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

Gain of chromatin loops marks the exit from naïve pluripotency – in-situ Hi-C data

ABSTRACT: In-situ Hi-C data for mouse embryonic stem cells (ES cells, grown in the presence of FBS and LIF) and for NS cells.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Mus musculus

SUBMITTER: Bernd Klaus

PROVIDER: E-MTAB-6591 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Genome-wide Chromatin Maps Derived from Limited Numbers of Hematopoietic Progenitors

Project description:Whole genome mapping of protein-DNA interactions can be performed by coupling chromatin immunoprecipitation (ChIP) with high-throughput sequencing (ChIP-Seq). However, current methods require large amounts of starting materials which precludes their application to rare cell types. Here, we combine a high-sensitivity ChIP assay with a novel library preparation procedure to map histone modifications in as few as 10,000 cells. We apply the technique to acquire genome-wide chromatin maps for an enriched population of hematopoietic progenitors, and thereby gain insight into their developmental program. An optimized ChIP protocol for small number of cells and a novel Librray preperation methods for high throughput sequencing of picograms amount of ChIP DNA.

2010-07-01 | E-GEOD-22075 | biostudies-arrayexpress

ATAC and sequencing of barallete progenitors and neurons during mouse brain development

Project description:Genome-wide measurements of chromatin accessibility in mouse barelette progenitors and neurons at different developmental stages.

2021-01-09 | E-MTAB-8313 | biostudies-arrayexpress

Cap analysis of gene expression (CAGE) of polysome-associated RNA against total RNA from human HEK293 cell line

Project description:In this study, we used CAGE followed by deep sequencing to globally profile the transcript 5’ isoforms in the translatome (i.e., polysome-associated RNA) and transcriptome (i.e., total RNA) of human HEK293 cells at single-nucleotide resolution. After removing low-quality sequencing reads, we obtained approximately 18 million and 14 million CAGE tags respectively for the translatome and transcriptome of HEK293 cells. These tags were then mapped to the human genome (assembly GRCh37) using bowtie with two mismatches allowed. Tags mapped to rRNA were less than 17.9% for translatome and 7.5% for transcriptome, indicating high quality of the two CAGE libraries. By comparing CAGE tags between HEK293's translatome and transcriptome, we revealed selective usage of the TSS-derived 5’ ends by polysome.

2019-06-13 | E-MTAB-7382 | biostudies-arrayexpress

A new transcription factor for mitosis: In S. pombe, the RFX transcription factor Sak1 works with forkhead factors to regulate mitotic expression

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

2014-08-25 | E-GEOD-60719 | biostudies-arrayexpress

HiC-sequencing in human monocyte differentiation (3D-MO)

Project description:This dataset consists of in situ HiC-seq data from human monocytes, monocyte-derived dendritic cells as well as monocyte-derived cells that were subjected to siRNA treatment targeting CTCF or RAD21. In total, the data set includes 42 samples.

2022-06-24 | E-MTAB-10848 | biostudies-arrayexpress

Chromatin profiling of dendritic cells in healthy and hyperglycaemic mice

Project description:The aim of the experiment was to compare chromatin states between healthy and hyperglycaemic mice. We focused on dendritic cells extracted from the lungs. Nuclei were extracted from 200.000 sorted dendritic cells per sample. H3K27me3 and H3K27ac were then profiled using CUT&RUN protocol.

2023-06-29 | E-MTAB-11390 | biostudies-arrayexpress

Genome-wide maps of nuclear lamina interactions in HeLa cells identified using MethylAdenine IDentification (MadID).

Project description:Mapping of lamina-associated domains using MadID experiment. A methyltransferase (M.EcoGII) targeted to the nuclear envelope is able to add methyl groups to adenine residues (m6A) on chromatin in contact to the nuclear periphery. A m6A-specific immunoprecipitation is performed on isolated genomic DNA, followed by Ilumina deep sequencing to identify contact sites.

2018-10-26 | E-MTAB-6888 | biostudies-arrayexpress

RNA-seq of Barrelette neurons and progenitors during mouse brain development

Project description:Bulk RNA-seq using the smartSeq2 protocol in mouse Barrelette neurons, progenitors and ESCs at different developmental stages and in different genotypes.

2021-01-09 | E-MTAB-8314 | biostudies-arrayexpress

Single-cell RNA-seq of mouse cerebral cortex

Project description:We have applied a recently developed, highly accurate and sensitive single-cell RNA-seq method (STRT/C1) to perform a molecular census of two regions of the mouse cerebral cortex: the somatosensory cortex and hippocampus CA1. We isolated cells fresh from somatosensory cortex (S1) and hippocampus CA1 area of juvenile (P22 - P32) CD1 mice, 33 males and 34 females. Cells were collected without selection, except that 116 cells were obtained by FACS from 5HT3a-BACEGFP transgenic mice. A total of 76 Fluidigm C1 runs were performed, each attempting 96 cell captures and resulting in 3005 high-quality single-cell cDNAs, containing Unique Molecular Identifiers allowing counting of individual mRNA molecules, even after PCR amplification.

2015-02-20 | E-GEOD-60361 | biostudies-arrayexpress

Diverse pathways generate microRNA-like RNAs and Dicer-independent small interfering RNAs in fungi

Project description:A variety of small RNAs, including the Dicer-dependent miRNAs and the Dicer-independent Piwi-interacting RNAs, associate with Argonaute family proteins to regulate gene expression in diverse cellular processes. These two species of small RNA have not been found in fungi. Here, by analyzing small RNA associated with the Neurospora Argonaute protein QDE-2, we show that diverse pathways generate miRNA-like small RNAs (milRNAs) and Dicer-independent small interfering RNAs (disiRNAs) in this filamentous fungus. Surprisingly, milRNAs are produced by at least four different mechanisms that use a distinct combination of factors, including Dicers, QDE-2, the exonuclease QIP and an RNAse III domain-containing protein MRPL3. In contrast, disiRNAs originate from loci producing overlapping sense and antisense transcripts, and do not require the known RNAi components for their production. Taken together, these results uncover several pathways for small RNA production in filamentous fungi, shedding light on the diversity and evolutionary origins of eukaryotic small RNAs. One small RNA library was generated using QDE-2 immunoprecipitate from Neurospora crassa.

2010-07-01 | E-GEOD-21175 | 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