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Sample GSM2881405 Query DataSets for GSM2881405
Status Public on Nov 28, 2018
Title C57_D300_F1_5 [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 GSM2309215
BioSample SAMN08149858
SRA SRX3457273

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

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