Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Quantification, dynamic visualization, and validation of bias in ATAC-seq data with ataqv

ABSTRACT: The assay for transposase-accessible chromatin using sequencing (ATAC-seq) has become the preferred method for mapping chromatin accessibility, due to its simplicity, speed, and low input material requirements. However, it can be difficult to evaluate data quality, particularly when processing many samples. Here, we present ataqv, a computational toolkit for efficiently measuring, visualizing, and comparing ATAC-seq quality control results. We perform controlled ATAC-seq experiments and utilize ataqv to show that the ratio of Tn5 transposase to nuclei and sequencing flowcell cluster density induce reproducible technical bias in ATAC-seq results, significantly changing the fragment length distribution and enrichment of reads in promoter and enhancer chromatin states.

ORGANISM(S): Homo sapiens

PROVIDER: GSE130450 | GEO | 2020/03/23

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Bos taurus ATAC-seq across 88 tissue samples to profile open chromatin regions in the cattle genome

Project description:We performed the assay for transposase-accessible chromatin using sequencing (ATAC-seq) using 88 tissue samples to profile open chromatin regions in the cattle genome.

2023-08-24 | E-MTAB-11825 | biostudies-arrayexpress

ATAC-seq data in mouse and zebrafish limbs

Project description:Assay for Transposable Accessible Chromatin (ATAC) reveals a genome wide view of areas of open chromatin at very high resolution, which are often associated with regulatory activity. The ATAC-seq technology uses a Tn5 transposase loaded with nex-generation sequencing primers in order to simultaneously fragment areas of open chromatin and ligate adapters.

2015-01-06 | E-GEOD-61065 | biostudies-arrayexpress

Enhancer Mapping in Chronic Lymphocytic Leukemia

Project description:<p>In this study we profile the epigenomic enhancer landscapes of CLL B cells (CD19+/CD5+) harvested from peripheral blood of patients from our Center. Included are results of ChIPseq profiling using chromatin immunoprecipitation of the enhancer histone mark H3K27ac (acetylated lysine 27 on histone H3), and open chromatin profiles using ATAC-seq (assay for transposase accessible chromatin). These profiles are used to define the global enhancer and super enhancer landscape of CLL B cells, and to derive active transcription factor networks associated with this disease. Also included are H3K27ac ChIP-seq and ATAC-seq datasets for non-CLL B cells obtained from the peripheral blood of normal adult donors.</p>

| phs001704 | dbGaP

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

Project description:We describe an assay for transposase-accessible chromatin using sequencing (ATAC-seq), based on direct in vitro transposition of sequencing adaptors into native chromatin, as a rapid and sensitive method for integrative epigenomic analysis. ATAC-seq captures open chromatin sites using a simple two-step protocol with 500–50,000 cells and reveals the interplay between genomic locations of open chromatin, DNA-binding proteins, individual nucleosomes and chromatin compaction at nucleotide resolution. We discovered classes of DNA-binding factors that strictly avoided, could tolerate or tended to overlap with the nucleosome. Using ATAC-seq maps of human CD4+ T cells from a proband obtained on consecutive days, we demonstrated the feasibility of analyzing an individual’s epigenome on a timescale compatible with clinical decision-making. We examined chromatin structure using ATAC-seq in 2 cell types (GM12878 cell line, purified CD4+ T cells).

2013-10-01 | E-GEOD-47753 | biostudies-arrayexpress

ATAC-seq of liver of a Holstein Friesian infant male.

Project description:We performed the assay for transposase-accessible chromatin using sequencing (ATAC-seq) on a liver sample collected from one Holstein Friesian healthy male at one month of age to profile open chromatin regions genome-wide to identify putative regulatory elements related to phenotype of interest.

2021-07-09 | E-MTAB-9872 | biostudies-arrayexpress

An integrated multi-omics analysis of identiﬁes distinct molecular characteristics in pulmonary infections of Pseudomonas aeruginosa

Project description:Pseudomonas aeruginosa (P. aeruginosa) can cause severe acute infections, including pneumonia and sepsis, and also cause chronic infections commonly in patients with structural respiratory diseases. However, the molecular and pathophysiological mechanisms of P. aeruginosa respiratory infection are largely unknown. Here, we profiled performed to assay for transposase-accessible chromatin using sequencing (ATAC-seq), transcriptomics, and quantitative mass spectrometry-based proteomics and ubiquitin-proteomics in P. aeruginosa-infected lung tissues for multi-omics analysis, while ATAC-seq and transcriptomics were also examined in P. aeruginosa-infected mouse macrophages. To find the pivotal transcription factors that are likely involved in host immune defense, we integrally investigated systematic changes in chromatin accessibility and gene expression in P. aeruginosa-infected lung tissues combined with proteomics and ubiquitin-proteomics studies. We discovered that Stat1 and Stat3 were altered in various omics and found similar results in mouse alveolar macrophages. Taken together, these findings indicate that these crucial transcription factors and their downstream signaling molecules play a critical role in the mobilization of host immune response against P. aeruginosa infection and may serve as potential targets for bacterial infections and inflammatory diseases, as well as provide clear insights and resources for using integrative histological analyses.

2023-07-27 | PXD038001 | Pride

An integrated multi-omics analysis of identiﬁes distinct molecular characteristics in pulmonary infections of Pseudomonas aeruginosa

2023-07-27 | PXD042381 | Pride

Fresh versus slow-frozen ATACseq samples for salmon tissues

Project description:When sampling many samples at locations with poor laboratory facilities, the ability of freezing samples for later processising is crucial. ATAC-seq on fresh tissue is still considered the star method. Freezing has shown to affect chromatin architecture and nucleosome pattern. However, the freezing method might determine the chromatin integrity. We therefore ask whether or not slow frozen samples give the same results as fresh samples when assaying tissues for transposase accessible chromatin?

2020-05-08 | E-MTAB-9001 | biostudies-arrayexpress

A simple and robust plate-based single-cell ATAC-seq on various tissues and cell lines

Project description:The assay for transposase-accessible chromatin using sequencing (ATAC-seq) is widely used to identify regulatory regions throughout the genome. However, only a few studies have been done at the single cell level (scATAC-seq) due to technical difficulties. Here we developed a simple and robust plate-based scATAC-seq method, combining upfront bulk tagmentation with single-nuclei sorting, to investigate open chromatin regions. We applied this method on mouse splenocytes and unbiasedly revealed key regulatory regions and transcription factors that define each cell (sub)type.

2018-10-10 | E-MTAB-6714 | biostudies-arrayexpress

ATAC-seq of subfractions within hematopoietic stem cells in bone marrow

Project description:Purpose: The goals of this study are to elucidate the underlying mechanism for the regulation of HSC divisions. Methods: Fifteen thousand cells subfractions within the HSC fraction were sorted. These cells were subjected to ATAC-seq using Hi-seq. The sequence reads that passed quality filters were analyzed by FASTX-toolkit.

2022-01-19 | GSE187014 | GEO

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