|
| Status |
Public on Aug 10, 2014 |
| Title |
Del Baf60c rep3 D5.3 |
| Sample type |
SRA |
| |
|
| Source name |
Differentiated embryonic stem cells (129 SvEv background), at cardiac precursor (d5.3) stage
|
| Organism |
Mus musculus |
| Characteristics |
barcode: TGTTGC
timepoint: day 5.3
genetic background: Baf60c null (homozygous Knockout)
replicate number: Replicate 3
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.
|
| 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.
|
| |
|
| 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.
|
| |
|
| 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 |
SAMN02911869 |
| SRA |
SRX652717 |
