{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":[null],"organism":["Drosophila melanogaster"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-14107"],"description":["Chromatin accessibility was assayed in control of salm/salr double knockdown third instar wing imaginal discs. Imaginal discs of the stated genotypes were fixed in PFA and treated for ATAC-seq. For each genotype, two biological replicates were collected and used to construct the ATAC libraries. Libraries were sequenced (paired-end) on Illumina NextSeq 500."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - paired-end sequencing on illumina NextSeq 500","Library Construction - Disk were permeabilization: Thaw disks on ice for 10 min and add 50ul PBT+PI; Add 50 ul of PBT + 0.4% IGEPAL CA-630; Incubate at 4C for 30 min on a nutator and Spin at 3200 xg for 5 min at 4C. Tagmentation and reverse-crosslinking: Resuspend the nuclei pellet in 50 ul tagmentation mix(5 uL TDE1 (Illumina, 15027865), 25 uL 2x buffer (Illumina, 15027866), 20 uL nuclease-free H2O). Incubate at 37C for 30 min. Add 50 ul STOP buffer, 5 ul of 1mg/ml RNase A and incubate at 55C for 10 min. Add 3 ul Proteinase K (20 mg/ml) incubate 65C for 1 hour. Purify with Zymo DNA clean and concentrator kit. Finally samples are PCR amplified and size selected with SPRI beads.","Growth Protocol - We used 20 imaginal wing discs per sample to make two technical replicates, and the larvae were of salEPV-Gal4 UAS-salm-i/+; UAS-salr-i/+ and salEPV-Gal4 UAS-GFP/+ genotypes. The discs were dissected in pre-cooled PBS, pipetted in PBT (PBS, 0.1 % Triton X-100) containing 1x proteases inhibitors (cOmplete™ Protease Inhibitor Cocktail tablets, Roche, 11873580001) and suspended in transposition solution containing."],"figure_sub":["MINSEQE Score","Assays and Data","organisation","MAGE-TAB Files"],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["NextSeq 500"],"study_type":["ATAC-seq"],"species":["Drosophila melanogaster"],"additional_accession":["ERP160391"],"pubmed_authors":["Jose F de Celis","Charles Girardot"]},"is_claimable":false,"name":"Comparison of ATAC seq between control wing imaginal discs and salm/salr knockdown wing imaginal discs","description":"Chromatin accessibility was assayed in control of salm/salr double knockdown third instar wing imaginal discs. Imaginal discs of the stated genotypes were fixed in PFA and treated for ATAC-seq. For each genotype, two biological replicates were collected and used to construct the ATAC libraries. Libraries were sequenced (paired-end) on Illumina NextSeq 500.","dates":{"release":"2025-05-05T00:00:00Z","modification":"2026-06-06T01:10:29.368Z","creation":"2024-05-20T16:41:55.414Z"},"accession":"E-MTAB-14107","cross_references":{"ENA":["ERP160391"],"EFO":["EFO_0007045","EFO_0004170","EFO_0005518","EFO_0004184"]}}