Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Mus musculus

ABSTRACT: Nuclear Lamins are Not Required for Genome Organization in Mouse Embryonic Stem Cells [RNA-Seq]

PROVIDER: PRJNA264802 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR1623081.fastq.gz	Fastqsanger.gz
	SRR1623082.fastq.gz	Fastqsanger.gz
	SRR1623083.fastq.gz	Fastqsanger.gz
	SRR1623084.fastq.gz	Fastqsanger.gz

Items per page:

1 - 4 of 4

Similar Datasets

Mus musculus

Project description:Nuclear Lamins are Not Required for Genome Organization in Mouse Embryonic Stem Cells [DamID]

| PRJNA264801 | ENA

Project description:Nuclear Lamins are Not Required for Genome Organization in Mouse Embryonic Stem Cells

| PRJNA264798 | ENA

Mus musculus

Project description:Chromatin decondensation is sufficient to alter nuclear organization in embryonic stem cells

| PRJNA263941 | ENA

B-type lamins differentially associate with specific genes during differentiation without directly affecting their expression

Project description:B-type lamins, the major structural component of the nuclear lamina, is thought to play a repressive role in the expression of many of its bound genes whose silencing are known to be critical for cell differentiation during early development. Using global mapping of lamin-B-chromatin interaction, we find that the binding to lamin-B indeed correlated with gene silencing in mouse embryonic stem cells (ESC) and ESC-derived trophectoderm (TE) lineage cells. To address whether lamin-B directly suppresses the expression of the bound genes, we have derived ESCs from lamin-B-null mouse blastocysts. Unexpectedly, microarray analyses of ESCs and TE cells show that B-type lamins do not repress the expression of their bound genes. Furthermore, the knockout mice that do not express any B-type lamins can develop to term but exhibit small body size and perinatal lethality. Our studies demonstrate that B-type lamins are not required for cell differentiation during early embryonic development. Instead, they are required for proper late embryonic and perinatal development. The availability of the null ESCs and mice opens the door to further define the functions of B-type lamins.

2011-10-31 | GSE24532 | GEO

Mus musculus embryonic germ cell transcriptome

Project description:Identification of the mouse embryonic germ cell transcriptome

2015-08-13 | GSE70360 | GEO

Mus musculus Stra8-deficient fetal ovary transcriptome

Project description:Identification of the mouse embryonic germ cell Stra8-/- transcriptome

2015-08-13 | GSE70359 | GEO

Mus musculus Dazl-deficient fetal ovary transcriptome

Project description:Identification of the mouse embryonic germ cell Dazl-/- transcriptome

2015-08-13 | GSE70358 | GEO

DamID-based chromatin profiling of dHey in Kc cells

Project description:Chromatin binding profiling showed that dHey binds to enhancers in order to maintain EC identity, and co-regulates nuclear organization by governing a switch in the expression of nuclear lamins. Moreover, like dHey loss, de-regulated expression of lamins override identity programs. Thus, a single TF concomitantly orchestrates chromatin state, enhancer activity, and nuclear organization safeguarding differentiated cell identity Chromatin profiling using Dam-dHey shows preferential recruitment to enhancers and transcriptionally active regions. Manuscript title: Specification and maintenance of enterocyte identity requires dHey and nuclear lamins

2019-07-15 | GSE87895 | GEO

Bidirectional Introgression between Mus musculus domesticus and Mus spretus.

Project description:Introgressed variants from other species can be an important source of genetic variation because they may arise rapidly, can include multiple mutations on a single haplotype, and have often been pretested by selection in the species of origin. Although introgressed alleles are generally deleterious, several studies have reported introgression as the source of adaptive alleles-including the rodenticide-resistant variant of Vkorc1 that introgressed from Mus spretus into European populations of Mus musculus domesticus. Here, we conducted bidirectional genome scans to characterize introgressed regions into one wild population of M. spretus from Spain and three wild populations of M. m. domesticus from France, Germany, and Iran. Despite the fact that these species show considerable intrinsic postzygotic reproductive isolation, introgression was observed in all individuals, including in the M. musculus reference genome (GRCm38). Mus spretus individuals had a greater proportion of introgression compared with M. m. domesticus, and within M. m. domesticus, the proportion of introgression decreased with geographic distance from the area of sympatry. Introgression was observed on all autosomes for both species, but not on the X-chromosome in M. m. domesticus, consistent with known X-linked hybrid sterility and inviability genes that have been mapped to the M. spretus X-chromosome. Tract lengths were generally short with a few outliers of up to 2.7 Mb. Interestingly, the longest introgressed tracts were in olfactory receptor regions, and introgressed tracts were significantly enriched for olfactory receptor genes in both species, suggesting that introgression may be a source of functional novelty even between species with high barriers to gene flow.

| S-EPMC8784167 | biostudies-literature

EDD: a program for detection of wide genomic enrichment domains robust against local variations [RNA-Seq]

Project description:Nuclear lamins contact the genome at the nuclear periphery through large domains and are involved in chromatin organization. Among broad peak calling algorithms available to date, none are suited for mapping lamin-genome interactions genome-wide. We disclose a novel algorithm, Enriched Domain Detector (EDD), for analysis of broad enrichment domains from ChIP-seq data. EDD enables discovery of genomic domains interacting with broadly distributed chromatin-associated proteins such as lamins. The main advantage of EDD over existing broad peak callers is sensitivity to domain width rather than enrichment strength at a particular site, and robustness against local variations. EDD is downloadable from http://github.com/eivindgl/edd. RNA-seq experiments in human normal dermal fibroblasts (Lonza CC-2511; LDFs) and human normal primary dermal fibroblasts (Norwegian Stem Cell Center AD04DFs).

2014-04-25 | E-GEOD-54333 | 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