|
| Status |
Public on Sep 25, 2017 |
| Title |
Knock-out Mouse 4 Oocyte 5 |
| Sample type |
SRA |
| |
|
| Source name |
mouse oocyte
|
| Organism |
Mus musculus |
| Characteristics |
genotype/variation: cKO-Zfp36l2 oocyte
|
| Treatment protocol |
No treatment. Either F/F- or cKO-Zfp36l2 oocytes were isolated.
|
| Growth protocol |
Five week-old F/F- and cKO-Zfp36l2 female mice were stimulated with 10 IU of PMSG by intraperitoneal injection. The mice were sacrificed 46 hrs after PMSG injection, ovaries were harvested and GV oocytes were collected following ovarian puncture in M2 media (Sigma) containing 5 μM Milrinone. Only oocytes completely enclosed in cumulus cells were collected and granulosa cells were mechanically removed using pipets of decreasing diameter. The zona pellucida was removed with a brief incubation in Acid Tyrode’s solution (Sigma) and the oocytes were immediately washed in PBS with 0.1% BSA.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated with Trizol and total RNA quality was assessed using an Agilent Bioanalyzer.
The RNA isolation and cDNA synthesis was carried out using the SMARTer® Ultra® Low Input RNA Kit for Sequencing - v3 (Clontech, Cat.no. 634851).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
processed data file header: KO4_5
|
| Data processing |
RNA-seq reads were mapped with the STAR pipeline against mm10 transcriptome hosted at TSCC.
The python script rpkmforgenes.py was used to quantify counts for each gene and scde was used to calculate differential expression.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file includes raw reads and RPKM values for each Sample.
|
| |
|
| Submission date |
Mar 15, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Heidi Cook-Andersen |
| E-mail(s) |
[email protected]
|
| Organization name |
University of California, San Diego
|
| Department |
Department of Reproductive Medicine
|
| Street address |
2880 Torrey Pines Scenic Drive, Rm 4811
|
| City |
La Jolla |
| State/province |
California |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE96638 |
Single-cell RNA sequencing of Zfp36l2 knock-out and floxed GV mouse oocytes. |
|
| Relations |
| BioSample |
SAMN06604023 |
| SRA |
SRX2642263 |
