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Title: Complex Interdependence Regulates Heterotypic Transcription Factor Distribution and Coordinates Cardiogenesis [RNA-Seq]      
keywords:
Transcriptome or Gene expression
ID:
PRJNA310768
description:
Analysis of the changes in gene expression during in vitro cardiomyocyte differentiation due to the lack of Tbx5, Nkx2-5 or both. 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).
accesstypes:
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landingpage: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA310768
authentication:
none
authorization:
none
ID:
pmid:26875865
name:
Mus musculus
ncbiID:
ncbitax:10090
abbreviation:
NCBI
homePage: http://www.ncbi.nlm.nih.gov
ID:
SCR:006472
name:
National Center for Biotechnology Information
homePage: http://www.ncbi.nlm.nih.gov/bioproject
ID:
SCR:004801
name:
NCBI BioProject
  • P01 HL089707/HL/NHLBI NIH HHS/United States

  • U01 HL098179/HL/NHLBI NIH HHS/United States

  • R01 HL114948/HL/NHLBI NIH HHS/United States

  • C06 RR018928/RR/NCRR NIH HHS/United States

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