 |
 |
GEO help: Mouse over screen elements for information. |
|
Status |
Public on Feb 26, 2023 |
Title |
HYMIIGC3 |
Sample type |
SRA |
|
|
Source name |
granulosa cells
|
Organism |
Homo sapiens |
Characteristics |
cell type: granulosa cells patient age: under 28
|
Extracted molecule |
total RNA |
Extraction protocol |
hGCs were isolated from donors under 28 (21-28) [HY] or over 38 (38-42) years old [HO]. The hGCs were washed with 500 μL phosphate buffered saline (PBS) (Gibco) and centrifuged at 3,000 rpm for 5 min. Then 50 μL hyaluronidase (Sigma) was added to digest hGCs at 37oC for 5 min. The cell suspensions were washed with 100 μL PBS and then 20 μL PBS was added to resuspend cell pellet. RNA-seq libraries were constructed as previously described (Liu et al., 2021). Discover-scTM WTA Kit V2 (Vazyme, N711) was used to obtain cDNA from single oocyte and GCs. The TruePrepTM DNA Library Prep Kit V2 for Illumina (Vazyme, TD503) was used for the purpose of constructing libraries. An Illumina HiSeq X platform (Shanghai, China) performs libraries sequencing. High-quality reads were aligned to Mus musculus UCSC mm9 references and FPKM value of each gene was calculated.
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
|
|
Data processing |
All RNA-seq raw data were trimmed to remove low-quality reads and adapters with Trim Galore (Version 0.6.5). The clean reads were then mapped to the human reference genome (hg38) using the STAR aligner(Dobin et al., 2013) with default parameters and the annotated genes were counted by HTSeq (Anders, Pyl, & Huber, 2015). The raw counts.txt files were normalized using the DESeq2 package and heatmaps was generated using the ggplot2 and pheatmap packages in R. Genome_build: hg38 Supplementary_files_format_and_content: counts
|
|
|
Submission date |
May 31, 2021 |
Last update date |
Feb 28, 2023 |
Contact name |
Qian Bian |
E-mail(s) |
qianbian@shsmu.edu.cn
|
Organization name |
Shanghai Jiao Tong University School of Medicine
|
Department |
Ninth People’s Hospital
|
Street address |
Pudong New District, Jinzun Rd, No.115
|
City |
Shanghai |
State/province |
Shanghai |
ZIP/Postal code |
200125 |
Country |
China |
|
|
Platform ID |
GPL24676 |
Series (2) |
GSE175832 |
Granulosa cell mevalonate pathway abnormalities contribute to oocyte meiotic defects and aneuploidy [RNA-seq Human Granulosa cells] |
GSE175836 |
Granulosa cell mevalonate pathway abnormalities contribute to oocyte meiotic defects and aneuploidy |
|
Relations |
BioSample |
SAMN19468691 |
SRA |
SRX11031606 |
Supplementary file |
Size |
Download |
File type/resource |
GSM5348577_HYMIIGC3.counts.txt.gz |
296.8 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
|
|
|
|
 |