biostudies-arrayexpressAlessandro VitrioloHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-16418This 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.biostudies-arrayexpressLibrary 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.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData 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)MetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina HiSeq 2500IEO HPCOmni ATAC kitATAC-seqHomo sapiensAlessandro VitriolofalseDisruption of ADNP-KDM1A-GTF2I complex drives neural differentiation imbalance in Helsmoortel-Van der Aa syndrome [ATAC]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.2026-01-26T00:00:00Z2026-05-27T16:32:22.604Z2025-12-18T17:12:17.131ZE-MTAB-16418ERP186782E-MTAB-15963EFO_0002944EFO_0007045EFO_0004170EFO_0005518EFO_0003816EFO_000418410.1101/2025.03.06.641037v1.full