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| 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
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| Summary |
TCF7L2 regulates multiple metabolic pathways in hepatocytes through a transcriptional network involving HNF4α
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| 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).
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| Contributor(s) |
Heikkinen S, Norton L |
| Citation(s) |
25414334 |
| Submission date |
Jan 07, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Sami Heikkinen |
| E-mail(s) |
sami.heikkinen@uef.fi
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| Organization name |
University of Eastern Finland
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| Department |
Institute of Biomedicine
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| Street address |
Yliopistonranta 1E
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| City |
Kuopio |
| ZIP/Postal code |
70211 |
| Country |
Finland |
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| Platforms (1) |
| GPL14844 |
Illumina HiSeq 2000 (Rattus norvegicus) |
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| Samples (44)
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| 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 |
| GSM1302240 |
RNA-seq sample for timecourse of siRNA knock-down of Tcf7l2: siRNA - Scrambled, 6 h, rep 2 |
| GSM1302241 |
RNA-seq sample for timecourse of siRNA knock-down of Tcf7l2: siRNA - Scrambled, 9 h, rep 1 |
| GSM1302242 |
RNA-seq sample for timecourse of siRNA knock-down of Tcf7l2: siRNA - Scrambled, 9 h, rep 2 |
| GSM1302243 |
RNA-seq sample for timecourse of siRNA knock-down of Tcf7l2: siRNA - Scrambled, 9 h, rep 3 |
| GSM1302244 |
RNA-seq sample for timecourse of siRNA knock-down of Tcf7l2: siRNA - Scrambled, 12 h, rep 1 |
| GSM1302245 |
RNA-seq sample for timecourse of siRNA knock-down of Tcf7l2: siRNA - Scrambled, 12 h, rep 2 |
| GSM1302246 |
RNA-seq sample for timecourse of siRNA knock-down of Tcf7l2: siRNA - Scrambled, 12 h, rep 3 |
| GSM1302247 |
RNA-seq sample for timecourse of siRNA knock-down of Tcf7l2: siRNA - Scrambled, 15 h, rep 1 |
| GSM1302248 |
RNA-seq sample for timecourse of siRNA knock-down of Tcf7l2: siRNA - Scrambled, 15 h, rep 2 |
| GSM1302249 |
RNA-seq sample for timecourse of siRNA knock-down of Tcf7l2: siRNA - Scrambled, 18 h, rep 1 |
| GSM1302250 |
RNA-seq sample for timecourse of siRNA knock-down of Tcf7l2: siRNA - Scrambled, 18 h, rep 2 |
| GSM1302251 |
RNA-seq sample for timecourse of siRNA knock-down of Tcf7l2: siRNA - Scrambled, 48 h, rep 1 |
| GSM1302252 |
RNA-seq sample for timecourse of siRNA knock-down of Tcf7l2: siRNA - Scrambled, 48 h, rep 2 |
| GSM1302253 |
RNA-seq sample for timecourse of siRNA knock-down of Tcf7l2: siRNA - Scrambled, 96 h, rep 1 |
| GSM1302254 |
RNA-seq sample for timecourse of siRNA knock-down of Tcf7l2: siRNA - Scrambled, 96 h, rep 2 |
| GSM1302255 |
RNA-seq sample for timecourse of siRNA knock-down of Tcf7l2: siRNA - Tcf7l2, 3 h, rep 1 |
| GSM1302256 |
RNA-seq sample for timecourse of siRNA knock-down of Tcf7l2: siRNA - Tcf7l2, 3 h, rep 2 |
| GSM1302257 |
RNA-seq sample for timecourse of siRNA knock-down of Tcf7l2: siRNA - Tcf7l2, 6 h, rep 1 |
| GSM1302258 |
RNA-seq sample for timecourse of siRNA knock-down of Tcf7l2: siRNA - Tcf7l2, 6 h, rep 2 |
| GSM1302259 |
RNA-seq sample for timecourse of siRNA knock-down of Tcf7l2: siRNA - Tcf7l2, 9 h, rep 1 |
| GSM1302260 |
RNA-seq sample for timecourse of siRNA knock-down of Tcf7l2: siRNA - Tcf7l2, 9 h, rep 2 |
| GSM1302261 |
RNA-seq sample for timecourse of siRNA knock-down of Tcf7l2: siRNA - Tcf7l2, 9 h, rep 3 |
| GSM1302262 |
RNA-seq sample for timecourse of siRNA knock-down of Tcf7l2: siRNA - Tcf7l2, 12 h, rep 1 |
| GSM1302263 |
RNA-seq sample for timecourse of siRNA knock-down of Tcf7l2: siRNA - Tcf7l2, 12 h, rep 2 |
| GSM1302264 |
RNA-seq sample for timecourse of siRNA knock-down of Tcf7l2: siRNA - Tcf7l2, 12 h, rep 3 |
| GSM1302265 |
RNA-seq sample for timecourse of siRNA knock-down of Tcf7l2: siRNA - Tcf7l2, 15 h, rep 1 |
| GSM1302266 |
RNA-seq sample for timecourse of siRNA knock-down of Tcf7l2: siRNA - Tcf7l2, 15 h, rep 2 |
| GSM1302267 |
RNA-seq sample for timecourse of siRNA knock-down of Tcf7l2: siRNA - Tcf7l2, 18 h, rep 1 |
| GSM1302268 |
RNA-seq sample for timecourse of siRNA knock-down of Tcf7l2: siRNA - Tcf7l2, 18 h, rep 2 |
| GSM1302269 |
RNA-seq sample for timecourse of siRNA knock-down of Tcf7l2: siRNA - Tcf7l2, 48 h, rep 1 |
| GSM1302270 |
RNA-seq sample for timecourse of siRNA knock-down of Tcf7l2: siRNA - Tcf7l2, 48 h, rep 2 |
| GSM1302271 |
RNA-seq sample for timecourse of siRNA knock-down of Tcf7l2: siRNA - Tcf7l2, 96 h, rep 1 |
| GSM1302272 |
RNA-seq sample for timecourse of siRNA knock-down of Tcf7l2: siRNA - Tcf7l2, 96 h, rep 2 |
| GSM1302273 |
Pooled RNA-seq sample for H4IIE-specific transcriptome generation |
| GSM1302274 |
Pooled Input chromatin |
| GSM1302275 |
ChIP-seq sample for siRNA knock-down of Tcf7l2: siRNA - Scrambled, 15 h, target protein - Tcf7l2, rep 1 |
| GSM1302276 |
ChIP-seq sample for siRNA knock-down of Tcf7l2: siRNA - Scrambled, 15 h, target protein - Tcf7l2, rep 2 |
| GSM1302277 |
ChIP-seq sample for siRNA knock-down of Tcf7l2: siRNA - Tcf7l2, 15 h, target protein - Tcf7l2, rep 1 |
| GSM1302278 |
ChIP-seq sample for siRNA knock-down of Tcf7l2: siRNA - Tcf7l2, 15 h, target protein - Tcf7l2, rep 2 |
| GSM1302279 |
ChIP-seq sample for siRNA knock-down of Tcf7l2: siRNA - Scrambled, 15 h, target protein - Hnf4a |
| GSM1302280 |
ChIP-seq sample for siRNA knock-down of Tcf7l2: siRNA - Tcf7l2, 15 h, target protein - Hnf4a |
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| Relations |
| BioProject |
PRJNA233591 |
| SRA |
SRP035209 |
| 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 |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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