Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

39 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

LRH-1 and PTF1-L coregulate an exocrine pancreas-specific transcriptional network for digestive function [RNA-Seq]

ABSTRACT: Two separate pools of three Flox or two Lrh1t-/- pancreas RNA preparations was subjected to the Illumina RNA-seq protocol. Examination of mRNA levels in induced Lrh1 pancreas knockout and wild-type mice.

ORGANISM(S): Mus musculus

SUBMITTER: Scott Ochsner

PROVIDER: E-GEOD-34030 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

LRH-1 and PTF1-L coregulate an exocrine pancreas-specific transcriptional network for digestive function.

Holmstrom Sam R SR Deering Tye T Swift Galvin H GH Poelwijk Frank J FJ Mangelsdorf David J DJ Kliewer Steven A SA MacDonald Raymond J RJ

Genes & development 20110801 16

We have determined the cistrome and transcriptome for the nuclear receptor liver receptor homolog-1 (LRH-1) in exocrine pancreas. Chromatin immunoprecipitation (ChIP)-seq and RNA-seq analyses reveal that LRH-1 directly induces expression of genes encoding digestive enzymes and secretory and mitochondrial proteins. LRH-1 cooperates with the pancreas transcription factor 1-L complex (PTF1-L) in regulating exocrine pancreas-specific gene expression. Elimination of LRH-1 in adult mice reduced the co ...[more]

PMID: 21852532

Similar Datasets

LRH-1 and PTF1-L coregulate an exocrine pancreas-specific transcriptional network for digestive function [ChIP-Seq]

Project description:We have determined the cistrome and transcriptome for the nuclear receptor liver receptor homolog-1 (LRH-1) in the exocrine pancreas. Chromatin immunoprecipitation (ChIP)-seq and RNA-seq analyses reveal that LRH-1 directly induces expression of genes encoding digestive enzymes and secretory and mitochrondrial proteins. LRH-1 cooperates with the pancreas transcription factor 1-L complex (PTF1-L) in regulationg exocrine pancreas-specific gene expression. Elimination of LRH-1 in adult mice reduced the concentration of several lipases and proteases in pancreatic fluid and impaired pancreatic fluid secretion in response to cholecystokinin. Thus, LRH-1 is a key regulator of the exocrine pancreas-specific transcriptional network required for the production and secretion of pancreatic fluid. input and Lrh1 ChIP

2011-12-09 | E-GEOD-34295 | biostudies-arrayexpress

LRH-1 and PTF1-L coregulate an exocrine pancreas-specific transcriptional network for digestive function

Project description:This SuperSeries is composed of the following subset Series: GSE34030: LRH-1 and PTF1-L coregulate an exocrine pancreas-specific transcriptional network for digestive function [RNA-Seq] GSE34295: LRH-1 and PTF1-L coregulate an exocrine pancreas-specific transcriptional network for digestive function [ChIP-Seq] Refer to individual Series

2011-12-09 | E-GEOD-34296 | biostudies-arrayexpress

Sel1L is Indispensable for Mammalian ERAD, ER Homeostasis and Survival

Project description:Sel1L is an adaptor protein for the E3 ligase Hrd1 involved in endoplasmic reticulum-associated degradation (ERAD). Its physiological importance in mammalian ERAD, however, remains to be established. Here, using the inducible Sel1L knockout mouse and cell models, we provide the first in vivo evidence that Sel1L is indispensable for Hrd1 stability, ER homeostasis and survival. Acute loss of Sel1L leads to premature death in adult mice within 3 weeks with profound pancreatic atrophy. Contrary to current belief, our data show that mammalian Sel1L is required for Hrd1 stability and ERAD function both in vitro and in vivo. Sel1L deficiency disturbs ER homeostasis, activates ER stress, attenuates translation and promotes cell death. Serendipitously, using biochemical approach coupled with mass spectrometry, we found that Sel1L deficiency causes the aggregation of both small and large ribosomal subunits. Thus, Sel1L is an indispensable component of mammalian ERAD and ER homeostasis, which is essential for protein translation, pancreatic function, cellular and organismal survival. Pancreas tissue of wild type and inducible Sel1L knockout mice were subjected to gene expression analysis.

2013-12-04 | E-GEOD-52929 | biostudies-arrayexpress

Nanostring microRNA microarry analysis of p53 and Mdm2 knockout mouse hearts compared to vehicle-injected negative controls

Project description:Adult cardiomyocytes (CM) are terminally differentiated cells with minimal regenerative capacity, making cardiac tissue particularly vulnerable to injury. Thus, defining the roadblocks responsible for adult CM cell cycle arrest lies at the core of developing therapies to regenerate myocyte loss following injurious events such as myocardial infarction. We have previously shown that inactivating the p53/Mdm2 tumor suppressor circuitry, specifically in the heart (using the Cre-loxP recombination system of bacteriophage P1), can allow differentiated CMs to regain proliferative capacity, through an upregulation of factors involved in cell cycle re-entry. These factors are repressed in quiescent CMs, in part through the action of microRNAs (miRNAs). Notably, knockout of either p53 or Mdm2 individually was insufficient to promote CM proliferation. Therefore, we hypothesized that inactivation of p53/Mdm2-regulated miRNAs could promote the expression of cell cycle activators and induce proliferation of adult murine CMs. To identify miRNAs regulated by both p53 and Mdm2, total miRNA expression profiles from cardiac specific p53/Mdm2 double knockout (DKO) mouse hearts were compared with those from cardiac-specific single knockouts (p53KO and Mdm2KO), and vehicle-injected controls using the Nanostring nCounter mouse miRNA expression assay. This revealed a profile of 11 significantly downregulated miRNAs in the proliferative DKO hearts (versus vehicle-injected control), that were enriched for mRNA targets involved in cell cycle regulation. In vitro studies have demonstrated that knockdown of these 11 miRNAs in neonatal rat cardiomyocytes can increase the occurrence of cytokinetic events. Ultimately, we aim to inject antagomirs targeting these miRNAs into animals post-myocardial infarction to determine the effect of p53/Mdm2-regulated miRNAs on heart function and CM proliferation in vivo.

2017-03-22 | E-MTAB-5531 | biostudies-arrayexpress

Calcineurin-dependent transcriptome in ICN1 (activated NOTCH1)-induced T cell acute lymphoblastic leukemia (T-ALL)

Project description:Activated NOTCH1 induces T-ALL in mice when transduced in bone marrow (BM) cells. T-ALL cells activate the calcineurin/NFAT pathway in vivo (Medyouf H. et al. Nat Med 2007 [PMID 17515895]). Through appropriate crosses, mouse ICN1-induced T-ALL were generated that include a ROSCreERT2 transgene and 2 copies of a CnB1 floxed alleles. Cohorts of secondary recipient mice were injected with these T-ALL cells, and when becoming leukemic, divided into 2 subgroups. Group 1 was treated with Tamoxifen (TAM), resulting in CnB1 gene deletion and inactivation of calcineurin. Group 2 was treated with carrier solvent (corn OIL), thus maintaining CnB1 and calcineurin activity. RNAs were extracted from flow cytometry-sorted leukemic cells. Details in Gachet S. et al. Leukemia 2013 (PMID 23689515).

2014-08-09 | E-GEOD-60258 | biostudies-arrayexpress

Characterization of the molecular signature associated with the ablation of integrin Î±6 in IECs in the Î±6ÎIEC-TAM mouse model

Project description:Transcriptome analysis of mRNAs extracted from the rectal mucosa of WT and Î±6ÎIEC-TAM mice, 15 days after tamoxifen treatment Inflammatory bowel diseases (IBD) in humans are characterized by chronic inflammation and gastrointestinal tissue damage, caused by a combination of genetic and environmental factors. We show that the specific ablation of integrin Î±6 in intestinal epithelial cells (IECs) results in spontaneous colorectal inflammation in mice. In order to characterize the earlier molecular signature involved in the onset of inflammation, we performed Affymetrix microarrays and compare control versus Î±6ÎIEC-TAM transcriptomes after tamoxifen treatment. RNAs were prepared from rectal mucosa of 3 control mice treated with tamoxifen, 4 mutant mice treated with tamoxifen and 4 mutant mice treated with NaCl. The transcriptome analysis was performed using the Affymetrix Mouse Gene 1.0 ST arrays. Images were processed using affymetrix GeneChipÂ® Command ConsoleÂ® Software (AGCC) (version 2.0) and numerical values were generated using Affymetrix Expression Consoleâ¢ Software (version 1.1).

2016-07-07 | E-GEOD-70700 | biostudies-arrayexpress

Genome-wide transcriptome analyses of transgenic mice, that express Cre recombinase flanked by mutated estrogen receptors (MerCreMer; mcm), and carry loxP-flanked sequences of p53 and Mdm2 was performed in the presence and absence of Tamoxifen

Project description:Genome-wide transcriptome analyses of transgenic mice, that express Cre recombinase flanked by mutated estrogen receptors (MerCreMer; mcm), and carry loxP-flanked sequences of p53 and Mdm2 was performed in the presence and absence of Tamoxifen.<br>The molecular mechanisms underlying heart failure remain poorly understood. As such, identifying the factors which effectively maintain cardiac tissue homeostasis is of great scientific and clinical importances. The tumor suppressor Trp53 (p53) inhibits cell growth after acute stress by regulating gene transcription. The mammalian genome contains hundreds of p53 binding sites. However, whether p53 participates in the regulation of cardiac tissue homeostasis under normal conditions is not known. To examine the physiologic consequences of p53 and Mdm2 ablation in adult cardiomyocytes in vivo, cardiac morphology and function were assessed in conditional mutant mice.

2017-02-23 | E-MTAB-5441 | biostudies-arrayexpress

Gene expression profile of mature plasmacytoid dendritic cells (PDC) after the deletion of transcription factor E2-2

Project description:The interferon-producing plasmacytoid dendritic cells (PDC) share common progenitors with antigen-presenting classical dendritic cells (cDC), yet they possess distinct morphology and molecular features resembling those of lymphocytes. It is unclear whether the unique cell fate of PDC is actively maintained in the steady state. We report that the deletion of transcription factor E2-2 from mature peripheral PDC caused their spontaneous differentiation into cells with cDC properties. This included the loss of PDC markers, increase in MHC class II expression and T cell priming capacity, acquisition of dendritic morphology and induction of cDC signature genes. Genome-wide chromatin immunoprecipitation revealed direct binding of E2-2 to key PDC-specific and lymphoid genes, as well as to certain genes enriched in cDC. Thus, E2-2 actively maintains the cell fate of mature PDC and opposes the “default” cDC fate, in part through direct regulation of lineage-specific gene expression programs. Inducible deletion of E2-2 (Tcf4) has been performed by administering tamoxifen to conditional E2-2flox/flox Rosa26-CreER+ mice or to E2-2flox/flox Rosa26-CreER- control littermates. Four or six days later total splenocytes were isolated, pooled from 2-3 mice and PDC (CD11b- B220+ CD11clow Bst2+) were isolated by sorting. Global gene expression profiles of E2-2-deficient (null) and control (Ctrl) PDC were compared using Affymetrix microarrays (GPL1261).

2010-12-21 | E-GEOD-24726 | biostudies-arrayexpress

A senescence-inflammatory switch from cancer-inhibitory to cancer-promoting mechanism

Project description:To elucidate the effect of senescence in mouse colorectal tumor, the transcriptome of enterocytes from CKI alpha deletion mutants (CKI alpha KO), CKI alpha/p53 double deletion mutants (CKI alpha/p53 DKO) and CKI alpha heterozygous mice (CKI alpha Het) were determined by RNAseq.

2013-06-12 | E-MTAB-1683 | biostudies-arrayexpress

Single-cell sequencing of tissue-resident CD4+ T cells that drive compartmentalized immunopathology in the CNS

Project description:In chronic inflammatory diseases of the central nervous system (CNS), immune cells persisting behind the blood-brain barrier are supposed to promulgate local tissue destruction. The drivers of such compartmentalized inflammation remain unclear, but tissue-resident memory T cells (TRM) represent a potentially important cellular player in this process

2022-02-19 | E-MTAB-11422 | biostudies-arrayexpress

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