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Sample GSM1723640 Query DataSets for GSM1723640
Status Public on Mar 24, 2016
Title ES si- (2)
Sample type SRA
 
Source name 46C ES cells
Organism Mus musculus
Characteristics cell type: 46C ES cells
knock in: Atad2 TAP-tag
si rna: si control
Treatment protocol 46C ES tag cells were treated with an active anti-Atad2 siRNA (si Atad2) and an inactive siRNA (si ctrl)
Growth protocol ES cells expressing a TAP-tagged Atad2 were cultured according to a standard in DMEM medium containing LIF (ESG1107, Millipore), non essential aminoacids, antibiotics (Penicillin and streptomycin), beta-mercaptoethanol and supplemented with 15% fetal bovine serum (Invitrogen), on 0.1% gelatin-coated tissue culture dishes at 37┬░C in CO2 incubator.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using RNAeasy kit from Quiagen following the manufacturer┬┤s instruction.
Approximately 500ng of total RNA were used for sequencing library preparation with the TruSeq RNA protocol from Illumina.
Four libraries were multiplexed in a single lane (10pm) and subsequently sequenced on a HiSeq1000 (Illumina) with the paired end protocol and 50 cycle each.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1000
 
Description ES cells transfected with scrambled siRNA ( replicate 2)
Data processing RNA-seq reads were aligned to the mm9 genome assembly using tophat (Galaxy Tool Version 1.1.2)
Cuffdiff (Galaxy Tool Version 2.2.1.2) was used to find genes differentially expressed between the two conditions
Genome_build: mm9
Supplementary_files_format_and_content: Cuffdiff output files corresponding to gene and transcript differential expression
 
Submission date Jun 26, 2015
Last update date May 15, 2019
Contact name Sophie Rousseaux
Organization name INSERM-UGA
Department IAB
Lab U1209
Street address Bd de la Chantourne
City La Tronche
ZIP/Postal code 38706
Country France
 
Platform ID GPL15103
Series (2)
GSE70314 Atad2 is a generalist facilitator of chromatin dynamics in embryonic stem cells [Atad2_ES_RNAseq_BI]
GSE70315 Atad2 is a generalist facilitator of chromatin dynamics in embryonic stem cells
Relations
BioSample SAMN03797963
SRA SRX1074421

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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