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Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling by array of mouse wild type and Nkx2.2 knock-out embryos

ABSTRACT: The goal: Investigate the genes differentlly expressed during pancreas development. The model: The Nkx2.2 null allele was generated using standard homologous recombination in ES cells. The Pgk:NeoR cassette was inserted into a 4.4 Kb deletion of the Nkx2.2 genomic locus, effectively deleting both coding exons. The mice are maintained on a Swiss Black strain background.

ORGANISM(S): Mus musculus

SUBMITTER: Lori Sussel

PROVIDER: E-MTAB-356 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Novel computational analysis of protein binding array data identifies direct targets of Nkx2.2 in the pancreas.

Hill Jonathon T JT Anderson Keith R KR Mastracci Teresa L TL Kaestner Klaus H KH Sussel Lori L

BMC bioinformatics 20110225

<h4>Background</h4>The creation of a complete genome-wide map of transcription factor binding sites is essential for understanding gene regulatory networks in vivo. However, current prediction methods generally rely on statistical models that imperfectly model transcription factor binding. Generation of new prediction methods that are based on protein binding data, but do not rely on these models may improve prediction sensitivity and specificity.<h4>Results</h4>We propose a method for predictin ...[more]

PMID: 21352540

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NKX2.2

Project description:NKX2.2

| PRJNA316849 | ENA

Gene expression profiling of wild-type, Nkx2.2 null, NeuroD null and Nkx2.2/NeuroD double KO E13.5 pancreata

Project description:The experiment consist of 16 one channel assays for analyzing embryonic pancreas at E13. There are four replicates per condition. We are looking at differential gene expression across four mouse lines: WT, Nkx2.2, NeuroD and Nkx2.2/NeuroD double mutants at E13.5.

2015-02-03 | E-MTAB-3350 | biostudies-arrayexpress

Functional analysis of the Nkx2.2 SD domain: gene expression profiling of E16.5 Nkx2.2 SD mutant pancreata versus wild-type littermate pancreata

Project description:The experiment consists of 7 one channel assays for analyzing embryonic pancreas at E16.5. There are three or four replicates per condition. At E16.5, we are looking at differential gene expression across two mouse lines, WT vs Nkx2.2 SD mutants.

2015-01-29 | E-MTAB-3349 | biostudies-arrayexpress

Transcription profiling of mouse wild type and Nkx2.2 mutant embryos at E12.5 and E13.5 to identify a transcripional program that Nkx2.2 regulation in the pancreas

Project description:The goal of this experiment was to analyze expression changes in the pancreas at embryonic days 12.5 and 13.5 between wild type and Nkx2.2 null mice. We know that Nkx2.2 is essential for pancreatic endocrine differentiation and development. At these early time points which are critical for endocrine cell specification, we would like to identify a transcriptional program that Nkx2.2 regulates. We would also like to identify direct and functional transcriptional targets of Nkx2.2.

2009-11-05 | E-CBIL-44 | biostudies-arrayexpress

Transcription profiling of mouse beta cells lacking NeuroD

Project description:The goal: Investigate NeuroD function in the mature beta cells. The model: Cross RIP-Cre to NeuroD flox/flox mouse to delete neuroD when insulin gene is activated; The methods: Islets are purified and RNA is extracted to see how the profile of gene expression is altered after neuroD is deleted from the beta cells. The comparison: Compare control with mutant; The hypothesis: Since neuroD is deleted, I would expect that neuroD mRNA will be decreased in the mutant samples; The samples: two types of samples will be submitted including control and conditional knockout (mutant); Flox/+,Ins (F/+,I) is the control and labled as group B; and Flox/-,Ins (F/-,I) is the conditional knockout and labled as group A

2010-03-03 | E-MTAB-152 | biostudies-arrayexpress

RNA-Seq analysis of E15.5 pancreas of both whole body Nkx2.2 mutant embryos and endocrine progenitor specific Nkx2.2 mutant embryos

Project description:Aim: Transcriptional analysis of E15.5 whole pancreas of Nkx2.2-LacZ/LacZ embryos versus control and Ngn3-Cre; Nkx2.2-flox/flox embryos versus control Methods: Embryonic pancreata were isolated at E15.5 from Nkx2.2 mutant mice and controls. Total RNA was extracted. Libraries were prepared from total RNA (RIN>8) with the TruSeq RNA prep kit (Illumina) and sequenced using the HiSeq2000 (Illumina) instrument. More than 20 million reads were mapped to the mouse genome (UCSC/mm9) using Tophat (version 2.0.4) with 4 mismatches and 10 maximum multiple hits. Significantly differentially expressed genes were calculated using DEseq. Results: There is significant overlap between the differentially expressed genes of whole body Nkx2.2 mutant embryos and endocrine progenitor specific Nkx2.2 mutant embryos; many of the downregulated genes (p-value < 0.05) are genes involved in beta cell function. Conclusion: Nkx2.2 functions within the endocrine progenitor lineage to activate beta cell genes

2017-01-09 | GSE80444 | GEO

Identification of dysregulated transcripts in nkx2.2(RNAi) planarians.

Project description:Nkx2.2 is an intestine-enriched transcription factor required for regeneration in planarians. The goal of this study was to identify differentially expressed transcripts in uninjured nkx2.2(RNAi) planarians.

2022-05-24 | GSE174228 | GEO

Genome-wide disclosure of the Nkx2.2 targets in oligodendrocytes and their progenitor cells suggests several novel target genes

Project description:The Nkx2.2 transcription factor contributes to regulate the timing of myelination in the CNS. Still, information about the regulon of Nkx2.2 in oligodendrocytes (Ols) and their progenitor cells (OPCs) is restricted to a few genes. Therefore we aimed to identify the entire regulon of Nkx2.2. We performed transcript profiling of postnatal Nkx2.2-/- mice, investigated the expression of selected transcripts in Ol lineage cells after siRNA induced Nkx2.2 knock-down, and identified the genome-wide active Nkx2.2 binding sites in murine OPCs and Ols by use of ChIP-sequencing technique. Thereby we have found 521 genes with active Nkx2.2 binding sites within 10,000 bp of their gene loci that furthermore are differently expressed in absence or lower expression of Nkx2.2. Functionally, the target genes are associated with mitosis, migration stop, protein transport, lipid metabolism, mitochondrial biogenesis, formation of Ca2+ waves, and WNT signalling. Furthermore, motif discovery techniques and tests for overlaps between sequencing reads suggest that MYRF, OLIG2, SOX10, and TCF3 interact or compete with Nkx2.2 in OPCs/Ols. However, the activator versus repressor activity of Nkx2.2 does not seem to depend on the potential interaction with either of the transcription factors. Test for overlaps with sites of specific histone 3 modifications show that the Nkx2.2 binding sites are more frequently associated H3K4me3 and H3K27ac in genes to which Nkx2.2 may act as an activator. This supports previous studies showing that Nkx2.2 acts in a HDAC1 dependent way. Together this provides new insight into how Nkx2.2 contributes to the timing of OPC differentiation and myelination in CNS.

2019-11-01 | GSE73921 | GEO

Genome-wide disclosure of the Nkx2.2 targets in oligodendrocytes and their progenitor cells suggests several novel target genes

2020-09-30 | GSE73664 | GEO

WT vs Nkx2.2-/- (null) cells at E15.5

Project description:Whole transcriptome analysis of Ngn3-expressing cells in WT and Nkx2.2 Null mouse embryos.

2015-02-24 | E-MTAB-3357 | biostudies-arrayexpress