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

Chromatin signature identifies monoallelic gene expression across mammalian cell types

ABSTRACT: This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

ORGANISM(S): Mus musculus

SUBMITTER: Sebastien Vigneau

PROVIDER: E-GEOD-67384 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Chromatin signature identifies monoallelic gene expression across mammalian cell types (RNA-seq)

Project description:Monoallelic expression of autosomal genes (MAE) is a widespread epigenetic phenomenon which is poorly understood, due in part to current limitations of genome-wide approaches for assessing it. Recently, we reported that a specific histone modification signature is strongly associated with MAE, and demonstrated that it can serve as a proxy of MAE in human lymphoblastoid cells (Nag et al. Elife. 2013 Dec 31;2:e01256). Here, we use murine cells to establish that this chromatin signature is conserved between mouse and human, and is associated with MAE in every tested cell type. Our analyses reveal extensive conservation in the identity of MAE genes between the two species. By applying MAE chromatin signature analysis to a large number of cell and tissue types, we show that the MAE state remains consistent during terminal cell differentiation and is predominant among cell-type specific genes, suggesting a link between MAE and specification of cell identity. PolyA RNA purification and subsequent high-throughput sequencing were performed on two independent B-lymphoid clonal cell line, derived from 129S1/SvImJ x CAST/EiJ F1 mice and immortalized with Abelson murine leukemia virus, and on two independent fibroblast clonal cell lines, derived from 129S1/Sv x CAST/EiJ F1 and immortalized with SV40.

2015-06-17 | E-GEOD-67379 | biostudies-arrayexpress

Chromatin signature identifies monoallelic gene expression across mammalian cell types (ChIP-seq)

Project description:Monoallelic expression of autosomal genes (MAE) is a widespread epigenetic phenomenon which is poorly understood, due in part to current limitations of genome-wide approaches for assessing it. Recently, we reported that a specific histone modification signature is strongly associated with MAE, and demonstrated that it can serve as a proxy of MAE in human lymphoblastoid cells (Nag et al. Elife. 2013 Dec 31;2:e01256). Here, we use murine cells to establish that this chromatin signature is conserved between mouse and human, and is associated with MAE in every tested cell type. Our analyses reveal extensive conservation in the identity of MAE genes between the two species. By applying MAE chromatin signature analysis to a large number of cell and tissue types, we show that the MAE state remains consistent during terminal cell differentiation and is predominant among cell-type specific genes, suggesting a link between MAE and specification of cell identity. Chromatin immunoprecipitation with antibodies specific for histone modifications H3K27me3 and H3K36me3 and subsequent high-throughput sequencing were performed on fixed chromatin from a B-lymphoid clonal cell line, derived from 129S1/SvImJ x CAST/EiJ F1 mice and immortalized with Abelson murine leukemia virus.

2015-06-17 | E-GEOD-67380 | biostudies-arrayexpress

scRNA-seq of human fetal duodenal enteroids grown in EGF and/or NRG1

Project description:The purpose of this study was to interrogate the role of EGF-family ligands, in particular Epidermal Growth Factor (EGF) and Neuregulin 1 (NRG1), as human intestinal stem cell niche factors. An established duodenal enteroid line derived from a 20.2 week post conception biological specimen was exposed to either EGF or NRG1 for five days, after which scRNA-seq was performed to assess changes in gene expression and cellular composition. In an independent experiment, scRNA-seq was performed on freshly isolated duodenal epithelium from a 15 week specimen cultured in the presence of EGF, NRG1, or both EGF and NRG1 after 2 passages.

2020-12-10 | E-MTAB-9720 | biostudies-arrayexpress

Bulk RNA-seq of Adult and Fetal Enteroids (Control or Treated with DBZ)

Project description:Bulk RNA sequencing data of both adult and fetal enteroid lines cultured for 1 or 3 days. Conditions include enteroids grown in control basal media and basal media with the notch inhibitor DBZ added.

2022-04-08 | E-MTAB-11619 | biostudies-arrayexpress

Trim24 ChIP-seq in embryonic stem (ES) cells grown by 2i+LIF (2iL) and serum media

Project description:ChIP followed by next generation sequencing against Trim24 was performed in mouse embryonic stem (ES) grown either in 2i+LIF (2iL) or serum media. Two biological replicates for each condition were sequenced using Illumina HiSeq. Two input controls (no IP) were also generated for each condition.

2016-11-08 | E-MTAB-3802 | biostudies-arrayexpress

Trim24 knock down in the 2i-state of the mouse ES cells

Project description:Differentially expressed genes were determined by single-end sequencing (stranded protocol) following Trim24 and/or p53 knock down in the mouse ES cells grown in 2i media. Triplicates were generated for treatment and control samples but for p53 knock down (duplicate).

2017-11-08 | E-MTAB-4893 | biostudies-arrayexpress

The gene expression changes by CID 70698683

Project description:CID 70698683 is a novel broad-spectrum antiviral compound. To understand the broad-spectrum antiviral mechanism, the cellular gene expression changes by the treatment of CID70698683 was measured. HEp-2 cells grown in 6-well plates were treated with 5 microM of CID 70698683 for overnight and the cellular RNA was extracted (Treatment group). For control, DMSO was used instead of CID 70698683 (final concentration of 0.25%). Three replicates per group used.

2015-11-25 | E-GEOD-72167 | biostudies-arrayexpress

Impact of MAREMO peptide MP5 on gene expression in tumor cells

Project description:After seeding and growth for 18 hours in 10%FBS/DMEM, NT193M cells were incubated with MP5 (50 microgr/ml) in 0.1% FCS/DMEM for 72 hours before collection of RNA and RNA seq analysis. Expression and p-values of the genes differentially expressed in MP5 (compared to PBS) treated NT193M cells with p-values < 0.05, N = 5 replicates per group.

2024-09-25 | E-MTAB-14437 | biostudies-arrayexpress

scRNA-seq of intestinal epithelial organoids derived from human fetal duodenum

Project description:Here, we used single-cell RNA-sequencing (scRNA-seq) to profile intestinal epithelial only organoids (also known as enteroids) from human fetal duodenum after one passage of in vitro growth. Organoids were grown in the standard 25% LWRN media with either 100 ng/ml of epidermal growth factor (EGF) or 1 ng/ml of EPIREGULIN (EREG) added.

2022-07-17 | E-MTAB-11912 | biostudies-arrayexpress

Acetylated histone H3K56 interacts with Oct4 to promote mouse embryonic stem cell pluripotency

Project description:The presence of acetylated histone H3K56 in human embryonic stem cells (ESCs) correlates positively with the binding of Nanog, Sox2 and Oct4 (NSO) transcription factors at their target gene promoters. However, the function of H3K56ac there has been unclear. We now report that Oct4 interacts with K56ac and it is functionally important since K56ac combines with NSO factors in ChIP-Seq to mark the regions associated with pluripotency better than NSO alone. Therefore, our data suggest that K56ac plays a critical role in binding to Oct4 to promote the pluripotency of ESCs. Genome wide location analysis ChIP-Seq was performed in mouse embryonic stem cell lines (E14Tg2a) for histone H3K56ac.

2013-06-25 | E-GEOD-47387 | 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