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Sample GSM1104441 Query DataSets for GSM1104441
Status Public on Mar 01, 2015
Title Day2_Rep2
Sample type SRA
 
Source name Differentiated embryonic stem cells
Organism Mus musculus
Characteristics cell line: Brg1f/f; Actin-CreER
timepoint: Day 2
brg1 levels: Normal
Treatment protocol On Day2, cultures were treated with either 200 nM 4-OHT in tetrahydrofuran (THF) or THF alone. 4-OHT induces CreER mediated deleted of Brg1 floxed alleles.
Growth protocol Mouse ES cells were cultured in feeder-free conditions under standard conditions. Mouse ES cells were aggregated into embryoid bodies (EB) and differentiated for two days in serum free media (Day2). Embryoid bodies were dissociated and reaggregated for 40 hours in the presence of VEGF, Activin A, and BMP4 to promote mesoderm differentiation (Day4).
Extracted molecule polyA RNA
Extraction protocol RNA was extracted using TRIzol according to the manufacturer's instructions.
8 ug of total RNA was used as input material for the preparation of the RNA-Seq libraries, according to Illumina RNA Seq library kit with minor modifications. Briefly, mRNA was isolated using Dynabeads® mRNA Purification Kit (Invitrogen) followed by fragmentation (Ambion) and ethanol precipitation. First and second strand synthesis were performed followed by end repair, A-tailing, adapter ligation and size selection on a Beckman Coulter SPRI TE nucleic acid extractor. 200-400 bp dsDNA was enriched by 13 cycles of PCR with Phusion® High-Fidelity DNA Polymerase (NEB). Amplified libraries were sequenced on an Illumina HiSeq 2000 system.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing Reads were aligned using Bowtie reporting uniquely aligned reads and allowing 2 bp mismatches
Generated .useq files using (USeq Version 8) Application Sam2USeq
USeq files were converted to BigWig format via GnomEx (https://hci-as3.hci.utah.edu/gnomex/gnomex.html)
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig values are per base read depth scaled per million mapped reads.
 
Submission date Mar 23, 2013
Last update date May 15, 2019
Contact name Jeffrey Michael Alexander
E-mail(s) jeffrey.alexander@ucsf.edu
Organization name Gladstone Institutes
Lab Bruneau Lab
Street address 1650 Owens St
City San Francisco
State/province CA
ZIP/Postal code 94158
Country USA
 
Platform ID GPL13112
Series (2)
GSE45446 Brg1 Modulates Enhancer Activation and Polycomb-mediated Repression in Mesoderm Differentiation [RNA-Seq]
GSE45448 Brg1 Modulates Enhancer Activation and Polycomb-mediated Repression in Mesoderm Differentiation
Relations
Reanalyzed by GSE80797
SRA SRX254791
BioSample SAMN01990868

Supplementary file Size Download File type/resource
GSM1104441_Day2_RNAseq_Rep2.bw 66.2 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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