ATAC
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ABSTRACT:
PROVIDER: EGAD00010001928 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:These ATAC-seq data were generated to correlate with genomic interaction data in a related Hi-C analysis. Analysis of ATAC-seq data revealed series of overlapping or specific open chromatin peaks in ATRA treated and control cells. Those specific peaks showed fewer overlapping with gene promoters than the overlapping peaks. Key transcription factor for blood cell differentiation GATA2 was found only bind in control specific peaks.
2018-03-07 | GSE93993 | GEO
Project description:A map of open chromatin in control and Irx3-KO beige ME3 preadipocytes cells on days 0, 1 and 7 of adipogenic differentiation. Cells were differentiated for indicated number of days, pelleted and snap-frozen in liquid nitrogen. After thawing, cells were treated with DNase to remove exogenous DNA released from cells that died prior to freezing. Remaining cells were lysed in ATAC-seq lysis buffer from the ATAC-seq. Crude nuclear extracts was isolated by centrifugation and resuspended in Tagmentation buffer. Nuclear integrety was verified under microscope, and 50,000 nuclei were transferred for tagmentation. Tagmentation and indexing was performed according to the instructions of the ATAC-seq Kit (Active Motif Catalog No. 53150). Library QC was performed on a Bioanalyzer, and the library was sequenced on a HiSeq4000 Illumina platform using 75 bp paired end sequencing. Reads were filtered to remove low quality mappings, duplicates and mitochondrial mappings. Peaks were called by Macs2 and ENCODE blacklisted regions were excluded. Differentially open chromatin was identified by featurecounts and DESeq2.
2025-05-16 | E-MTAB-13525 | biostudies-arrayexpress
Project description:ATAC-seq data. Dataset includes FASTQ files, BAM files, and analysis files with the ATAC-seq peaks determined using MACS2.
| EGAD00001008962 | EGA
Project description:Purpose: Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq) is a method for mapping chromatin accessibility genome-wide. The goals of this study are to investigate chromatin accessibility of C57BL/6J mice through ATAC-seq. Results: ATAC-seq reads were aligned to the UCSC mm10 reference genome with BWA-MEM. ATAC-seq peaks were called through MACS2 . Peaks were annotated and known transcription factor binding motifs were further analyzed in the ATAC-seq peaks by HOMER.
2020-07-08 | GSE153993 | GEO
Project description:Generation of genome-wide maps of putative regulatory regions in human airway smooth muscle cells (ASMC) to aid in fine mapping of asthma GWAS. The cells were cultured and maintained in 10% FBS in PBS for 24 hours with no additional treatment given. MACS2 peaks provided in this submission were mapped to hg19.
2025-03-11 | E-MTAB-14267 | biostudies-arrayexpress
Project description:Purpose: Zinc Finger MIZ-Type Containing 1 (Zmiz1) is a member of the PIAS family of protein and function as a transcriptional coactivator of Notch, Androgen Receptor (AR), p53, Estrogen Receptor (ER), and Smad3/4 . Despite Zmiz1 critical role in angiogenesis, its role in lymphatic vasculature is unknown. Here, we use HDLECs cell line to profileepigenetic changes upon Zmiz1 knockdown using siRNA. Methods: ATAC sequencing library was prepared as per manufacturer instruction (Active Motif, 53150). Briefly, intact nuclei were isolated from control and Zmiz1 siRNA transfected HDLECs. Samples were treated with a hyperactive Tn5 transposase which tag the target DNA with sequencing adapters and fragment the DNA simultaneously. Library was then quantified using Qubit dsDNA High Sensitivity Assay Kit (Thermo Fisher Scientific, Q32851) and verified using the Bioanalyzer DNA High Sensitivity Assay Kit (Agilent, 5067-4626). Validated samples were sequenced using the NextSeq1000/2000 P2 Reagents (100 Cycles) v3 (Illumina, 20046811) on a Nextseq1000/2000. Resulting sequencing data were analyzed using basepairtech ATAC-Seq pipeline (www.basepairtech.com). Briefly, sequenced reads were aligned to the human (hg19) reference genome using Bowtie2. ATAC-Seq peaks and differentially accessible regions were quantified using MACS2 and DESeq2. Results: ATAC seq peaks analysis using MACS2 identified 576 peaks of which are mostly located in intergenic regions followed by introns. We found significantly reduced open chromatin near Prox1 loci upol loss of Zmiz1. Conclusions: We identify Zmiz1 regulates chromatin accessibility near Prox1 genomic loci in lymphatic endothelial cells
2023-11-29 | GSE225130 | GEO
Project description:We have studied the impact of T2D on open chromatin in human pancreatic islets. We used assay for transposase-accessible chromatin using sequencing (ATAC-seq) to profile open chromatin in islets from T2D and non-diabetic donors. We identified ATAC-seq peaks representing open chromatin regions in islets of non-diabetic and diabetic donors. The majority of ATAC-seq peaks mapped near transcription start sites. Additionally, peaks were enriched in enhancer regions and in regions where islet-specific TFs bind. Islet ATAC-seq peaks overlap with SNPs associated with T2D and with additional SNPs in LD with known T2D SNPs. There was enrichment of open chromatin regions near highly expressed genes in human islets.
2019-04-06 | GSE129383 | GEO
Project description:For ATAC-seq data processing, we used the ENCODE ATAC-seq pipeline (https://www.encodeproject.org/atac-seq/). In detail, for each sample, ATAC-seq reads were first checked for adaptor contamination. Then, adaptor trimmed reads were aligned to hg19 using Bowtie2 under paired-end mode with parameter “-X2000”, which permits 2000 bp for the maximum allowable insert size between two paired ends of each read. Using the ENCODE ATAC-seq pipeline, duplicated reads were properly filtered out. ATAC-seq enriched peaks were called using MACS2 (Zhang et al., 2008) based on remaining unique reads with parameters “-f BAMPE -q 0.05 --nomodel”. In total, we collected 45,569 peaks for the ARID1AWT sample and 27,480 peaks for the ARID1AKO sample.
2020-06-08 | GSE106660 | GEO
Project description:ATAC-seq was performed for T-cell blasts for the following study groups: healthy controls (HC, n=6) and patients with AIOLOS E82K (n=6) and Q402X (n=1). ATAC-Seq was performed using the Active Motif ATAC-Seq Kit following the manufacturer’s protocol and sequenced using the Illumina NextSeq 2000 with 42-bp paired end reads. Using Basepair bioinformatics tools and pipelines (https://www.basepairtech.com/), reads were aligned using Bowtie2, and peaks were called with MACS2 and annotated using Homer. Differential testing, annotation, and visualization were performed using R (v.4.3.1) and the following Bioconductor R packages (https://bioconductor.org/): DESeq2 (v.1.40.2), DiffBind (v.3.10.1), ChIPQC (v.1.36.1), ChIPseeker (v.1.36.0), clusterProfiler (v.4.8.2), and goseq (v.1.52.0).
2023-12-21 | GSE244038 | GEO
Project description:The "Assay for Transposase Accessible Chromatin sequencing" (ATAC-seq) is an efficient and easy to implement protocol to measure chromatin accessibility that has been widely used in multiple applications studying gene regulation. While several modifications or variants of the protocol have been published since it was first described, there has not yet been an extensive evaluation of the effects of specific protocol choices head-to-head in a consistent experimental setting. In this study, we tested multiple protocol options for major ATAC-seq components (including three reaction buffers, two reaction temperatures, two enzyme sources, and the use of either native or fixed nuclei) in a well-characterized cell line. In addition, the native conditions were tested in a primary sample type (mouse lung tissue) with two different input amounts. In general, native samples yielded more peaks (particularly at loci not overlapping transcription start sites) than fixed samples, and the temperature at which the enzymatic reaction was carried out had a major impact on data quality metrics for both fixed and native nuclei. However, the effect of various conditions tested was not always consistent between the native and fixed samples. For example, the Nextera and Omni buffers were largely interchangeable across all other conditions, while the THS buffer resulted in markedly different profiles in native samples. In-house and commercial enzymes performed similarly. We found that the relationship between commonly used measures of library quality differed across temperature and fixation, and so evaluating multiple metrics in assessing the quality of a sample is recommended. Notably, we also found that these choices can bias the functional class of elements profiled and so we recommend evaluating several formulations in any new experiments. Finally, we hope the ATAC-seq workflow formulated in this study on crosslinked samples will help to profile archival clinical specimens.
2022-03-23 | GSE174280 | GEO