Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

DHS NS5 Cells

ABSTRACT: Here we performed DNAse-seq experiments on samples of adherent cultures of mouse neural stem cells (NS5 cell line) under normal growth conditions and upon differentiation by expression of an inducible version of the proneural factor Mash1/Ascl1 (Ascl1-ERT2). This resulted in the generation of genome-wide maps of regions of chromatin accessibility in both conditions.

INSTRUMENT(S): Illumina Genome Analyzer II

ORGANISM(S): Mus musculus

SUBMITTER: Raposo Alexandre

PROVIDER: E-MTAB-2270 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Histone ChIP NS5 Ascl1-ERT2

Project description:Here we performed a ChIP-seq experiment on a sample of adherent cultures of mouse neural stem cells (NS5 cell line) expressing an inducible version of the proneural factor Mash1/Ascl1 (Ascl1-ERT2) under normal growth conditions and after 24 hours of activation by 4-Hydroxytamoxifen. This resulted in the generation of a genome-wide map of histone modifications H3K27ac and H3K4me1.

2015-02-16 | E-MTAB-3104 | biostudies-arrayexpress

ChIP NS5 Ascl1-ERT2

Project description:Here we performed a ChIP-seq experiment on a sample of adherent cultures of mouse neural stem cells (NS5 cell line) under normal growth conditions and upon short term activation (30 minutes) of an inducible version of the proneural factor Mash1/Ascl1 (Ascl1-ERT2). This resulted in the generation of a genome-wide map of Ascl1 binding to chromatin.

2015-02-16 | E-MTAB-2384 | biostudies-arrayexpress

Genome-wide identification of regulatory elements in preSertoli cells based on DNaseI hypersensitivity

Project description:Identifying transcriptional networks active during development has been hindered by the slow pace at which regulatory elements are identified, and by the difficulty in purifying cells from developing tissues. We used DNaseI-seq to identify functional regulatory elements in purified fetal preSertoli cells and uncovered thousands of preSertoli-specific DNaseI hypersensitive sites (DHSs) that are likely to activate or repress genes required for Sertoli cell development and function. To demonstrate their functional significance, we validated the preSertoli-specific enhancer activity of a DHS located 50 kb upstream of the Wt1 gene. This genome-wide data will guide many future studies into gene-regulatory mechanisms that operate in the fetal gonad and may lead to the identification of non-coding mutations leading to DSDs. One biological replicate was analyzed for each of the seven mouse samples using DNase-seq.

2013-12-07 | E-GEOD-53076 | biostudies-arrayexpress

Extensive Evolutionary Changes in Regulatory Element Activity during Human Origins Are Associated with Altered Gene Expression and Positive Selection [Dnase-seq]

Project description:The human genome shares a remarkable amount of genomic sequence with our closest living primate relatives. Researchers have long sought to understand what regions of the genome are responsible for unique species-specific traits. Previous studies have shown that many genes are differentially expressed between species, but the regulatory elements contributing to these differences are largely unknown. Here we report a genome-wide comparison of active gene regulatory elements in human, chimpanzee, and macaque, and we identify hundreds of regulatory elements that have been gained or lost in the human or chimpanzee genomes since their evolutionary divergence. These elements contain evidence of natural selection and correlate with species-specific changes in gene expression. Polymorphic DNA bases in transcription factor motifs that we found in these regulatory elements may be responsible for the varied biological functions across species. This study directly links phenotypic and transcriptional differences between species with changes in chromatin structure. One biological replicate was analyzed for each of the 15 primate samples using DNase-seq.

2014-02-13 | E-GEOD-54907 | biostudies-arrayexpress

Defining principles of gene and regulatory element imprinting in mouse trophoblast stem cells

Project description:An undefined number of mammalian genes are expressed preferentially from one parental allele, in a process termed genomic imprinting. To shed light on the general principles of this process in a single cell type, we profiled allelic gene expression, DNaseI hypersensitivity (DHS), and CTCF binding in genetically defined murine trophoblast stem cells (TSCs). The data deposited in this entry are from CTCF ChIP-Seq and DNase-Seq experiments performed in the BC.1 cell line. All other data has been previously deposited as part of GEO Series GSE39406. The F1 TSC line profiled was generated from a cross between a C57BL/6J (B6) female and CAST/EiJ (Cast) male mouse.

2016-07-03 | E-GEOD-51610 | biostudies-arrayexpress

Site-specific silencing of regulatory elements as a mechanism of X-inactivation

Project description:The inactive X chromosome’s (Xi) physical territory is microscopically devoid of transcriptional hallmarks and enriched in silencing-associated modifications. How these microscopic signatures relate to specific Xi sequence is unknown. This study reports the profiling of Xi gene expression and chromatin states at high-resolution via allele-specific sequencing in F1 hybrid mouse trophoblast stem cells (TSCs). Datasets provided include those generated from strand-specific RNA-Seq, ChIP-Seq, FAIRE-Seq, and DNase-Seq protocols. Included for each dataset are FASTQ files, BED alignments and WIG files with coordinates relative to UCSC genome build mm9, and _snp files that report the location of all SNP-overlapping reads. The F1 TSC lines profiled were generated from crosses between CAST/EiJ (Cast) and C57BL/6J (B6) mice. C/B denotes a Cast mother and B6 father, and B/C denotes a B6 mother and Cast father.

2012-11-21 | E-GEOD-39406 | biostudies-arrayexpress

ChIP-seq NS5 Zeb1

Project description:Here we performed a ChIP-seq experiment on a sample of adherent cultures of mouse neural stem cells (NS5 cell line) under normal growth conditions. This resulted in the generation of a genome-wide map of Zeb1 binding to chromatin.

2016-07-01 | E-MTAB-3560 | biostudies-arrayexpress

ChIP-seq NS5 RBPJ

2016-09-09 | E-MTAB-4494 | biostudies-arrayexpress

ChIP-Seq MyT1-HA in NS5

Project description:Here we performed a ChIP-seq experiment on a sample of adherent cultures of mouse neural stem cells (NS5 cell line) expressing an inducible HA-tagged version of the proneural factor MyT1 (MyT1-HA, under TetON control) after activation by doxycycline hyclate (DOX). This resulted in the generation of a genome-wide map of MyT1-HA binding to chromatin.

2016-09-09 | E-MTAB-4330 | biostudies-arrayexpress