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Series GSE213216 Query DataSets for GSE213216
Status Public on Oct 11, 2022
Title A single-cell transcriptomic analysis of endometriosis
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary We profiled transcriptomes of >370,000 individual cells from endometriomas (n=8), endometriosis (n=28), eutopic endometrium (n=10), unaffected ovary (n=4) and endometriosis-free peritoneum (n=4) to create a cellular atlas of endometrial-type epithelial cells, stromal cells, and microenvironmental cell populations across tissue sites.
 
Overall design Single cells are captured and barcoded using the 10X Chromium platform (10X Genomics). scRNA-seq libraries were prepared following the instructions from Chromium Single Cell 3' Reagent Kits User Guide (v2 or v3). Briefly, Gel Bead-In EMulsions (GEMs) are generated using single cell preparations. After GEM-RT and cleanup, the cDNA from barcoded single cell RNAs were amplified before quantification using Agilent Bioanalyzer High Sensitivity DNA chips. The single cell 3' gene expression libraries were constructed and cDNA corresponding to an insertion size of around 350 bp selected. Libraries were quantified using Agilent Bioanalyzer High Sensitivity DNA chips and pooled together to get similar numbers of reads from each single cell before sequencing on the NovaSeq S4 (by Fulgent Genomics or Novogene).
 
Contributor(s) Lawrenson K, Fonseca MA
Citation(s) 36624343, 38370978
Submission date Sep 12, 2022
Last update date Feb 26, 2024
Contact name Marcos Fonseca
Organization name Cedars-Sinai Medical Center
Department Division of Gynecologic Oncology, Department of Obstetrics and Gynecology
Lab Lawrenson LAB
Street address 8000 Beverly Boulevard
City Los Angeles
State/province CA
ZIP/Postal code 90048
Country USA
 
Platforms (1)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (51)
GSM6574509 Sample 1
GSM6574510 Sample 5
GSM6574511 Sample 7
Relations
BioProject PRJNA879764

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Supplementary file Size Download File type/resource
GSE213216_RAW.tar 15.7 Gb (http)(custom) TAR (of CSV, JSON, MTX, PNG, TAR, TIFF, TSV)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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