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Sample GSM2309216 Query DataSets for GSM2309216
Status Public on Jan 09, 2017
Title C57_CTL_F1_1
Sample type SRA
 
Source name epididymis extracted sperm
Organism Mus musculus
Characteristics strain: C57BL/6J
prenatal exposure: CTL
age: 14 weeks
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
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes FPKM
 
Submission date Sep 12, 2016
Last update date May 15, 2019
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)
GSE86837 Testicular dysgenesis syndrome and long-lasting epigenetic silencing of mouse sperm genes involved in the reproductive system after prenatal exposure to DEHP
Relations
Reanalyzed by GSM2881406
BioSample SAMN05763201
SRA SRX2160044

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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