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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
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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.
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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).
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Contributor(s) |
Lawrenson K, Fonseca MA |
Citation(s) |
36624343, 38370978 |
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Submission date |
Sep 12, 2022 |
Last update date |
Feb 26, 2024 |
Contact name |
Marcos Fonseca |
Organization name |
Cedars-Sinai Medical Center
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Department |
Division of Gynecologic Oncology, Department of Obstetrics and Gynecology
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Lab |
Lawrenson LAB
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Street address |
8000 Beverly Boulevard
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City |
Los Angeles |
State/province |
CA |
ZIP/Postal code |
90048 |
Country |
USA |
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Platforms (1) |
GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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Samples (51)
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Relations |
BioProject |
PRJNA879764 |
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 Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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