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Series GSE125852 Query DataSets for GSE125852
Status Public on Jun 28, 2019
Title Effect of the twelve isoforms of Hepatocyte nuclear factor 4 alpha on HCT116 cell line transcriptome
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary The nuclear receptor HNF4alpha is regulating a wide set of genes associated with development, cell differentiation, inflammation and metabolism. In human, 12 variants of HNF4α can be expressed by the use of two promoters and by alternative splicing. Until now, the characterization of this transcription factor has ignored this diversity and has remained confined to the study of a fraction of the isoforms. We therefore wanted to clarify the situation by specifically characterizing the transcriptional functions of the 12 isoforms of HNF4α. We have generated for this purpose stable lines expressing each isoform of HNF4α in HCT 116 cells. The expression of each isoform was then induced for 48 hours and the whole transcriptome was analyzed by RNA sequencing. The transcriptome associated with each specific isoform was then compared to empty control cells to determine the specific transcriptional functions of HNF4alpha's isoforms.
 
Overall design Stable HCT116 cell lines containing a single insertion of the different human HNF4alpha isoforms (1 to 12) fused to GFP at its C-terminal were generated through the Flp-In T-REx system. Expression of HNF4alpha isoforms was induced for 48 hours with 2.5 ug/ml of doxycycline before analyzing the transcriptome by RNA sequencing on Illumina NovaSeq 6000 system. Experiments were realized in triplicate for all isoforms of HNF4alpha and transcripts expression was compared to the one of the parental empty HCT116 cell line.
 
Contributor(s) Lambert É, Babeu J, Simoneau J, Lévesque D, Jolibois É, Scott M, Boudreau F, Boisvert F
Citation(s) 32123031
Submission date Jan 29, 2019
Last update date Aug 07, 2020
Contact name Francois Boudreau
E-mail(s) [email protected]
Organization name Université de Sherbrooke
Department Anatomie et biologie cellulaire
Street address 3201 rue Jean-Mignault
City Sherbrooke
State/province Quebec
ZIP/Postal code J1E 4K8
Country Canada
 
Platforms (1)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (39)
GSM3583169 Empty Control, replicate 1 [A0N1]
GSM3583170 Empty Control, replicate 2 [A0N2]
GSM3583171 Empty Control, replicate 3 [A0N3]
Relations
BioProject PRJNA517705
SRA SRP182835

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SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE125852_A0.tsv.gz 678.7 Kb (ftp)(http) TSV
GSE125852_HNF4A10.tsv.gz 2.3 Mb (ftp)(http) TSV
GSE125852_HNF4A11.tsv.gz 2.3 Mb (ftp)(http) TSV
GSE125852_HNF4A12.tsv.gz 2.3 Mb (ftp)(http) TSV
GSE125852_HNF4A2.tsv.gz 2.3 Mb (ftp)(http) TSV
GSE125852_HNF4A3.tsv.gz 2.2 Mb (ftp)(http) TSV
GSE125852_HNF4A4_2.tsv.txt.gz 1.6 Mb (ftp)(http) TXT
GSE125852_HNF4A5_2.tsv.txt.gz 1.6 Mb (ftp)(http) TXT
GSE125852_HNF4A6.tsv.gz 2.2 Mb (ftp)(http) TSV
GSE125852_HNF4A7.tsv.gz 2.3 Mb (ftp)(http) TSV
GSE125852_HNF4A8.tsv.gz 2.3 Mb (ftp)(http) TSV
GSE125852_HNF4A9.tsv.gz 2.3 Mb (ftp)(http) TSV
GSE125852_HNFA1.tsv.gz 2.3 Mb (ftp)(http) TSV
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