|
| Status |
Public on Dec 15, 2016 |
| Title |
XY-KO rep3 |
| Sample type |
SRA |
| |
|
| Source name |
testis
|
| Organism |
Mus musculus |
| Characteristics |
tissue: testis
strain: C57BL/6
genotype: XY AMH-Cre; Sox9flox/flox
developmental stage: E13.5
|
| Growth protocol |
All animal work was performed under Monash Medical Centre Animal Ethics approval (MMCB/2012/23). Microdissected gonads were separated from mesonephros of E13.5 embryos, snap frozen and stored at −80°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the RNeasy kit (QIAGEN GmbH, D-40725 Germany).
Libraries were generated using NuGEN Mondrian Technology, utilising SPIA amplification methodology (which specifically selects and linearly reverse transcribes nonribosomal RNA). 6pM of bar-coded libraries per lane were sequenced using the Illumina HiSeq1500. Paired-end RNA sequencing chemistry, using 150 nt read lengths, at 50 million reads per sample was performed.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Data processing |
Trimmomatic (version 0.30)
Tophat2 (version 2.0.8)
HTSeq-count (version 0.6.1p1)
voom' from ‘limma’ R package (version 3.24.0)
Genome_build: Mus_musculus.GRCm38.77
Supplementary_files_format_and_content: Voom output of all differentially expressed genes
|
| |
|
| Submission date |
May 16, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Francis Poulat |
| E-mail(s) |
francis.poulat@igh.cnrs.fr
|
| Phone |
(+33) 4 3435 9940
|
| Organization name |
IGH CNRS-UM UMR9002
|
| Department |
Genetic and Development
|
| Street address |
141 rue de la Cardonille
|
| City |
Montpellier |
| ZIP/Postal code |
34396 |
| Country |
France |
| |
|
| Platform ID |
GPL18480 |
| Series (2) |
| GSE81489 |
In fetal testis, SOX9 acts on transcription and splicing of its targets genes through binding to genomic regions with conserved signatures [RNA-seq] |
| GSE81490 |
In fetal testis, SOX9 acts on transcription and splicing of its targets genes through binding to genomic regions with conserved signatures |
|
| Relations |
| BioSample |
SAMN05003701 |
| SRA |
SRX1769369 |
