullary multiple myeloma (MM) with limited therapeutic options and poor outcomes. …

Single-cell transcriptomes of corpus cavernosum from three males with normal erections and five organic erectile dysfunction (ED) patients.

Cutaneous squamous cell carcinoma (cSCC) is the second most frequent of the keratinocyte-derived malignancies with actinic keratosis (AK) as…

Myeloblast expansion is a hallmark of disease progression in leukemias and comprises of CD34+ hematopoeitic stem and progeneitor cells. We u…

Immune checkpoint inhibitors (ICI) represent the cornerstone for treatment of patients with metastatic clear-cell renal cell carcinoma (ccRC…

Cerebrospinal fluid (CSF) protects the central nervous system (CNS) and analyzing CSF aids the diagnosis of CNS diseases, but our understand…

We performed single-cell/nuclei RNA-sequencing (sc/snRNA-seq) of 22 treatment-naïve melanoma brain metastases (MBM; 5 samples using scRNA-se…

The oral mucosa remains an understudied barrier tissue rich in exposure to antigens, commensals and pathogens. Moreover, it is the tissue wh…

Schinzel-Giedion syndrome (SGS) is a developmental syndrome, due to SETBP1 gene mutations inducing the accumulation of the relative protein,…