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Sample GSM1464535 Query DataSets for GSM1464535
Status Public on Jul 21, 2015
Title Tbx3 N/N RNASeq
Sample type SRA
 
Source name mESCs
Organism Mus musculus
Characteristics cell type: embryonic stem cells
cell line: R1
genotype: Tbx3 -/-
Growth protocol R1 mESCs were cultured in mESC media containing serum and LIF without feeders
Extracted molecule total RNA
Extraction protocol For ChIP cells were fixed with 11% formaldehyde in mESC media for 10 minutes on a rotating platform. The fixation was stopped by addition of 125nM of Glycine for 5 minutes on a rotating platform. Cells were scraped, quick-frozen and stored at -80°C. ChIP was done by pulling down the bfTbx3 protein using Dynabeads conjugated to streptavidin (SA) in Tbx3N/N+NBirA+bfTbx3 cells. Pull down in Tbx3N/N+NBirA cells was used as negative control. For mRNA-Seq sample preparation, the total RNA was isolated using Trizol reagent following the manufacturer’s instructions. Quality and quantity of total RNA was assayed using Nanodrop and Agilent Bioanalyzer.
For ChIPSeq, DNA library preparation was done using the Illumina ChIP-seq sample prep kit. The libraries were run on HiSeq 2000 machine. For mRNA-seq, libraries were prepared using the TrueSeq protocol from Illumina. The concentration of the libraries was assayed using Agilent Bioanalyzer and sequenced either using 1*26bp or 1*100bp on an Illumina Genome analyzer II or HiSeq 2000 platform
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer II
 
Description Tbx3 null mESCs
Data processing RNASeq: Fastq files were mapped to the genome using Tophat: tophat -o -p 4
RNASeq: Tophat output files were processed through Cufflinks (cufflinks -p 4 -L -o) and Cuffdiff (cuffdiff -o -L) programs to conduct differential gene expression analysis.
RNASeq: Homer package was used to generate the bedGraph files using the commands: makeTagDirectory and makeUCSCfile.
Genome_build: mm9
Supplementary_files_format_and_content: bed file with peaks; bedGraph files with read counts
 
Submission date Aug 04, 2014
Last update date May 15, 2019
Contact name avinash waghray
E-mail(s) avinash.waghray@gmail.com
Organization name Massachussets General Hospital
Department Center for Regenerative Medicine
Lab Rajagopal
Street address 185 Cambridge Street, CPZN Room 4254A
City Boston
State/province MA
ZIP/Postal code 02114
Country USA
 
Platform ID GPL9250
Series (1)
GSE60066 Tbx3 controls Dppa3 levels to regulate exit from pluripotency towards mesodermal lineage
Relations
BioSample SAMN02951512
SRA SRX669206

Supplementary file Size Download File type/resource
GSM1464535_Tbx3N_N-Rep1.ucsc.bedGraph.gz 51.7 Mb (ftp)(http) BEDGRAPH
GSM1464535_Tbx3N_N-Rep2.ucsc.bedGraph.gz 49.1 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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