|
Status |
Public on Feb 26, 2023 |
Title |
HYMIIO5 |
Sample type |
SRA |
|
|
Source name |
oocytes
|
Organism |
Homo sapiens |
Characteristics |
tissue: oocytes patient age: under 28
|
Treatment protocol |
Oocytes were isolated from donors under 28 (21-28) [HY] or over 38 (38-42) years old [HO].
|
Extracted molecule |
total RNA |
Extraction protocol |
Human MII oocytes were obtained from patients undergoing in vitro fertilization and embryo transfer procedure due to a sperm quality issue or tubal obstruction. 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 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) |
GSE175833 |
Granulosa cell mevalonate pathway abnormalities contribute to oocyte meiotic defects and aneuploidy [RNA-seq Human oocytes] |
GSE175836 |
Granulosa cell mevalonate pathway abnormalities contribute to oocyte meiotic defects and aneuploidy |
|
Relations |
BioSample |
SAMN19468709 |
SRA |
SRX11031664 |