{"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-15963"],"description":["Our 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)."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample 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 kit","Sequencing - 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 sample","Sequencing - 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."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Sequence Alignment - salmon v1.2 was used to quasimap reads on GENCODE v35 hg38 transcriptome 30bp-length k-mers, to directly quantify read counts","Data Transformation - reads were normalized for PCA and differential expression analysis with TMM using the edgeR v3 R library"],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina HiSeq 2500","Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA"],"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","description":"Our 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).","dates":{"release":"2026-01-31T00:00:00Z","modification":"2026-05-31T01:40:21.75Z","creation":"2025-11-03T15:59:23.671Z"},"accession":"E-MTAB-15963","cross_references":{"ENA":["ERP183595"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184","EFO_0003969"]}}