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Status |
Public on Jan 21, 2025 |
Title |
GV oocytes from Rpa1 OcKO mouse 2 |
Sample type |
SRA |
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|
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).
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
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|
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
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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 |