EGAS00001003522-sc-2019-05-08T09:27:45Z - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001005002 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:This dataset maps gene expression regulation in human primary regulatory CD4+ T cells (Tregs). It includes whole genome sequence data for ChM-seq (118 H3K4me3, 118 H3K27ac and 6 inputs), ATAC-seq (114 samples) and whole transcriptome (141 samples). All individuals were genotyped (130 samples) using coreExome Illumina SNP chip array. The final quality filtered set included 123 individuals with RNA-seq data, 73 with ATAC-seq, 91 with H3K27ac ChM-seq and 88 with H3K4me3 ChM-seq data. A total of 62 individuals had QCed data for all the assays.
| EGAS00001003516 | EGA
Project description:This dataset maps gene expression regulation in human primary regulatory CD4+ T cells (Tregs). It includes whole transcriptome data for141 samples. The final quality filtered set included 123 individuals with RNA-seq data.
| EGAD00001004830 | EGA
Project description:This dataset maps gene expression regulation in human primary regulatory CD4+ T cells (Tregs). It includes whole genome sequence data for ChM-seq (118 H3K4me3, 118 H3K27ac and 6 inputs). The final quality filtered set included 91 individuals with H3K27ac ChM-seq and 88 with H3K4me3 ChM-seq.
| EGAD00001004828 | EGA
Project description:ATAC-seq data from naïve Tregs, memory Tregs and CD161+ Tregs
| PRJNA489004 | ENA
Project description:ATAC-seq open chromatin maps for HepG2 cells (3 biological replicates), a liver model.
2019-03-20 | E-MTAB-7543 | biostudies-arrayexpress
Project description:Genome Wide Association Studies (GWAS) have been successful in yielding >60 loci for Systemic Lupus Erythematosus (SLE). However, it is known that GWAS just reports genomic signals and not necessarily the precise localization of culprit genes, with eQTL efforts only able to infer causality to a minority of such loci. Thus, we sought to carry out physical and direct ‘variant to gene mapping’ by integrating results from high-throughput chromatin conformation capture and ATAC-seq assays. This experiment refers to the ATAC-seq part of our work. To determine informative proxy SNPs for each of the SLE GWAS sentinel loci, we generated ATAC-seq open chromatin maps for primary human T Follicular Helper (TFH) cells from tonsils of healthy volunteers (3 biological replicates), a model relevant to SLE as TFH operate upstream of the activation of pathogenic autoantibody-producing B cells during the disease. We also generated open chromatin maps for naive CD4-positive helper T cells (3 biological replicates).
2020-05-12 | E-MTAB-6617 | biostudies-arrayexpress
Project description:Foxp3 expressing regulatory T cells (Tregs) are the central regulator of immune homeostasis and tolerance. As it is believed that proper Treg function is compromised under inflammatory conditions, exploring a pathway that enhances Treg function is of great importance. In this study, we report that IL-27, an IL-12 family cytokine known to play both pro- and anti-inflammatory role in T cells, plays a pivotal role in Treg function to control T cell-induced colitis. Unlike WT Tregs capable of inhibiting colitogenic T cell expansion and inflammatory cytokine expression, IL-27R-deficient Tregs were unable to downregulate inflammatory T cell responses. Tregs stimulated with IL-27 expressed substantially enhanced suppressive function both in vitro and in vivo. IL-27 stimulation of Tregs induced expression of LAG3, a surface molecule implicated in negatively regulating immune responses. LAG3 expression in IL-27-stimulated Tregs was critical to mediate suppressive Treg function. Finally, human Tregs also displayed enhanced suppressive function and LAG3 expression in response to IL-27 stimulation. Taken together, our results highlight a novel function of the IL-27/LAG3 axis in Treg regulation of inflammatory responses in the intestine. FACS purified Foxp3+ Tregs were stimulated in the presence of media or IL-27 to compare IL-27 induced gene profiles. Four samples (media stimulated or IL-27-stimulated) were collected from four independent experiments. Genes altered by IL-27 treatment were compared to those of media stimulated Tregs.
2015-11-01 | E-GEOD-63455 | biostudies-arrayexpress
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
Project description:ATAC-seq profiles of Tregs isolated from spleen and LN in Flicr WT and KO mice
2017-03-28 | GSE97085 | GEO
Project description:The ATAC histone acetyl-transferase (HAT) and the Mediator coactivator complexes regulate independent and distinct steps during transcription initiation and elongation. Here we report the identification of a new stable molecular assembly formed between the ATAC and the Mediator complex in mouse embryonic stem cells. Moreover, we identify LUZP1 as a subunit of this meta coactivator complex (MECO). Finally, we demonstrate that MECO regulates a subset of RNA polymerase II transcribed non-coding RNA genes. Our findings establish that transcription coactivator complexes can form stable sub-complexes in order to facilitate their combined actions on specific target genes. For ChIP-seq analysis, 300µg of chromatin (DNA) was incubated with GST (mock), LUZP1 and GCN5 antibodies. Retrieved purified DNA was sequenced using Illumina Genome Analyzer II following manufacturer recommendations. Illumina raw files were aligned against reference (mouse mm9) genome using the eland program allowing one mismatch. Enrichment clusters were detected using MACS (Zhang et al., 2008). The retrieved peaks were filtered (max size 1000bp, min size 100bp) and repeat masked, to establish the final binding sites lists. Peaks were annotated using the GPAT web server (Krebs et al., 2008) using ENSEMBL gene 57 database.
2010-06-24 | E-GEOD-21717 | biostudies-arrayexpress