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Sample GSM5348591 Query DataSets for GSM5348591
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

Supplementary file Size Download File type/resource
GSM5348591_HYMIIO5.counts.txt.gz 291.5 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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