Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

High resolution analysis of epigenetic changes associated with X inactivation, ChIP-Seq

ABSTRACT: This study describes the epigenetic profiling of the X chromosome during X inactivation. It includes H3K4me3 and H3K27me3 ChIP-Seq profiles of male (E14) and female (LF2 and XT67E1) mouse ES cells, together with their differentiated derivatives (either 4d atRA or 10d EB). It also includes ChIP-chip profiles around the Xic on chromosome X of H3K4me3, H3K27me3, H3K9me2, H3K36me3, Pol II, TBP, H3-Core as well as expression, using male (E14) and female (LF2) mouse ES cells, together with their differentiated derivatives (either 4d atRA or 10d EB).

ORGANISM(S): Mus musculus

PROVIDER: GSE15814 | GEO | 2009/06/06

SECONDARY ACCESSION(S): PRJNA123057

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

High resolution analysis of epigenetic changes associated with X inactivation, ChIP-chip

2009-06-06 | GSE15883 | GEO

High resolution analysis of epigenetic changes associated with X inactivation, ChIP-Seq

Project description:This study describes the epigenetic profiling of the X chromosome during X inactivation. It includes H3K4me3 and H3K27me3 ChIP-Seq profiles of male (E14) and female (LF2 and XT67E1) mouse ES cells, together with their differentiated derivatives (either 4d atRA or 10d EB). It also includes ChIP-chip profiles around the Xic on chromosome X of H3K4me3, H3K27me3, H3K9me2, H3K36me3, Pol II, TBP, H3-Core as well as expression, using male (E14) and female (LF2) mouse ES cells, together with their differentiated derivatives (either 4d atRA or 10d EB). Examination of two different histone modifications in 3 cell lines under 3 conditions using ChIP-Seq. Examination of five different histone modifications two transcription factors and gene expression under three conditions in 2 cell lines using ChIP-chip.

2009-06-06 | E-GEOD-15814 | biostudies-arrayexpress

High resolution analysis of epigenetic changes associated with X inactivation, ChIP-chip

2010-05-18 | E-GEOD-15883 | biostudies-arrayexpress

A stepwise mode of TGFβ-SMAD signaling and DNA methylation regulates naïve-to-primed pluripotency and differentiation

Project description:This E14-EB-S2-4-Mass-spec-data dataset includes both raw data and processed matrices for peptides and proteins.

2024-10-22 | PXD057083 |

Comprehensive analysis of genome-wide transcriptome modification during neuronal differentiation of mouse embryonic stem cells by all-trans retinoic acid

Project description:Total RNA from 4 sample which are control and differentiation stage after treated ATRA with 4days (Embryonic body, Embryonic body + ATRA (0D), Embryonic body + ATRA (6D), Embryonic body + ATRA (10D))

2017-03-01 | GSE93581 | GEO

PAR-TERRA RNA directs homologous sex chromosome pairing

Project description:In mammals, homologous chromosomes rarely pair outside meiosis. One exception is the X chromosome, which transiently pairs during X-chromosome inactivation (XCI). How two chromosomes find each other in 3D space is not known. Here, we reveal a required interaction between the X-inactivation center (Xic) and the telomere in mouse embryonic stem (ES) cells. The subtelomeric, pseudoautosomal regions (PARs) of the two sex chromosomes (X and Y) also undergo pairing in both female and male cells. PARs transcribe a class of telomeric RNA, dubbed PAR-TERRA, which accounts for a vast majority of all TERRA transcripts. PAR-TERRA binds throughout the genome, including to the PAR and Xic. During X-chromosome pairing, PAR-TERRA anchors the Xic to the PAR, creating a ‘tetrad’ of pairwise homologous interactions (Xic–Xic, PAR–PAR, and Xic–PAR). Xic pairing occurs within the tetrad. Depleting PAR-TERRA abrogates pairing and blocks initiation of XCI, whereas autosomal PAR-TERRA induces ectopic pairing. We propose a ‘constrained diffusion model’ in which PAR-TERRA creates an interaction hub to guide Xic homology searching during XCI.

2017-07-10 | GSE69887 | GEO

Influence of Water Chemistry on Toxicogenomics of Chronic Lead Toxicity to the Fathead Minnow (Pimephales promelas)

Project description:Despite major successes in reducing the risks of lead (Pb) exposure over the past few decades, two issues of considerable importance remain unresolved: (1) how differences in water chemistry influence acute and chronic Pb toxicity, and (2) the elucidation of specific toxic mechanisms and modes of action (MOA). To more clearly define the water chemistry parameters mediating Pb toxicity we evaluated the effects of hardness (as CaSO4) and DOC (as humic acid (HA)) during chronic (150d) exposures to the fathead minnow (Pimephales promelas). Traditional toxicological endpoints were examined alongside gene expression analyses to help clarify the underlying mechanisms and MOA of Pb toxicity and to identify robust molecular markers of exposure and effect. Keywords: time course, chronic lead (Pb) exposure To analyze the gene expression responses to low-level Pb exposures fish were exposed +/- Pb in low ionic strength base water and fish collected at 2d, 4d, 10d, and 30d for microarray analysis. Equal amounts of RNA from all no lead controls were pooled (18 fish total for 2d & 4d exposures; 12 fish total for 10d & 30d exposures) as reference samples for hybridization with each of 3 separate biological replicate pools (6 fish total for 2d & 4d exposures; 4 fish total for 10d & 30d exposures) of RNA from age-matched, lead-exposed fish. Each pair of hybridizations was repeated with dye-swaps. Additional repeats were performed for various arrays to ensure quality of data obtained from initial hybridization.

2008-04-06 | E-GEOD-8404 | biostudies-arrayexpress

Jarid2 methylation is required for PRC2 functioning during ES cells differentiation

Project description:We report that Jarid2 is methylated at K116 by the polycomb complex PRC2. We analyzed Jarid2 versus Methylated Jarid2 genomic localization by ChIP-seq. We also study H3K27 enrichment in Jarid2 knock out ES cells and in cells rescued for Jarid2 or a mutant that cannot be methylated. ChIP-seq for H3K27me3 was perfomed in undiffrentiated ES cells as well as after 8 days of diffrentiation toward Embroyid Bodies (Hanging Drop method). Experiment 1: Jarid2 vs Jarid2me ChIP-seq in undifferentiated mouse ES cells (E14). Experiment 2: H3K27me3 ChIP-seq in Jarid2 -/- ES cells (peng, 2009, Cell), or the same cells rescue with a BAC expressing JARID2 or a mutant of K116 to A. H3K27me3 Chip-seq were perfomed in undifferentiated ES cells and in EB after 8 days of differentiation (hanging Drop method).

2015-01-22 | E-GEOD-55630 | biostudies-arrayexpress

The effects of oxygen treatments on angiogenesis and lymphangiogenesis in mouse embryoid bodies

Project description:This study investigates the processes of angiogenesis and lymphangiogenesis in an in vitro mouse Embryoid Body (EB) model while maintaining as closely as possible an in vivo environment that is observed in human and murine placental development. Several studies have documented that human placental development is profoundly influenced by oxygen tension. Further the developing murine embryo also experiences hypoxic conditions prior to parturition, which regulates early organogenesis and embryonic blood vessel formation in vivo. Embryonic stem (ES) cells derived from 129/SvJ mice were differentiated into embryoid bodies (EBs) and were subjected to two oxygen treatments: normoxia (21% O2) and hypoxia (2.6%). Hypoxia was achieved in a humidified chamber flushed with 95% N2/5% CO2 until the oxygen level was stably maintained at 2.6%. EBs were transferred on days E8, E12, E15 and E18 to hypoxia or maintained in normoxia. After 2 days of differential oxygen treatments, these EBs were analyzed at E10, E14, E17 and E20 respectively. A 4 x 2, reference-based, experimental design was utilized consisting of 4 timepoints (E10, E14, E17 and E20) subjected to 2 oxygen treatments (normoxia, hypoxia) with n=4 biological replicates present in each group. All EB samples were handled in parallel through all experimental steps. Each EB RNA sample was amplified, labeled with Cy5, and compared to the same Mouse Universal Reference RNA sample (Stratagene, La Jolla, CA) that was amplified and labeled with Cy3 dye. No dye swaps were utilized.

2012-08-11 | E-GEOD-17613 | biostudies-arrayexpress

Transcription profiling of mouse embryonic fibroblasts (MEF) during adipocyte differentiation timeseries

Project description:Gene expression timeseries analysis of mouse embryonic fibroblasts (MEF) during differentiation to mature adipocytes with a 27.648 element murine cDNA microarray. Three independent time series experiments of MEF adipocyte differentiation were performed in reference design. RNA from 7 time points (0d, 1d, 2d, 3d, 4d, 6d, 10d) was hybridized against RNA from the preconfluent stage to study the gene expression profile over the whole differentiation process.

2010-01-20 | E-MARS-13 | 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