Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

42 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ChIP-seq profiling of H3K27 tri-methylation in Ezh2-deficient and control murine lung epithelium at day E16.5

ABSTRACT: Epithelial (CD31-CD45-EpCAM+) lung cells were derived by FACS from ShhCre;Ezh2fl/fl and control ShhCre;Ezh2fl/+ mouse embryos at day E16.5 (2 biological replicates per genotype). Chromatin from each of the replicates was immunoprecipitated with H3K27me3 antibody (Millipore #07-449) and subjected to NGS library preparation using TruSeq Nano DNA Sample Preparation Kit (Illumina). Completed libraries from different samples were sequenced on HiSeq 2500 TruSeq with SBS Kit v3 - HS reagents (Illumina) as 100 bp single end reads at the Australian Genome Research Facility. ChIP-seq profiles of H3K27 tri-methylation from Ezh2 deficient and control lung epithelium (2 replicates per genotype).

ORGANISM(S): Mus musculus

SUBMITTER: Marie-Liesse Asselin-Labat

PROVIDER: E-GEOD-57392 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Repression of Igf1 expression by Ezh2 prevents basal cell differentiation in the developing lung.

Galvis Laura A LA Holik Aliaksei Z AZ Short Kieran M KM Pasquet Julie J Lun Aaron T L AT Blewitt Marnie E ME Smyth Ian M IM Ritchie Matthew E ME Asselin-Labat Marie-Liesse ML

Development (Cambridge, England) 20150319 8

Epigenetic mechanisms involved in the establishment of lung epithelial cell lineage identities during development are largely unknown. Here, we explored the role of the histone methyltransferase Ezh2 during lung lineage determination. Loss of Ezh2 in the lung epithelium leads to defective lung formation and perinatal mortality. We show that Ezh2 is crucial for airway lineage specification and alveolarization. Using optical projection tomography imaging, we found that branching morphogenesis is a ...[more]

PMID: 25790853

Similar Datasets

RNA-seq profiling of gene expression in Ezh2-deficient and control murine lung epithelial and stromal cell populations at day E16.5

Project description:Epithelial (CD31-CD45-EpCAM+) and stromal (CD31-CD45-EpCAM-) lung cells were derived by FACS from ShhCre;Ezh2fl/fl and control ShhCre;Ezh2fl/+ mouse embryos at day E16.5 (3 biological replicates per genotype-tissue combination). Total RNA extracted from the samples was subjected to NGS library preparation using TruSeq Stranded Total RNA with Ribo-Zero (Illumina). Completed libraries from different samples were sequenced on HiSeq 2000 TruSeq with SBS Kit v3 - HS reagents (Illumina) as 100 bp single end reads at the Australian Genome Research Facility. RNA-seq gene expression profiles from Ezh2 deficient and control lung epithelial and stromal cell populations at day E16.5 (3 replicates per genotype-tissue combination).

2015-05-11 | E-GEOD-57391 | biostudies-arrayexpress

ChIP-seq profiling of H3K27 tri-methylation in Ezh2-deficient and control murine lung epithelium at day E16.5

Project description:Epithelial (CD31-CD45-EpCAM+) lung cells were derived by FACS from ShhCre;Ezh2fl/fl and control ShhCre;Ezh2fl/+ mouse embryos at day E16.5 (2 biological replicates per genotype). Chromatin from each of the replicates was immunoprecipitated with H3K27me3 antibody (Millipore #07-449) and subjected to NGS library preparation using TruSeq Nano DNA Sample Preparation Kit (Illumina). Completed libraries from different samples were sequenced on HiSeq 2500 TruSeq with SBS Kit v3 - HS reagents (Illumina) as 100 bp single end reads at the Australian Genome Research Facility.

2015-05-11 | GSE57392 | GEO

RNA-seq profiling of gene expression in Ezh2-deficient and control murine lung epithelial and stromal cell populations at day E16.5

2015-05-11 | GSE57391 | GEO

Repression of Igf1 expression by Ezh2 prevents basal cell differentiation in the developing lung

Project description:Gene expression (RNA-seq) and H3K27me3 binding (ChIP-seq) profiling of wild type and Ezh2-deficient mouse lung epithelium. Lungs from wild type and Ezh2-deficient mice (Ezh2 deletion is specific to lung epithelium) were collected at day e16.5. Lung cells were separated into epithelial and stromal populations based on EpCAM expression. Epithelial cells were profiled for both gene expression (Total RNA-seq) and H3K27me3 binding (ChIP-seq). Additionally, stromal cells were also profiled for gene expression.

2015-05-11 | E-GEOD-57393 | biostudies-arrayexpress

Defining the genomic occupancy of the general regulatory factor Abf1 in budding yeast

Project description:Abf1 has been defined as a general regulatory factor involved in determining chromatin structure in the yeast Saccharomyces cerevisiae. As such, it plays a major role in a range of functions including DNA replication, transcriptional activation and gene silencing, as well as DNA repair. Previous studies have identified an Abf1 DNA consensus binding sequence and Abf1 binding at up to several hundred locations throughout the genome. Depletion of Abf1 in the cell, however, results in altered nucleosome structure at many thousands of sites throughout the yeast genome, suggesting a far greater role for Abf1 in chromatin structure and dynamics. Here, we examine genome-wide Abf1 binding using ChIP-Chip to measure its chromatin occupancy. Using a novel software package, Sandcastle, we detect 3,821 genomic positions at which Abf1 binds. We conducted a detailed bioinformatic analysis of these novel Abf1 binding sites, defining variations in the current consensus sequence and identifying many more genomic locations at which Abf1 can be found. These observations define the sites at which Abf1 occupancy determines chromatin structure, providing a framework for understanding how processes such as replication, transcription and DNA repair are organised within the genome.

2017-12-31 | E-MTAB-3890 | biostudies-arrayexpress

Differential gene expression in embryonic lung and small intestine after epithelial deletion of centrioles

Project description:Epithelial specific disruption of centrioles but not cilia results in severe phenotype in the lung but not in the intestine. Compare gene expression in lung and small intestine of control (ShhCre Cenpj+/lox), epithelial centriole disrupted (ShhCre Cenpj-/lox), and epithelial cilia disrupted (ShhCre Ift88-/lox).

2021-12-31 | GSE188585 | GEO

Chromatin contact maps of 24 and 48 hours post-fertilisation zebrafish (Danio rerio) embryos and 48 hours post-fertilisation fibroblasts

Project description:In this experiment, we've examined chromatin conformation of zebrafish embryos at 24 and 48 hours post-fertilization (hpf), as well as 48 hpf fibroblasts. The aim of this study was to characterise the 3D chromatin structure of zebrafish and perform an evolutionary comparison with mammalian genomes (Homo sapiens and Mus musculus) focusing on syntenic regions and zebrafish ohnologs (duplicated genes that were kept in the genome after the third round of whole-genome duplication).

2023-11-17 | E-MTAB-6313 | biostudies-arrayexpress

Four Hi-C datasets from mESCs and 2C-like cells generated by knocking down the histone chaperone CAF-1 in mESCs

Project description:In this experiment, we've examined chromatin conformation of mESCs and 2C-like cells generated from a CAF-1 knockdown. The method to generate the knockdown was described in (). We performed a modified in situ Hi-C protocol from (Rao et al., 2014) and that can be found in detail at (Díaz et al., 2017, under revision). Samples were digested with MboI restriction enzyme having as starting material 100k cells with two biological replicates per sampling point. The aim of the experiment was to analyze the potential chromatin conformational changes that accompany the mESC to 2C-like transition.

2023-11-16 | E-MTAB-6330 | biostudies-arrayexpress

Low input Hi-C datasets for a diffuse large B-cell lymphoma sample, healthy control human B-cells and mouse embryonic stem cells

Project description:In this experiment, we've examined chromatin conformation of OG2 (B6; CBA-Tg(Pou5f1-EGFP)2Mnn/J; stock number 004654) mouse stem cells cultured as described in (Shi et al., 2008), using different amounts of starting cells. We performed a modified in situ Hi-C protocol for 6 samples digested with MboI restriction enzyme having as starting material 1 million (M), 100 thousand (k), 50k, 25k, 10k or 1k cells. As well as, to 2 samples digested with HindIII restriction enzyme that had as starting material 5M or 100k cells. Traditional in situ Hi-C protocols recommend 5-10 million starting cells. The aim of the experiment was to assess the impact of decreasing the cell number on reproducibility, library complexity, chromatin structure visualization in order to adapt the method to the study of rare cell populations. Furthermore, we have characterised the 3D structure of peripheral blood mononuclear cells (PBMCs) obtained from a blood extraction from a healthy donor and from a lymph node biopsy from a DLBCL patient as a proof of concept for the suitability of Low-C for rare cell population analysis.

2018-11-30 | E-MTAB-5875 | biostudies-arrayexpress

Six in situ Hi-C libraries of control and mESC auxin-inducible degrons for Scc1 and Ring1b.

Project description:In this experiment, we've examined chromatin conformation differences of E14 mESC against cohesin and Ring1b degrons. We performed a modified in situ Hi-C protocol from (Rao et al., 2014) that can be found in detail at (Díaz et al., 2018). Samples were digested with MboI restriction enzyme. The aim of the experiment was to characterize the role of cohesin and polycomb on the 3D structure of mouse chromatin.

2020-01-23 | E-MTAB-7816 | 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