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

ATAC-seq of human embryonic stem cells during cell cycle progression

ABSTRACT: The experiment was designed to look into chromatin accessibility changes during cell cycle progression in human embryonic stem cells (hESCs). For this, FUCCI hESCs are sorted in Early G1 (EG1), Late G1 (LG1), G1/S transition and S/G2/M phases in duplicates. 100,000 were used per sample, as described in 2.4. Library preparation and sequencing were performed at the Wellcome Trust Sanger Institute next-generation sequencing facility. 8 ATAC-seq libraries were prepared with one of i5 and i7 Nextera tags combination (see 2.4), and pooled equimolarly. Sequencing was performed on Illumina HiSeq 2000, 2 X 75bp paired-end reads obtaining more than 60M mapped reads per library.

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Homo sapiens

SUBMITTER: Anna Osnato

PROVIDER: E-MTAB-8348 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

ATAC-seq of definitive endoderm differentiation of human embryonic stem cells in early G1 phase of the cell cycle

Project description:The experiment was designed to look into chromatin accessibility changes during cell cycle progression in human embryonic stem cells (hESCs) during definitive endoderm differentiation. For this, FUCCI hESCs were sorted in Early G1 (EG1), and differentiation into endoderm was performed for up to 72 hours with a combination of cytokines as described in Pauklin and Vallier (2013) and Pauklin et al. (2016). Samples at 0, 12, 24, 36, 48 and 72 hours were generated from two independent experiments, with 100,000 cells per sample, as previously described in Kumasaka et al. (2016). Library preparation and sequencing were performed at the Wellcome Sanger Institute next-generation sequencing facility. ATAC-seq libraries were prepared with one of i5 and i7 Nextera tags combination (see protocol details), and pooled equimolarly. Sequencing was performed on Illumina HiSeq 2000, 2 x 75bp paired-end reads.

2020-09-07 | E-MTAB-9124 | 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

ATAC-seq of mouse luminal progenitors isolated from wild-type or Blg-Cre;Brca1f/f;p53+/- mouse models

Project description:One of the major hurdles for the early detection of cancer is our poor understanding of tumour initiating events. Historically, cancer research has focused on histological and molecular characterisation of established tumours which has led to the identification of hundreds of putative driver mutations. It is currently unclear how these genetic aberrations impact the cell state of nascent tumour cells and their microenvironment. BRCA1 driven triple negative breast cancer (TNBC) for example has been shown to arise from luminal progenitor cells yet little is known about how BRCA1 loss-of-function (LOF) and concomitant mutations affect the luminal progenitor cell state. This repository contains ATAC-sequencing dataset of luminal progenitors isolated from 6-months old Brca1/p53 and wild-type mice. This data was used to show that the perturbation of Brca1/p53in luminal progenitors induces an aberrant alveolar differentiation pre-malignancy. Unlike alveolar differentiation occurring during gestation, this process is cell autonomous and characterised by the dysregulation of transcription factors driving alveologenesis. The ATAC-sequencing data supports a model where transcriptional and epigenetic changes driven by Brca1/p53 inadvertently promote a differentiation program hardwired in luminal progenitors, highlighting the deterministic role of the cell of origin and offering a potential explanation for the tissue specificity of BRCA1 tumours.

2021-02-02 | E-MTAB-10054 | 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

Chromatin immuno-precipitation and sequencing of barallete progenitors and neurons during mouse brain development

Project description:Genome-wide measurements of histone modifications and transcription factor binding in mouse barelette progenitors, neurons and ESCs at different developmental stages and in different genotypes.

2021-01-09 | E-MTAB-8317 | biostudies-arrayexpress

ATAC-seq of HepG2 cells

Project description:ATAC-seq open chromatin maps for HepG2 cells (3 biological replicates), a liver model.

2019-03-20 | E-MTAB-7543 | biostudies-arrayexpress

T helper cell type 2 ATAC-seq time-course

Project description:CD4+ T cells were extracted from mouse and human. They were activated in vitro with CD3/28 and cultured with Il4. ATAC-seq was then performed at different time points

2017-12-14 | E-MTAB-6292 | biostudies-arrayexpress

Dose-dependent role of the cohesin complex in normal and malignant hematopoiesis [ATAC-Seq]

Project description:Cohesin complex members have recently been identified as putative tumor suppressors in hematologic and epithelial malignancies. The cohesin complex guides chromosome segregation, however cohesin-mutant leukemias do not show genomic instability. We hypothesized reduced cohesin function alters chromatin structure and disrupts cis-regulatory architecture of hematopoietic progenitors. We investigated the consequences of Smc3 deletion in normal and malignant hematopoiesis. Bi-allelic Smc3 loss induced bone marrow aplasia with premature sister chromatid separation, and revealed an absolute requirement for cohesin in hematopoietic stem cell function. In contrast, Smc3 haploinsufficiency increased self-renewal in vitro and in vivo including competitive transplantation. Smc3 haploinsufficiency reduced coordinated transcriptional output, including reduced expression of transcription factors and other genes associated with lineage commitment. Smc3 haploinsufficiency cooperated with Flt3-ITD to induce acute leukemia in vivo, with potentiated Stat5 signaling and altered nucleolar topology. These data establish a dose-dependency for cohesin in regulating chromatin structure and hematopoietic stem cell function. ATAC-seq in murine c-kit+ cells for the following genotypes: Smc3 fl/+, Smc3 del/+, Flt3-ITD, Smc3 fl/del Flt3-ITD

2015-09-21 | E-GEOD-73215 | biostudies-arrayexpress

ATAC-seq for L3.6pl cells

Project description:Identification of open chromatin regions in L3.6pl cells by ATAC-seq

2018-12-18 | E-MTAB-7035 | biostudies-arrayexpress

ATAC-seq of primary mammalian aortic endothelial cells before and after TNFα stimulation

Project description:To identify conserved TNFα-induced changes in chromatin-accessibility in mammals, we performed ATAC-seq in primary vascular endothelial cells (ECs) isolated from the aortas of human (HAEC), mouse (MAEC) and cow (BAEC), before and after TNFα. We overlay our data with multi-species NF-κB binding data and identify multiple modes of NF-κB-chromatin interactions that are conserved during mammalian TNFα response. Our cross-species approach identifies conserved changes in chromatin-accessibility at NF-κB binding sites that are disease-relevant and essential during mammalian acute inflammation.

2020-06-01 | E-MTAB-7878 | 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