Transcriptomics

Dataset Information

0

ATAC-seq of primary human T Follicular Helper (TFH) cells and naive CD4-positive helper T cells from tonsils of healthy volunteers


ABSTRACT: 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).

INSTRUMENT(S): Illumina HiSeq 4000

ORGANISM(S): Homo sapiens  

SUBMITTER: Matthew E Johnson   Sumei Lu   Andrew D Wells   Neil D Romberg   Alessandra Chesi   Struan FA Grant   Kenyaita M Hodge   Elisabetta Manduchi  

PROVIDER: E-MTAB-6617 | ArrayExpress | 2020-05-12

SECONDARY ACCESSION(S): ERP107647

REPOSITORIES: ArrayExpress, ENA

Similar Datasets

2020-05-12 | E-MTAB-6621 | ArrayExpress
2019-04-01 | E-MTAB-6637 | ArrayExpress
1000-01-01 | S-EPMC6054970 | BioStudies
1000-01-01 | S-EPMC3925141 | BioStudies
1000-01-01 | S-EPMC4570857 | BioStudies
2020-01-01 | S-EPMC7324209 | BioStudies
2020-01-01 | S-EPMC7387970 | BioStudies
2015-01-01 | S-EPMC4450082 | BioStudies
2019-03-20 | E-MTAB-7543 | ArrayExpress
1000-01-01 | S-EPMC5859360 | BioStudies