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Series GSE53862 Query DataSets for GSE53862
Status Public on Nov 24, 2014
Title Chromatin occupancy and target genes of TCF7L2 in hepatocytes
Organism Rattus norvegicus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary TCF7L2 regulates multiple metabolic pathways in hepatocytes through a transcriptional network involving HNF4α
Overall design For the identification of Tcf7l2 target genes using a RNA-seq timecourse, and for identifying the binding sites of Tcf7l2 and Hnf4a, Tcf7l2 was silenced in rat H4IIE hepatocytes using siRNA for Tcf7l2 with a scrambled siRNA as control. Treatment times for RNA-seq samples were 3, 6, 9, 12, 15, 18, 48, and 96 hours, and for ChIP-seq samples 15 h. RNA-seq timecourse was performed in duplicate or triplicate, and the ChIP-seq in duplicate for Tcf7l2 and in singlicate for Hnf4a. The H4IIE-specific transcriptome was defined from an independent set of pooled 24 h siRNA treated samples (N=3 for siRNA for Tcf7l2 and N=3 for scrambled siRNA).
Contributor(s) Heikkinen S, Norton L
Citation(s) 25414334
Submission date Jan 07, 2014
Last update date May 15, 2019
Contact name Sami Heikkinen
Organization name University of Eastern Finland
Department Institute of Biomedicine
Street address Yliopistonranta 1E
City Kuopio
ZIP/Postal code 70211
Country Finland
Platforms (1)
GPL14844 Illumina HiSeq 2000 (Rattus norvegicus)
Samples (44)
GSM1302237 RNA-seq sample for timecourse of siRNA knock-down of Tcf7l2: siRNA - Scrambled, 3 h, rep 1
GSM1302238 RNA-seq sample for timecourse of siRNA knock-down of Tcf7l2: siRNA - Scrambled, 3 h, rep 2
GSM1302239 RNA-seq sample for timecourse of siRNA knock-down of Tcf7l2: siRNA - Scrambled, 6 h, rep 1
BioProject PRJNA233591
SRA SRP035209

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Supplementary file Size Download File type/resource
GSE53862_gene_exp_03h.diff.gz 655.8 Kb (ftp)(http) DIFF
GSE53862_gene_exp_06h.diff.gz 656.5 Kb (ftp)(http) DIFF
GSE53862_gene_exp_09h.diff.gz 662.2 Kb (ftp)(http) DIFF
GSE53862_gene_exp_12h.diff.gz 662.5 Kb (ftp)(http) DIFF
GSE53862_gene_exp_15h.diff.gz 656.2 Kb (ftp)(http) DIFF
GSE53862_gene_exp_18h.diff.gz 682.3 Kb (ftp)(http) DIFF
GSE53862_gene_exp_48h.diff.gz 652.5 Kb (ftp)(http) DIFF
GSE53862_gene_exp_96h.diff.gz 670.4 Kb (ftp)(http) DIFF
GSE53862_siRNA_scramble-TCF7L2_H4IIE_rep1-3.lane6_LukeNorton-1-6_1_CLEAN.rn4.combined.gtf.gz 2.9 Mb (ftp)(http) GTF
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