{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Thomas Boutet"],"organism":["Drosophila melanogaster"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16072"],"description":["Investigate changes in chromatin accessibility in rad50 KO CNS compared to control."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - Tagmentation was performed on extracted nuclei at 37°C for 30’ at 800 rpm in tagmentation buffer (Tris-HCl pH 8 33mM, DMF 16%, K-Ac 66mM, MgCl2 10mM, digitonin 0.001%, Tween-20 0.01%, PBS 0.4X) using pre-indexed assembled Tn5 transposomes (Active Motif, ref 53152). DNA was recovered using MinElute purification kit (Qiagen ref: 28004).","Library Construction - Libraries were prepared from the whole tagmented DNA using Q5® High-Fidelity 2X Master Mix (NEB) and P5/P7 primers at 1µM final concentration in 50µL total reaction volume and following PCR procedure: 72°C 5’/ 98°C 30’’/ (98°C 10’’, 63°C 30’’, 72°C 1’)*12. PCR clean-up was performed using SPRIselect size selection beads (Beckman coulter) with a ratio of 1.2. Library quality was assessed on bioanalyzer using High sensitivity Chips. If adapters remained, those were removed with another size selection step with 1.2 or 1.1 ratio according to amount of contamination.","Sample Collection - ATAC-seq was performed on Wl3 CNS from rad50∆5.1 or w1118 animals in triplicates. 20 CNS for each replicate were dissected on ice in PBS supplemented with 1% BSA. Cells were extracted in 200µL collagenase IV (Gibco ref: 17104019) at 1mg/mL at 37°C for 30’. To enhance dissociation, samples were pipetted 50 times every 10’ and 100 times at t=30’. Cells were counted on hemocytometer and 200.000 cells for each reaction were used. Upon dissociation, cells were pellet for 10’ at 600g 4°C and nuclei were extracted in nuclei extraction buffer (HEPES pH8.0 20mM, KCl 10mM, Glycerol 20%, triton X-100 0.1%, spermidine trihydrochloride 0.5mM) for 10’ on ice. Nuclei were pellet at 1200g for 10’ at 4°C.","Sequencing - Libraries were sequenced on an Illumina NextSeq 2000 sequencer as paired-end 50 base reads. Image analysis and base calling were performed using RTA version 4.12.2 and BCL Convert version 4.2.7. ”Sequencing was performed by the GenomEast platform, a member of the ’France Genomique’ consortium (ANR-10-INBS-0009)"],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Sequence Alignment - Sequencing reads were trimmed using Trim Galore (paired-end mode, minimum length 25 bp, --trim1 option). Trimmed reads were aligned to the D. melanogaster reference genome (dm6/BDGP6) using Bowtie2 with parameters: --very-sensitive-local, --dovetail, --no-unal, -I 25, -X 500, and --fr. Alignments were filtered for high-quality reads (mapping quality ≥10) and unmapped, secondary, and supplementary alignments were removed using samtools. Mitochondrial reads were quantified and removed. Peaks were called on individual samples using MACS2 (parameters: -f BAMPE, --gsize 120000000, --keep-dup=all, p-value cutoff 1e-5). Reproducible peaks were identified using Irreproducible Discovery Rate (IDR) analysis performed on all pairwise comparisons (sample 1 vs 2, 1 vs 3, and 2 vs 3), with peaks passing IDR threshold in all comparisons defined as significant. FRiP scores were calculated using bedtools intersect for quality control. Normalized bigWig files were generated using deepTools bamCoverage. Alignment and peak calling stats are described in Supplementary table 1. A consensus peak set of 26,996 regions was generated by merging all peaks detected across samples.","Data Transformation - Bigwig files were generated from bam files (filtered for small fragments) and normalized by library size."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["NextSeq 2000"],"study_type":["ATAC-seq"],"species":["Drosophila melanogaster"],"pubmed_authors":["Thomas Boutet"],"additional_accession":[]},"is_claimable":false,"name":"ATAC-seq on rad50∆5.1/rad50∆5.1 and w1118 CNS","description":"Investigate changes in chromatin accessibility in rad50 KO CNS compared to control.","dates":{"release":"2026-01-01T00:00:00Z","modification":"2026-05-27T02:01:08.326Z","creation":"2025-11-13T15:09:39.115Z"},"accession":"E-MTAB-16072","cross_references":{"ENA":["ERP184139"],"EFO":["EFO_0002944","EFO_0007045","EFO_0004170","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0004184"]}}