{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Alessandro Vitriolo"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16418"],"description":["This work attempt at characterizing the chromatin accessibility of control and HVDAS lines. We profiled 5 control and 5 HVDAS lines with bulk ATAC-seq, to reconstruct the molecular basis of HVDAS at early stages of development. This data was then integrated with HPTMs and TF ChIP-seq generated from the same lines to identify chromatin accessibility changes connected with ADNP binding changes in HVDAS."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - DNA fragments obtained at the end of library preparation underwent a double-sided size selection to remove primer dimers and fragments larger than 1000bp. To remove DNA fragments > 1000bp, 0.5X volumes of Agencourt AMPure beads XP (Beckman Coulter) were added to the samples, then incubated for 10 minutes at RT. The supernatant, containing DNA fragments < 1000bp, was transferred in a new tube and incubated for 10 minutes at RT with 1.3X original volume AMPure beads. Supernatant, containing primer dimers, was discarded and the DNA-beads complex was washed 3X with Ethanol 80% and eluted in water.","Sequencing - Libraries were quantified by Qubit DNA High sensitivity (Thermo Fisher), checked with Bioanalyzer high-sensitivity kit, and sequenced on an Illumina NovaSeq 6000 at 50bp paired-end read length and a coverage of 60 million reads per sample.","Sample Collection - 50,000 iPSCs were collected and centrifuged at 500g for 5 minutes in a pre-chilled centrifuge and then briefly resuspended in ice-cold ATAC Resuspension Buffer (ATAC-RSB buffer: Tris-HCl pH 7.4 10mM, NaCl 10mM, MgCl2 3mM) supplemented with NP-40 0.1%, Tween-20 0.1% and Digitonin 0.01%. Samples were incubated on ice for 3 minutes. Lysis was washed out with ATAC-RSB supplemented with Tween-20 0.1% without NP-40 or Digitonin. Nuclei were then centrifuged for 10 minutes at 500g in a pre-chilled centrifuge. To allow transposase reaction, samples were resuspended in 50ul of ice-cold transposition mixture (TD buffer 2X, MEDS-loaded Tn5 100nM, PBS 33%, digitonin 0.01%, Tween-20 0.1%) and then incubated for 30 minutes at 37 C on agitation (1000 rpm). Tn5 was pre-loaded with pre-annealed Mosaic End double-stranded (MEDS) oligonucleotides as described in Picelli et al89.","Nucleic Acid Extraction - To clean up the transposase reaction, samples were purified with Zymo DNA Clean and Concentrator-5 kit (Zymo Research), according to manufacturer instructions. Eluted tagmented DNA was PCR amplified for 5 cycles using NEBNext Master Mix (NEB) and barcoded with Unique Dual Indexes (UDIs) which mitigate sample misassignment due to index hopping during de-multiplexing. 5 ul of the total 50 ul PCR reaction were collected for qPCR quantification using Viia7 Real-Time PCR system in order to assess the right number of additional cycles required to obtain optimal complexity during library amplification. 8 final PCR cycles (5 pre-amplification + 3 extra cycles) was established as the gold standard for iPSCs samples, using the following condition: 72°C for 5 min, 98°C for 30s, and thermocycling for 98°C for 10s, 63°C for 30s and 72°C for 1 min."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Library size normalization was performed only for plotting, using DeepTools (e.g. bamCoverage -b sample.shifted.bam -o sample.rpgc.bw \\   --normalizeUsing RPGC --effectiveGenomeSize 2913022398 \\   --binSize 25 --ignoreDuplicates --minMappingQuality 30 -p 8)"],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina HiSeq 2500","IEO HPC","Omni ATAC kit"],"study_type":["ATAC-seq"],"species":["Homo sapiens"],"pubmed_authors":["Alessandro Vitriolo"],"additional_accession":[]},"is_claimable":false,"name":"Disruption of ADNP-KDM1A-GTF2I complex drives neural differentiation imbalance in Helsmoortel-Van der Aa syndrome [ATAC]","description":"This work attempt at characterizing the chromatin accessibility of control and HVDAS lines. We profiled 5 control and 5 HVDAS lines with bulk ATAC-seq, to reconstruct the molecular basis of HVDAS at early stages of development. This data was then integrated with HPTMs and TF ChIP-seq generated from the same lines to identify chromatin accessibility changes connected with ADNP binding changes in HVDAS.","dates":{"release":"2026-01-26T00:00:00Z","modification":"2026-05-27T16:32:22.604Z","creation":"2025-12-18T17:12:17.131Z"},"accession":"E-MTAB-16418","cross_references":{"ENA":["ERP186782"],"Biostudies":["E-MTAB-15963"],"EFO":["EFO_0002944","EFO_0007045","EFO_0004170","EFO_0005518","EFO_0003816","EFO_0004184"],"doi":["10.1101/2025.03.06.641037v1.full"]}}