Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

45 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq in control and Haster-deficient mouse livers

ABSTRACT: The HASTER promoter region is a cis-regulatory element that stabilizes the transcription of HNF1A, preventing silencing or overexpression. We have generated a mouse model where the promoter of Haster has been specifically deleted in liver (Haster loxP/loxP; AlbCre). In liver the prevailing consequence is upregulation of HNF1A. We performed RNA-seq from control and KO livers to assess the transcriptional impact of the HNF1A upregulation in the Haster KO liver.

INSTRUMENT(S): Illumina HiSeq 4000

ORGANISM(S): Mus musculus

SUBMITTER: Anthony Beucher

PROVIDER: E-MTAB-11463 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

HNF1A, H3K4me3 and H3K27ac ChIP-seq in control and Haster-deficient mouse livers

Project description:The HASTER promoter region is a cis-regulatory element that stabilizes the transcription of HNF1A, preventing silencing or overexpression. We have generated a mouse model where the promoter of Haster has been specifically deleted in liver (Haster loxP/loxP; AlbCre). In liver the prevailing consequence is upregulation of HNF1A. We performed HNF1A, H3K4me3 and H3K27ac ChIP-seq to assess the impact of HNF1A upregulation on the chromatin landscape of Haster KO liver.

2022-05-01 | E-MTAB-11471 | biostudies-arrayexpress

UMI-4C in control and Haster-deficient mouse livers

Project description:The HASTER promoter region is a cis-regulatory element that stabilizes the transcription of HNF1A, preventing silencing or overexpression. We have generated a mouse model where the promoter of Haster has been specifically deleted in liver (Haster loxP/loxP; AlbCre). In liver the prevailing consequence is upregulation of HNF1A. We performed UMI-4C experiments to assess how Haster inactivation remodel 3D chromatin interactions of the Hnf1a promoter using the Hnf1a promoter as viewpoint (V1, Hnf1a promoter upstream CTCF site viewpoint; V2, Hnf1a promoter VP).

2022-05-01 | E-MTAB-11472 | biostudies-arrayexpress

scRNA-seq of pancreatic islets from control and Haster-pKO mice

Project description:Pancreas specific deletion of the Haster promoter region results in a variegated phenotype in pancreatic islets with overexpression or silencing of the Hnf1a gene. To determine the transcriptional consequence of the overexpression or silencing of Hnf1a is islet cells from the Haster pKO mice (Haster loxP/loxP;Pdx1-Cre), we performed scRNA-seq of pancreatic islets from control and adult female Haster pKO mice.

2022-05-01 | E-MTAB-11477 | biostudies-arrayexpress

UMI-4C in control and HASTER-deficient EndoC-betaH3 cells overexpressing HNF1A

Project description:The HASTER promoter region is a cis-regulatory element that stabilizes the transcription HNF1A. If HASTER is deleted after beta cells have been formed and HNF1A is already stably expressed, HASTER is not required to maintain HNF1A activity, and is only required to provide negative feedback on HNF1A. HNF1A binding to the HASTER promoter mediates the repression of the HNF1A gene itself. To determine whether HNF1A binding to the HASTER promoter remodels 3D chromatin interactions of the HNF1A promoter, we performed UMI-4C experiments in wild type and HASTER-promoter KO EndoC-betaH3 cells with or without doxycycline-induced HNF1A overexpression using the HNF1A promoter as viewpoint.

2022-05-01 | E-MTAB-11473 | biostudies-arrayexpress

Strain-specific RNA-seq in Haster Stop/+ C57BL/6;PWK/PhJ F1 mice

Project description:Germ-line deletion of the Haster promoter region results in overexpression of Hnf1a in liver, while a variegated phenotype is observed in pancreatic islets, with overexpression or silencing of the Hnf1a gene in different cells. Mouse hybrid experiments show that both activation and silencing mechanisms occur in cis. To assess whether HASTER transcription or RNA transcripts are involved in the regulation of Hnf1a, we have generated a mouse model where the 4xSV40 polyA signal has been inserted downstream of Haster promoters (Haster-Stop allele) to terminate Haster transcription, but leaving the Haster promoter intact. Haster Stop/+ F1 mice with the Haster Stop allele from C57BL/6 origin and wild type allele from the PWK/PhJ origin were used for stain-specific RNA-seq in pancreatic islets and liver. Allele-specific quantification of Hnf1a exon 1 were used to assess the requirement of the Haster transcripts/transcription for Hnf1a expression.

2022-05-01 | E-MTAB-11475 | biostudies-arrayexpress

UMI-4C in control and HASTER-deficient EndoC-betaH3 cells overexpressing HNF1A

Project description:UMI-4C in control and HASTER-deficient EndoC-betaH3 cells overexpressing HNF1A

| PRJEB51139 | ENA

HNF1A, H3K4me3 and H3K27ac ChIP-seq in control and Haster-deficient mouse livers

Project description:HNF1A, H3K4me3 and H3K27ac ChIP-seq in control and Haster-deficient mouse livers

| PRJEB51128 | ENA

RNA-seq in control and Haster-deficient mouse livers

Project description:RNA-seq in control and Haster-deficient mouse livers

| PRJEB51114 | ENA

UMI-4C in control and Haster-deficient mouse livers

Project description:UMI-4C in control and Haster-deficient mouse livers

| PRJEB51135 | ENA

Liver transcriptome profiling of liver specific miR-122 knockout and control male mice

Project description:Liver transcriptome profiling of liver specific miR-122 knockout (miR-122loxP/loxP Alb-Cre) and control (miR-122loxP/loxP) male mice. Expression profile of several hundred mRNAs that include miR-122 targets were altered in miR-122 KO livers. Loss of miR-122 in the germ line resulted in significant changes in hepatic gene expression profile. Among the upregulated genes many are direct targets of miR-122

2012-03-03 | GSE20610 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data