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Sample GSM8741945 Query DataSets for GSM8741945
Status Public on Jan 21, 2025
Title GV oocytes from Rpa1 OcKO mouse 2
Sample type SRA
 
Source name germinal vesicle (GV) oocytes
Organism Mus musculus
Characteristics cell type: germinal vesicle (GV) oocytes
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from the GV oocytes without any cumulus cells using the RNeasy Plus Micro Kit (QIAGEN), followed by Agilent 2100 Bioanalyzer RNA 6000 Pico Assay (Agilent Technologies Inc).
RNA-seq libraries were prepared using the NEBNext Single Cell/Low Input RNA Library Prep Kit (New England Biolabs) following the manufacturer’s protocols. The quantity of library was evaluated by Qubit dsDNA HS Assay (Thermo Fisher Scientific) and the quality was analyzed by the Bioanalyzer (Agilent).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description Library name: Sample 17
x17 in raw_counts.csv
Data processing RNA-seq was undertaken by Azenta Life Sciences (NJ, USA) under ultra-low input RNA-seq workflow. Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2 and only unique reads that fell within exon regions were counted.
Assembly: Mus musculus GRCm38
Supplementary files format and content: sample.counts.txt: unique hit counts for each sample
Supplementary files format and content: raw_counts.csv: raw gene hit counts of all samples
 
Submission date Jan 16, 2025
Last update date Jan 21, 2025
Contact name Wei Cui
E-mail(s) wcui@umass.edu
Phone 413-545-0673
Organization name University of Massachusetts Amherst
Street address 240 Thatcher Road
City Amherst
State/province Massachusetts
ZIP/Postal code 01003
Country USA
 
Platform ID GPL24247
Series (1)
GSE287236 Replication Protein A1 is essential for DNA damage repair during mammalian oogenesis
Relations
BioSample SAMN46283615
SRA SRX27379662

Supplementary file Size Download File type/resource
GSM8741945_17.counts.txt.gz 3.3 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA

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