{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":[null],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15048"],"description":["ATAC-seq was conducted to map open chromatin regions in five individual primary human melanocyte cultures. The ATAC libraries were sequenced using paired-end sequencing on an Illumina NovaSeq platform. In total, we sequenced 15 ATAC libraries from these five independent primary melanocyte cultures (C24, C27, C56, C140, C205), with three technical replicates for each culture."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - The isolated nuclei were treated with Tn5 Transposes from Nextera DNA Sample Preparation Kit and the transposed DNA was purified using a Qiagen MinElute Kit. The transposed DNA libraries were amplified by PCR for 12 cycles and isolated by Ampure XP beads.","Sample Collection - Early passages of primary human melanocytes were isolated from foreskin healthy newborn males, following an established protocol (Halaban et al, J Exp Med (2000) 191(6):1005-1016) from the Specialized Programs of Research Excellence (SPORE) in Skin Cancer Specimen Resource Core at Yale University. Cells were grown in Dermal Cell Basal Medium (American Type Culture Collection/ATCC PCS-200-030) supplemented with Melanocyte Growth Kit (ATCC PCS-200-041) and 1% amphotericin B/penicillin/streptomycin (120-096-711, Quality Biological). C56, C140 and C205 are of European ancestry(CEU) and C24 and C27 are of African descent(YRI). For each library, 50,000 live cells were harvested.","Sequencing - 15 ATAC-seq libraries were sequenced on Illumina NovaSeq 6000","Nucleic Acid Extraction - The ATAC-seq libraries were generated following a previously published protocol (Buenrostro et al., Nature Methods, 2013). The nuclei were isolated from the 50,000 cells."],"figure_sub":["MINSEQE Score","Assays and Data","Processed Data","organisation","MAGE-TAB Files"],"data_protocol":["Data Transformation - The ATAC-seq reads from the technical replicates were merged for each melanocyte culture. The ATAC sequencing (ATAC-seq) data was processed using the ENCODE ATAC-seq pipeline version 1.6.1 (https://www.encodeproject.org/atac-seq/), treating five melanocyte cultures as biological replicates. The ATAC overlap and idr reproducibility peaks were identified via the optimal criteria assessing peak overlap between individual biological replicates, pooled biological replicates, and the pseudo biological replicates."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["ATAC-seq"],"species":["Homo sapiens"],"pubmed_title":["Mapping chromatin interactions at melanoma susceptibility loci and cell-type specific dataset integration uncovers distant gene targets of cis-regulation"],"additional_accession":["ERP171757"],"pubmed_authors":["Rohit Thakur","Kevin Brown","Rohit Thakur, Mai Xu, Hayley Sowards, Joshuah Yon, Lea Jessop, Timothy Myers, Tongwu Zhang, Raj Chari, Erping Long, Thomas Rehling, Rebecca Hennessey, Karen Funderburk, Jinhu Yin, Mitchell J. Machiela, Matthew E. Johnson, Andrew D. Wells, Alessandra Chesi, Struan F.A. Grant, Mark M. Iles, Maria Teresa Landi, Matthew H. Law, Melanoma Meta-Analysis Consortium, Jiyeon Choi, Kevin M. Brown"]},"is_claimable":false,"name":"Assay for Transposase-Accessible Chromatin sequencing (ATAC-seq) of primary melanocytes from five human donors","description":"ATAC-seq was conducted to map open chromatin regions in five individual primary human melanocyte cultures. The ATAC libraries were sequenced using paired-end sequencing on an Illumina NovaSeq platform. In total, we sequenced 15 ATAC libraries from these five independent primary melanocyte cultures (C24, C27, C56, C140, C205), with three technical replicates for each culture.","dates":{"release":"2025-04-24T00:00:00Z","modification":"2026-05-27T18:02:21.492Z","creation":"2025-04-17T09:47:44.172Z"},"accession":"E-MTAB-15048","cross_references":{"ENA":["ERP171757"],"EFO":["EFO_0002944","EFO_0007045","EFO_0004170","EFO_0005518","EFO_0003816","EFO_0004184"],"doi":["10.1101/2024.11.14.24317204"]}}