|
| Status |
Public on Mar 16, 2017 |
| Title |
Control_ovary_rep1_7707_S27 |
| Sample type |
SRA |
| |
|
| Source name |
6 week Ovary
|
| Organism |
Mus musculus |
| Characteristics |
age: 6 weeks old
genotype/variation: Dmrt1 +/+; Rara f/f; Rarb f/f; Rarg f/f; Sf1-Cre-
strain: C57BL/6; 129 Mixed
cell type: ovary
|
| Treatment protocol |
None.
|
| Growth protocol |
Animals were raised in conventional housing.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Whole gonads were dissected and homogenized in Trizol. RNA was purified using RNAeasy Micro Kit ( Qiagen 74004).
polyA+ mRNA using KAPA Stranded mRNA-Seq Kit, with KAPA mRNA Capture Beads (Kapa Biosystems KK8420/1)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Minkina_etal_normalized_FPKM.csv
Minkina_etal_raw_counts.csv
Supplementary_Table_1.csv
|
| Data processing |
Reads were trimmed with Trimmomatic Version 0.32, parameters:ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:5 MINLEN:25
Trimmed reads were mapped to the GRCm38 build of the mouse genome with STAR (version STAR_2.4.2a_modified)
Mapped reads were indexed and sorted with samtools 1.0
Gene quantification and deferential expression was performed using the GenomicAlignments (1.8.4) and DESeq2 (1.12.3) packages in Bioconductor.
Genome_build: mm10/GRCm38
Supplementary_files_format_and_content: bigWig, normalized FPKMs, raw counts, log2FoldChange
|
| |
|
| Submission date |
Feb 11, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Micah Gearhart |
| E-mail(s) |
gearh006@umn.edu
|
| Organization name |
University of Minnesota
|
| Department |
Genetics, Cell Biology and Development
|
| Street address |
6-160 Jackson Hall, 321 Church St.
|
| City |
Minneapolis |
| State/province |
MN |
| ZIP/Postal code |
55455 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE94802 |
Retinoic acid signaling is dispensable for somatic development and function of the developing ovary |
|
| Relations |
| BioSample |
SAMN06323316 |
| SRA |
SRX2553720 |
