biostudies-arrayexpressMetabolomicsUnknownTranscriptomicsGenomicsProteomicsKatja BaerenfallerIllumina HiSeq 4000RNA-seq of coding RNAHomo sapiensHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-16535This RNA-seq experiment profiles peripheral blood mononuclear cells from AmaXhosa children aged 12–36 months with clinically diagnosed moderate-to-severe atopic dermatitis and matched healthy controls living in rural or urban South African settings. The main goal is to capture systemic immune transcriptional programs associated with early-life atopic dermatitis while accounting for the strong contextual influence of environment. By comparing disease status across rural/urban strata, the dataset is designed to distinguish disease-linked expression patterns from location-associated immune signatures, and to identify gene sets reflecting pathways plausibly involved in atopic inflammation, barrier/immune regulation, and related mechanisms. The resulting transcriptomic signatures are intended for downstream integration with cytokine and antibody measurements and environmental exposure data to support mechanistic interpretation and endotype definition.biostudies-arrayexpressSample Collection - Whole blood samples were collected from participating individuals (n=149) in lithium heparin tubes and PBMCs were isolated according to standard protocols. The PBMCs were separated was using Ficoll‐Paque 1.077 g/mL density gradient centrifugation. Washed PBMCs were resuspended in freezing medium (DMSO, heat‐inactivated FCS, and RPMI). Cells were then transferred to a −80 C freezer and afterwards into liquid nitrogen the following day.Sequencing - RNA‐Seq analysis was performed on samples from all children (n = 149) using HiSeq 4000.Nucleic Acid Extraction - Total mRNA was isolated from PBMCs using the RNeasy Mini Kit (Qiagen), and RNA levels were quantified by NanoDrop (Thermo Fisher Scientific). RNA integrity was confirmed using the Agilent 2100 BioAnalyzer (Agilent).Library Construction - Libraries were prepared with Illumina's Truseq stranded mRNA library prep kit with polyA enrichment.OrganizationMINSEQE ScoreAssays and DataMAGE-TAB FilesKatja BaerenfallerDamir ZhakparovfalseBulk RNA-seq of Peripheral Blood Mononuclear Cells from AmaXhosa Children with Atopic Dermatitis and Healthy Controls in Rural and Urban South AfricaThis RNA-seq experiment profiles peripheral blood mononuclear cells from AmaXhosa children aged 12–36 months with clinically diagnosed moderate-to-severe atopic dermatitis and matched healthy controls living in rural or urban South African settings. The main goal is to capture systemic immune transcriptional programs associated with early-life atopic dermatitis while accounting for the strong contextual influence of environment. By comparing disease status across rural/urban strata, the dataset is designed to distinguish disease-linked expression patterns from location-associated immune signatures, and to identify gene sets reflecting pathways plausibly involved in atopic inflammation, barrier/immune regulation, and related mechanisms. The resulting transcriptomic signatures are intended for downstream integration with cytokine and antibody measurements and environmental exposure data to support mechanistic interpretation and endotype definition.2026-03-03T00:00:00Z2026-06-16T14:20:33.532Z2026-01-16T18:13:26.157ZE-MTAB-16535ERP187666EFO_0002944EFO_0004170EFO_0005518EFO_0003738EFO_0004184