Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Expression profile (nanoCAGE-seq), chromatin accessibility (ATAC-seq) profile, and histone modification profile (ChIP-seq for H3K4me3, H3K9me3, and H3K27me3) during the course of mouse gonocyte development

ABSTRACT: How de novo DNA methylation over heterochromatin is introduced in mouse gonocyte remains obscure. We performed nanoCAGE-seq, ChIP-seq for three major histone marks (H3K4me3, H3K9me3, H3K27me3), ATAC-seq, Hi-C during the course of mouse gonocyte development (E13.5, E17.5, E19.5, P2)

ORGANISM(S): Mus musculus

PROVIDER: GSE121118 | GEO | 2019/08/29

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Expression profile (nanoCAGE-seq), chromatin accessibility (ATAC-seq) profile, and histone modification profile (ChIP-seq for H3K4me3, H3K9me3, and H3K27me3) during the course of mouse gonocyte development

Project description:Expression profile (nanoCAGE-seq), chromatin accessibility (ATAC-seq) profile, and histone modification profile (ChIP-seq for H3K4me3, H3K9me3, and H3K27me3) during the course of mouse gonocyte development

| PRJNA495765 | ENA

Transcriptome profiling of derived-hepatocyte progenitors from human iPSCs with nanoCAGE

Project description:We investigated the human induced pluripotent stem cells (hiPSCs) during a sequential in vitro step-by-step differentiation into hepatocyte-like cells (HLCs) using nanoCAGE, a method for promoters, transcription factors, and transcriptome analysis.

2019-09-05 | GSE136841 | GEO

NanoCAGE in ERα knockdown BM67 cells

Project description:NanoCAGE in ERα knockdown BM67 cells

| PRJNA494966 | ENA

Effect of Morc1 knock out on gonocyte chromatin and transcriptome [ChIP-Seq]

Project description:To investigate the function of Morc1 to chromatin state during gonocyte stage when around 10,000 copies of transposons are deregulated.

2024-02-05 | GSE235426 | GEO

Effect of Morc1 knock out on gonocyte chromatin and transcriptome [ATAC-Seq]

Project description:To investigate the function of Morc1 to chromatin state during gonocyte stage when around 10,000 copies of transposons are deregulated.

2024-02-05 | GSE235425 | GEO

Effect of Morc1 knock out on gonocyte chromatin and transcriptome [RNA-Seq 2]

Project description:To investigate the function of Morc1 to chromatin state during gonocyte stage when around 10,000 copies of transposons are deregulated.

2024-02-05 | GSE235428 | GEO

Effect of Morc1 knock out on gonocyte chromatin and transcriptome [RNA-Seq 1]

Project description:To investigate the function of Morc1 to chromatin state during gonocyte stage when around 10,000 copies of transposons are deregulated.

2024-02-05 | GSE235427 | GEO

nanoCAGE reveals 5â UTR features that define specific modes of translation of functionally related mTOR-sensitive mRNAs

Project description:mTOR regulates mRNA translation. Whereas ribosome-profiling suggested that mTOR exclusively stimulates translation of TOP (containing a 5â-terminal oligopyrimidine [5âTOP] motif) and TOP-like mRNAs, polysome-profiling implied that mTOR also modulates translation of non-TOP mRNAs. We show that ribosome-, but not polysome-profiling, is biased towards identification of TOP mRNAs as differentially translated while obscuring detection of changes in non-TOP mRNA translation. Transcription start site profiling by Nano-Cap Analysis of Gene Expression (nanoCAGE) revealed that many mTOR-sensitive mRNAs do not have 5âTOP motifs. Moreover, nanoCAGE showed that 5â UTR features distinguish two functionally and translationally distinct subsets of mTOR-sensitive mRNAs: i) those with short 5â UTRs enriched for mitochondrial functions such as respiration, that are translated in an eIF4E, but not eIF4A1-dependent manner and ii) mRNAs encoding proliferation- and survival-promoting proteins, that harbor long 5â UTRs, and require both eIF4E and eIF4A1 for their efficient translation. Selective inhibition of translation of mRNAs harboring long 5â UTRs via suppression of eIF4A leads to uncoupling of expression of proteins involved in respiration (e.g. ATP5O) from those protecting mitochondrial integrity (e.g. BCL-2) ultimately resulting in apoptosis. Conversely, simultaneous translational downregulation of both long and short 5â UTR mRNAs by mTOR inhibitors results in suppression of mitochondrial respiration and predominantly cytostatic effects. Therefore, 5â UTR features define differential modes of translation of functionally distinct mTOR-sensitive mRNAs, which explains discrepancies between the effects of mTOR and eIF4A inhibitors on neoplastic cells. Determination of 5'UTR lengths using nanoCAGE in MCF7 cells

2016-03-14 | E-GEOD-77033 | biostudies-arrayexpress

Constitutive expression of activated NOTCH1 in fetal Sertoli cells dysregulates factors required for proper gonocyte maintenance and survival.

Project description:Genome-wide analysis of whole embryonic day 14.5 mouse testes constitutively expressing the activated intracellular domain of NOTCH1 in Sertoli cells. The goal of the study was to identify Sertoli cell expressed genes regulated by Notch signaling, which are critical to gonocyte maintenance and survival. The mouse model was generated by intercrossing anti-Müllerian hormone (Amh)-cre transgenic mice and RosaNICD transgenic mice. Testes were dissected free from mesonephroi and testis pairs from a single fetus were pooled to generate a single sample. Littermates not expressing Amh-cre were used as controls. Testes from one control and one overexpressor fetus per dam from three separate dams were used for analysis.

2013-02-08 | E-GEOD-37073 | biostudies-arrayexpress

SLIC-CAGE (Super-Low Input Carrier-CAGE) development: comparison with Saccharomyces cerevisiae nAnTi-CAGE and nanoCAGE libraries and validation of SLIC-CAGE on Mus musculus total RNA

Project description:We developed SLIC-CAGE (Super-Low Input Carrier-CAGE) approach to capture 5'end of RNA polymerase II transcripts from as little as 5-10 ng of total RNA. The dramatic increase in sensitivity compared to existing CAGE methods is achieved by specially designed, selectively degradable carrier RNA. We tested SLIC-CAGE on Saccharomyces cerevisiae (BY4741 strain) and produced libraries from 1-100 ng of total cellular RNA. We also produced S. cerevisiae nAnT-iCAGE libraries as the current gold-standard CAGE libraries using the recommended 5 micrograms of total cellular RNA to assess the quality of SLIC-CAGE libraries produces with up to 1000-fold less material. We provide a direct comparison between SLIC-CAGE and the latest nanoCAGE protocol (libraries created using S. cerevisiae total RNA) and show that SLIC-CAGE produces unbiased libraries of higher complexity and quality than nanoCAGE. Finally, we provide SLIC-CAGE libraries on mouse embryonic stem cells (E14) using 5-100 ng of total cellular RNA as starting material.

2018-10-25 | E-MTAB-6519 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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