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Sample GSM3897904 Query DataSets for GSM3897904
Status Public on Aug 14, 2019
Title RF117
Sample type SRA
 
Source name RNA in water
Organism Mus musculus
Characteristics genotype: Rfx6f/+
time: 3_months
Treatment protocol Adult mice were given tamoxifen (10mg) (Sigma) by gavage twice per day, every second day during 5 days.
Growth protocol Mutant (Rfx6f/f; Vilin-CreERT2) and control mice (Rfx6f/+, or Rfx6f/f) were generated starting from Rfx6f/+ (Piccand et al, 2014) and Vilin-CreERT2 mice (El Marjou et al 2004)
Extracted molecule polyA RNA
Extraction protocol Ileon was harvested at 8 days and 3 months after tamoxifen gavage. Total RNA was extracred using TRI-reagent or RNeasy® Midi Kit (Qiagen).
Library prep for total RNA-seq Ribozero/standard quantity
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description rawdata_3months.txt
Data processing Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Reads mapping to rRNA and ERCC spikes were identified using Bowtie version 1.0.0 and removed from the analysis.
Remaining reads were mapped onto the mm9 assembly of mouse genome using Tophat version 2.0.10 and the Bowtie2 version 2.1.0 aligner.
Quantification of gene expression was performed using HTSeq version 0.6.1 (parameter “--intersection_nonempty”) and gene annotations from Ensembl release 67
Genome_build: mm9
Supplementary_files_format_and_content: The two tab-delimited text file include raw read counts for the two experiments (at 8 days and 3 months)
 
Submission date Jun 19, 2019
Last update date Aug 14, 2019
Contact name Gérard Gradwohl
E-mail(s) gradwohl@igbmc.fr
Organization name IGBMC
Street address 1 rue Laurent Fries
City Illkirch-Graffenstaden
State/province -
ZIP/Postal code 67400
Country France
 
Platform ID GPL17021
Series (2)
GSE132997 Identification of Rfx6-dependent genes in the adult mouse ileon by RNAseq
GSE133038 Rfx6-regulated genes in the mouse intestine
Relations
BioSample SAMN12095381
SRA SRX6094147

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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