|
Status |
Public on Aug 10, 2014 |
Title |
Brg1 rep1 D10 |
Sample type |
SRA |
|
|
Source name |
Differentiated embryonic stem cells (129 SvEv background), at cardiomyocyte (d10) stage.
|
Organism |
Mus musculus |
Characteristics |
barcode: AAGACG timepoint: day 10 genetic background: WT (Wildtype) replicate number: Replicate 1 strain: 129 SvEv
|
Treatment protocol |
Both WT (Brg1) and Baf60c KO cardiac precurosor and cardiomyocytes were harvested by treating with TrpLE (cell dissociation reagent, life technologies, cat no. 12604-013). The cells were washed 2x with cold PBS, flash frozen in liquid nitrogen ans stored at -80C before total RNA isolation.
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Growth protocol |
Es cells were grown in DMEM media supplemented with fetal bovine serum and LIF. ES cells were differentiated to Cardiac precursor and Cardiomyocyte by following a directed differentiation protocol (Kattman et al, 2011). Briefly ES cells were cultured in suspension / low attachement dishes to form embryoid bodies (EBs). EBs were induced in presence of VEGF, BMP4 and Activin A and cultured in monolayers in presence of VEGF, FGF-b and FGF-10 to form cardiac precursors and cardiac myocytes.
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was isolated from the samples using miRNeasy micro kit (Qiagen, cat no. 217084) following manufacture protocol with on-column DNase I digestion. Total RNA was qunatified using nanodrop and quality checked using bioanalyser. RNA-seq libraries were prepared with ovation RNA-seq system v2 kit (NuGEN). The double-stranded DNA was then amplified using single primer isothermal amplification (SPIA). Random hexamers were used to amplify the second-strand cDNA linearly. Finally, libraries from the SPIA amplified cDNA were made using the Ultralow DR library kit (NuGEN). The RNA-seq libraries were analyzed by Bioanalyzer and quantified by qPCR (KAPA). All 12 indexed samples were sequenced in each of three lanes on an Illumina HiSeq 2500.
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|
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
|
|
Data processing |
Per-gene counts and FPKM values provided by "DefinedRegionDifferentialSeq" version 8.6.4, part of the USeq software package (http://useq.sourceforge.net/). Gene annotation used was ENSEMBL version 65.
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|
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Submission date |
Jul 14, 2014 |
Last update date |
May 15, 2019 |
Contact name |
Gladstone Bioinformatics |
Organization name |
Gladstone Institutes
|
Department |
Data Science and Biotechnology
|
Lab |
Bioinformatics Core
|
Street address |
1650 Owens St
|
City |
San Francisco |
State/province |
CA |
ZIP/Postal code |
94158 |
Country |
USA |
|
|
Platform ID |
GPL17021 |
Series (1) |
GSE59383 |
RNA-seq data: Baf60c homozygous deletion vs. WT at two time points in cardiac differentiation |
|
Relations |
BioSample |
SAMN02911858 |
SRA |
SRX652706 |