biostudies-arrayexpressAlessandro VitrioloHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15963Our experimental workflow was designed to study the role of ADNP in pluripotency and neuronal differentiation. Collectivelty, we profiled 12 iPSC, 2 NSC and 10 cortical brain organoids lines. This dataset contains RNA-seq profiling of iPSC and NSC, respectively capturing patient-derived transcriptional differences between control and ADNP-mutant individuals in pluripotency and transcriptional differences between control and ADNP-KO neural precursors. iPSC were generated by somatic reprogramming of fibroblasts from patients diagnosed with Helsmortel Van-der-Aa syndrome (HVDAS) and NSC were derived from a reference line. Both the NSC line, one control and one HVDAS lines were genetically engineered to carry a FLAG-tag at the n-terminus of ADNP coding sequence, to allow the profiling of ADNP DNA-binding activity through chromatin immunoprecipitation followed by sequencing (ChIP-seq).biostudies-arrayexpressSample Collection - Total RNA was extracted from fresh pellets of iPSC or NCS using the RNeasy Mini Kit (Qiagen, 74104).Growth Protocol - The hNSCs were cultured on Geltrex-coated dishes (Geltrex LDEV-free reduced growth factor membrane matrix, Thermo Fisher Scientific, A1413202) in KnockOut DMEM/F12 (Invitrogen, 12660012) supplemented with 2 mM L-Glutamine (Thermo Fisher Scientific, 25030024), 20 ng/ml EGF (Peprotech, 315-09), 20 ng/ml FGF (Peprotech, 100-18B) and 2% of StemPro Neural Supplement (Thermo Fisher Scientific, A1050801). The media was refreshed every other day and cells were routinely passaged with Accutase (Sigma-Aldrich, A6964).Sample Treatment - no treatment protocol was required nor performed on any cell line.Sample Collection - The H9 human embryonic stem cell (hESC) derived neural stem cells (hNSCs) were purchased from Invitrogen (N7800-100).Nucleic Acid Extraction - RNA was isolated using the GenElute™ Mammalian Total RNA Miniprep Kit (Sigma-Aldrich, RTN350-1KT)Library Construction - Library preparation for RNA sequencing was performed according to TruSeq Total RNA sample preparation protocol (Illumina, RS-122-2202), starting from 250 ng - 1 μg of total RNA. cDNA library quality was assessed on Agilent 2100 Bioanalyzer, using the high sensitivity DNA kit (Agilent 5067-4626)Nucleic Acid Extraction - Total RNA was extracted from fresh pellets of iPSC or NCS using the RNeasy Mini Kit (Qiagen, 74104). Purified RNA was quantified using a NanoDrop spectrophotometer and RNA quality was checked with an Agilent 2100 Bioanalyzer using the RNA nano kit (Agilent, 5067-1512).Library Construction - Total RNA was prepared using the Illumina TruSEq Stranded mRNA library Prep kitSequencing - sequenced according to the Illumina TruSeq Rapid v2 protocol on an HiSeq2500 sequencer (Illumina) at the Erasmus MC Center for Biomics at a read length of 50 bp single-end and a minimum coverage of 20 million reads per sampleSequencing - Libraries were sequenced with the Illumina Novaseq 6000 machine at a read length of 50 bp paired-end and a coverage of 35 million reads per sample.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesSequence Alignment - salmon v1.2 was used to quasimap reads on GENCODE v35 hg38 transcriptome 30bp-length k-mers, to directly quantify read countsData Transformation - reads were normalized for PCA and differential expression analysis with TMM using the edgeR v3 R libraryMetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina HiSeq 2500Illumina NovaSeq 6000RNA-seq of coding RNAHomo sapiensAlessandro VitriolofalseDisruption of ADNP-KDM1A-GTF2I complex drives neural differentiation imbalance in Helsmoortel-Van der Aa syndromeOur experimental workflow was designed to study the role of ADNP in pluripotency and neuronal differentiation. Collectivelty, we profiled 12 iPSC, 2 NSC and 10 cortical brain organoids lines. This dataset contains RNA-seq profiling of iPSC and NSC, respectively capturing patient-derived transcriptional differences between control and ADNP-mutant individuals in pluripotency and transcriptional differences between control and ADNP-KO neural precursors. iPSC were generated by somatic reprogramming of fibroblasts from patients diagnosed with Helsmortel Van-der-Aa syndrome (HVDAS) and NSC were derived from a reference line. Both the NSC line, one control and one HVDAS lines were genetically engineered to carry a FLAG-tag at the n-terminus of ADNP coding sequence, to allow the profiling of ADNP DNA-binding activity through chromatin immunoprecipitation followed by sequencing (ChIP-seq).2026-01-31T00:00:00Z2026-05-31T01:40:21.75Z2025-11-03T15:59:23.671ZE-MTAB-15963ERP183595EFO_0002944EFO_0004170EFO_0003789EFO_0004917EFO_0005518EFO_0003816EFO_0003738EFO_0004184EFO_0003969