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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Sep 15, 2024 |
| Title |
Ovary, Chek2KO, IR, rep1 |
| Sample type |
SRA |
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| Source name |
ovary
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| Organism |
Mus musculus |
| Characteristics |
tissue: ovary
genotype: Chek2-/-
treatment: irradiated 0.5Gy
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted using miRNeasy micro extraction kit (Qiagen)
Libraries were constructed using the KAPA mRNA HyperPrep Kit (KAPA Biosystems)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
nf-core/rnaseq (version1.4.3dev)
FastQC (version 0.11.9) was used to determine the quality of the FASTQ files. Adapter trimming was conducted with Trim Galore (version 0.6.5). Salmon (version 1.3.0) was used transcript-level quantitation. RNA-seq data quality control was performed with RSeQC (version 3.0.1) An aggregation of the quality control for the RNA-seq analysis was performed with MultiQC (version 1.9).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes row counts for each sample
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| Submission date |
Feb 04, 2024 |
| Last update date |
Sep 15, 2024 |
| Contact name |
Ewelina Bolcun-Filas |
| Organization name |
The Jackson Laboratory
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| Street address |
600 Main St
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| City |
Bar Harbor |
| State/province |
ME |
| ZIP/Postal code |
04609 |
| Country |
USA |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE255032 |
Single-cell and bulk transcriptional profiling of mouse ovaries reveals novel genes and pathways associated with DNA damage response in oocytes |
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| Relations |
| BioSample |
SAMN39824857 |
| SRA |
SRX23531036 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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