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Series GSE206240

Query DataSets for GSE206240

Status

Public on Feb 29, 2024

Title

Comprehensive characterisation of HNF4A and HNF1A genomic targets in pancreatic beta cells and hepatic cells reveals common and tissue-specific pathways and genes

Organism

Experiment type

Genome binding/occupancy profiling by high throughput sequencing

Summary

To determine the downstream regulatory network of HNF4A and HNF1A, two transcription factors that play important roles in the pancreas and liver and that are associated with diabetes, we generated a comprehensive genome-wide map of the binding targets of HNF4A and HNF1A in hiPSC-derived pancreatic and hepatic cells and relevant cell lines using ChIP-Seq and molecular validation. We report binding targets of HNF4A and HNF1A that map to both known and novel gene promoters, that are common or differentially bound across different cell types and developmental stages. Overall, the detailed characterisation of the regulatory roles of HNF4A and HNF1A in pancreatic beta cells and hepatic cells will potentially shed light on how dysregulation of these factors can contribute to altered tissue development and function, and thus pathogenesis of both monogenic diabetes and T2D.

Overall design

Chromatin immunoprecipitation and sequencing (ChIP-Seq) was performed using antibodies against HNF4A and HNF1A in multiple cell types (EndoC-βH1 cells, human islets, hiPSC-derived pancreatic progenitors, hiPSC-derived endocrine progenitors, hiPSC-derived beta-like cells, hiPSC-derived hepatoblasts and HepG2 cells). ChIP-Seq was also conducted using the antibody against FLAG in EndoC-βH1 cells stably overexpressing FLAG-tagged HNF4A8 WT or T117I variant. Validation by ChIP-qPCR confirmed binding at selected targets.

Contributor(s)

NG NH, GHOSH S, TEO AK

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Submission date

Jun 16, 2022

Last update date

Mar 02, 2024

Contact name

Adrian Kee Keong Teo

E-mail(s)

ateo@imcb.a-star.edu.sg

Organization name

IMCB, A*STAR

Department

Stem Cells and Diabetes Laboratory

Street address

61 Biopolis Drive, Proteos

City

Singapore

State/province

Singapore

ZIP/Postal code

138673

Country

Singapore

Platforms (1)

Illumina NextSeq 500 (Homo sapiens)

Samples (42)

More...

GSM6248567	EndoC-βH1 HNF4A sc-8987 - chip
GSM6248568	EndoC-βH1 HNF1A sc-6547 - chip
GSM6248569	HepG2 HNF4A ab41898 - chip

GSM6248570	HepG2 HNF4A sc-8987 - chip
GSM6248571	EndoC-βH1 HNF4A H1415 - chip
GSM6248572	HepG2 HNF4A H1415 - chip
GSM6248573	D14 PP HNF4A H1415 biological replicate 1 - chip
GSM6248574	Islets HNF4A H1415 - chip
GSM6248575	D20 EP HNF1A ab96777 - chip
GSM6248576	Islets HNF1A ab96777 - chip
GSM6248577	HepG2 HNF1A ab96777 - chip
GSM6248578	D14 PP HNF4A H1415 biological replicate 2 - chip
GSM6248579	D8 Hep HNF4A H1415 - chip
GSM6248580	D20 EP HNF4A H1415 - chip
GSM6248581	D35 beta-like cells HNF4A H1415 - chip
GSM6248582	EndoC-βH1 GFP (Empty) FLAG biological replicate 1 - chip
GSM6248583	EndoC-βH1 HNF4A8 WT FLAG biological replicate 1 - chip
GSM6248584	EndoC-βH1 HNF4A8 T117I FLAG biological replicate 1 - chip
GSM6248585	EndoC-βH1 GFP (Empty) FLAG biological replicate 2 - chip
GSM6248586	EndoC-βH1 HNF4A8 WT FLAG biological replicate 2 - chip
GSM6248587	EndoC-βH1 HNF4A8 T117I FLAG biological replicate 2 - chip
GSM6248588	EndoC-βH1 HNF4A sc-8987 - input
GSM6248589	EndoC-βH1 HNF1A sc-6547 - input
GSM6248590	HepG2 HNF4A ab41898 - input
GSM6248591	HepG2 HNF4A sc-8987 - input
GSM6248592	EndoC-βH1 HNF4A H1415 - input
GSM6248593	HepG2 HNF4A H1415 - input
GSM6248594	D14 PP HNF4A H1415 biological replicate 1 - input
GSM6248595	Islets HNF4A H1415 - input
GSM6248596	D20 EP HNF1A ab96777 - input
GSM6248597	Islets HNF1A ab96777 - input
GSM6248598	HepG2 HNF1A ab96777 - input
GSM6248599	D14 PP HNF4A H1415 biological replicate 2 - input
GSM6248600	D8 Hep HNF4A H1415 - input
GSM6248601	D20 EP HNF4A H1415 - input
GSM6248602	D35 beta-like cells HNF4A H1415 - input
GSM6248603	EndoC-βH1 GFP (Empty) FLAG biological replicate 1 - input
GSM6248604	EndoC-βH1 HNF4A8 WT FLAG biological replicate 1 - input
GSM6248605	EndoC-βH1 HNF4A8 T117I FLAG biological replicate 1 - input
GSM6248606	EndoC-βH1 GFP (Empty) FLAG biological replicate 2 - input
GSM6248607	EndoC-βH1 HNF4A8 WT FLAG biological replicate 2 - input
GSM6248608	EndoC-βH1 HNF4A8 T117I FLAG biological replicate 2 - input

Relations

BioProject

Download family	Format
SOFT formatted family file(s)	SOFT
MINiML formatted family file(s)	MINiML
Series Matrix File(s)	TXT

Supplementary file	Size	Download	File type/resource
GSE206240_RAW.tar	950.0 Kb	(http)(custom)	TAR (of BED)
SRA Run Selector
Raw data are available in SRA
Processed data provided as supplementary file

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