|
| Status |
Public on Nov 28, 2018 |
| Title |
C57_D300_F1_1 [re-analysis] |
| Sample type |
SRA |
| |
|
| Source name |
C57_D300_F1_CASA extracted sperm from cauda epididymis
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
prenatal exposure: DEHP 300mg/kg/day
age: 14 weeks
tissue: sperm from cauda epididymis
|
| Treatment protocol |
Prenatal exposure per os to 300 mg/kg/day of bis(2-ethylhexyl)phthalate (D300) or corn oil vehicle (CTL) was administered to pregnant mice during embryonic days 9th to 19th
|
| Growth protocol |
animal core facility of Geneva University under conventional accommodation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TRIZOL
RiboZero, fragmentation, Pyrophosphatase, kinase, TruSeq small RNA
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Base-calling (HiSeq Control Software 2.2.58, RTA 1.18.64.0, CASAVA-1.8.2)
RA3 clipped and reads > 18 bp from Fastq files using fastx_clipper
mapping to mm10 using TopHat
differential analysis using CuffDiff
analysis using CummeRbund
genes.count_tracking.txt tracks the summed counts of transcripts sharing each gene_id
http://cole-trapnell-lab.github.io/cufflinks/cuffdiff/
Genome_build: mm10
|
| |
|
| Submission date |
Dec 08, 2017 |
| Last update date |
Nov 28, 2018 |
| Contact name |
Ludwig Stenz |
| E-mail(s) |
ludwig.stenz@unige.ch
|
| Phone |
+41223795036
|
| Organization name |
University of Geneva
|
| Department |
Department of Genetic Medecine and Development
|
| Lab |
Giacobino
|
| Street address |
Rue Michel-Servet 1
|
| City |
Geneva |
| ZIP/Postal code |
CH-1211 Genève 4 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE107839 |
All-RNA-seq data used in "Genetic resistance to DEHP-induced transgenerational endocrine disruption" |
|
| Relations |
| Reanalysis of |
GSM2309211 |
| BioSample |
SAMN08149831 |
| SRA |
SRX3457269 |
