|
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
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|
|
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 |