Seq-Scope analysis of human acne(Dataset ID: STDS0000146)

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PMID: 35867799
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Dataset information
Summary:
Skin samples were analyzed through Seq-Scope.
Overall design:
A 6 mm punch skin biopsy was frozen in OCT medium and stored at -80°C until sectioning. The current study utilized Seq-Scope[HISEQ], which is similar to the previously described version of Seq-Scope [MISEQ] (PMID: 34115981), but utilized the HISEQ2500 flow cells for Seq-Scope array generation, instead of the MISEQ flow cells. All the procedures are extensively described in the former paper, and current study was performed almost identically; however, following things were different between the two studies: (1) To perform the 1st-Seq process, HISEQ2500 sequencing was performed with 100 pM of HDMI32-oligo library, and generated 1.1 million clusters/mm^2 fully sequenced pixel density (PF clusters). (2) HISEQ2500 tiles have a rectangular shape and are arranged to form a minimally interrupted large imaging area. Therefore, images from individual tiles were assembled to present a larger image that can be aligned with the hematoxylin and eosin histology results. (3) To accommodate the larger imaging area, volume of the solutions was proportionally increased during the experiment. (4) During the secondary strand synthesis, we used an updated Randomer sequence (5’-TCAGACGTGTGCTCTTCCGATCTNNNNNNNNB-3’). Compared to the original Randomer (5’-TCAGACGTGTGCTCTTCCGATCTNNNNNNNNN-3’), the updated Randomer sequence does not anneal to the poly-A region, enabling more efficient transcriptome alignment. (5) To further substantiate our former results from scRNA-seq and spatial-seq, we focused on one acne sample, which presented an ideal spatial orientation that reveals the relationship between diverse inflammatory populations (including TREM2 macrophages) and hair follicle pathology. Other experi
Technology:
Seq-Scope
Platform:
Illumina HiSeq 2500 (synthetic construct), HiSeq X Ten (Homo sapiens)
Species:
Homo sapiens(hg38)
Tissues:
Skin
Disease:
Acne
Submission date: 2021-10-26Update date: 2022-07-25
Sample number: 1Section number: 1
DOI: To be continue
Contributors
Hsu, Jer-En,Cho, Chun-Seok,Kim, Myungjin,Xi, Jingyue,Gudjonsson, Johann E,Lee, Jun Hee
Accessions
GEO Series Accessions: GSE186601
How to cite
  • Cite database of STOmicsDB:
    [1] Xu, Zhicheng et al. "STOmicsDB: a comprehensive database for spatial transcriptomics data sharing, analysis and visualization." Nucleic acids research vol. 52,D1 (2024): D1053-D1061. doi: 10.1093/nar/gkad933'
  • Cite visualization dataset:
    [2] Hsu, Jer-En,Cho, Chun-Seok,Kim, Myungjin,Xi, Jingyue,Gudjonsson, Johann E,Lee, Jun Hee. Seq-Scope analysis of human acne[DS/OL]. STOmicsDB, 2021[2021-10-26]. https://db.cngb.org/stomics/datasets/STDS0000146/. doi: xxxxxx
    #Format: {contributors}. {title}[DS/OL]. STOmicsDB, {the year of submission data}[{submission data}]. {dataset link}. doi: {doi ID}
  • Cite original data article:
    Citation: Do, Tran H et al. “TREM2 macrophages induced by human lipids drive inflammation in acne lesions.” Science immunology vol. 7,73 (2022): eabo2787. doi:10.1126/sciimmunol.abo2787