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| Status |
Public on Feb 11, 2016 |
| Title |
Complex Interdependence Regulates Heterotypic Transcription Factor Distribution and Coordinates Cardiogenesis [RNA-Seq] |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Analysis of the changes in gene expression during in vitro cardiomyocyte differentiation due to the lack of Tbx5, Nkx2-5 or both.
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| Overall design |
We performed RNA-seq in WT, Tbx5KO (TKO), Nkx2-5KO (NKO) and Tbx5KO;Nkx2-5KO (DKO) cells at the cardiac precursor (CP) and cardiomyocyte (CM) differentiation stages.
Total RNA was isolated from 3 mill cells using TRizol Reagent. RNA-seq libraries were prepared according to NuGEN Ultralow V2 kit and paired-end 100bp sequenced on an Illumina HiSeq 2500 instrument.
Reads were trimmed using the fastq-mcf program (Aronesty, 2011), and then aligned to the mm9 mouse genome assembly using tophat2 (RNA-seq) (Kim et al., 2013). For each gene, reads were counted, and counts-per-million (CPM) calculated using featureCounts (Liao et al., 2014). Finally, edgeR was used to perform differential expression analyses (Robinson et al., 2010).
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| Contributor(s) |
Luna-Zurita L, Bruneau BG |
| Citation(s) |
26875865 |
| |
| Submission date |
Feb 03, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Benoit G. Bruneau |
| E-mail(s) |
bbruneau@gladstone.ucsf.edu
|
| Organization name |
GLADSTONE INSTITUTES
|
| Street address |
1650 OWENS STREET
|
| City |
SAN FRANCISCO |
| ZIP/Postal code |
94158 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
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| Samples (24)
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| This SubSeries is part of SuperSeries: |
| GSE72223 |
Complex Interdependence Regulates Heterotypic Transcription Factor Distribution and Coordinates Cardiogenesis |
|
| Relations |
| BioProject |
PRJNA310768 |
| SRA |
SRP062699 |
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