{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Alessandro Vitriolo"],"organism":["Homo sapiens"],"software":["Cellranger Arc"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16422"],"description":["Here, to characterize HVDAS in a developmental setting, we generated cortical brain organoids of 5 control and 5 HVDAS lines and profiled them by single-cell RNA- and ATAC-seq. Organoids were grown for 30 days using the protocol 10.1016/j.stem.2019.08.002. To reduce batch effects and costs, and maximize coverage in terms of cell number and detected genes, we performed 3 downstream multiplexing 10.1038/s41592-024-02555-5. We grew each line independently, then single-cell dissociated 3 organoids per line, than mixed the cells and performed multiomic (10x GEX+ATAC) on 3 pools of multiple individuals. In silico sample deconvolution was performed by using ScanSNP on bulk RNA-seq from E-MTAB-15963."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Growth Protocol - Cortical organoids were generated using an adaptation of the previously described protocol published by Trujillo et al.","Sample Collection - Cortical organoids were dissociated using Dissociation Buffer composed of 0.5% BSA, 2 mM EDTA, 0.1% Accutase, 0.4 mg/ml Collagenase/Dispase (Sigma-Aldrich, 10269638001), 0.05 mg/ml DNAse I (Sigma-Aldrich, 10104159001) diluted into final volume of PBS, and filtered with 0.22 μm filters. Few homogeneous-sized organoids were incubated for approximately 40 minutes on a rotating wheel at 37°C with 1 ml of Dissociation Buffer, manually pipetting every 10 minutes. Organoids were transferred to a new Eppendorf leaving behind undissociated pieces, and then centrifuged at 300g for 5 minutes at 4°C. Cells were resuspended in 1 ml of PBS-BSA 0.04% and filtered with 40 μm Flowmi cell strainer (Bel-Art, H13680-0040) to remove the majority of debris. Cells were counted manually and then multiplexed together with other samples to obtain a final number of 1 million cells, with equal representation from each sample (e.g., 250K cells in case of 4 samples multiplexed).","Sequencing - DNA libraries were prepared by Genomic Unit at the IFOM/IEO/IIT campus according to manufacturer’s protocol and sequenced on the Illumina Novaseq 6000 instrument at a coverage of 50,000 reads per nucleus.","Nucleic Acid Extraction - Multiplexed cell solution was washed twice with PBS-BSA 0.04% and pellet was resuspended in 100 μL of Lysis Buffer [10mM Tris-HCl (pH 7.4), 10mM NaCl, 3mM MgCl2, 0.1% Tween-20 (Bio-Rad, 1662404), 0.1% Nonidet P40 Substitute (Sigma-Aldrich, 74385), 0.01% Digitonin (Thermo Fisher, BN2006), 1% BSA, 1 mM DTT (Sigma-Aldrich, 646563), 1U/μL RNase inhibitor (Sigma-Aldrich, 3335399001), nuclease-free water], and incubated 5 minutes on ice. Lysis Buffer was washed away three times with 1 ml of Wash Buffer [10mM Tris-HCl (pH 7.4), 10mM NaCl, 3mM MgCl2, 1% BSA, 0.1% Tween-20, 1 mM DTT, 1U/μL RNase inhibitor, nuclease-free water]. Assuming 50% nuclei loss during lysis, nuclei were resuspended in Diluted Nuclei Buffer [1X 10x Genomics Nuclei Buffer, 1 mM DTT, U/μL RNase inhibitor, nuclease-free water] according to the reference table provided by 10X protocol appendix.","Library Construction - The volume of Nuclei Diluted Buffer is critical to fit the right range of concentration based on the number of targeted nuclei recovery, therefore avoiding overcrowding of the Chromium machine during tagmentation and GEM preparation steps. Resuspended nuclei were passed again through a Flowmi cell strainer and counted to check for the right concentration feasible for the number of targeted nuclei. 5,000 was the number of targeted nuclei recovery for each multiplexed sample in all the experiments (e.g., 20,000 nuclei were targeted in the reactions with 4 multiplexed samples)."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Multiomic data was split into Gene Expression (RNA) and Chromatin Accessibility (ATAC) components before quality control. RNA was analysed using Scanpy 1.9.1 and ATAC was analysed using ArchR release 1.0.2. They were separately filtered according to the type of observable (counts per cell, mitochondrial genes expression/percentage of mitochondrial reads, percentage of reads in peaks, TSS enrichments, etc). The two modes were normalised independently following best practices (normalization on UMI and log-transformation, following Scanpy guidelines for RNA-seq, TF-IDF for ATAC-seq following ArchR pipeline).","Sequence Alignment - Reads were aligned using cellranger-arc v.2.11. In silico demultiplexing has been performed on each batch of sequencing using single nucleotide variants (SNP) called from bulk RNA-seq using internal pipelines (alignment with STAR on cellranger reference, followed by GATK)."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["IEO HPC","Illumina NovaSeq 6000","none"],"pubmed_abstract":["<h4>ABSTRACT</h4>  Mutations in ADNP (Activity-Dependent Neuroprotective Protein) are among the most frequent monogenic causes of autism spectrum disorder (ASD) and lead to Helsmoortel-Van der Aa syndrome (HVDAS). Yet how ADNP dysfunction leads to HVDAS is unclear. We employed patient-derived induced pluripotent stem cells, cortical organoids and ADNP KO human neural stem cells (hNSCs) to clarify the cellular and molecular mechanism of HVDAS onset. We purified an ADNP-KDM1A-GTF2I (AKG) protein complex from hNSCs and show that it targets transposable elements (TEs) to repress nearby gene transcription. Upon ADNP KO, KDM1A binding is lost at promoters targeted by AKG, pointing to ADNP as the anchoring subunit of the AKG complex. HVDAS cortical organoids show impaired progenitor proliferation and accelerated neuronal differentiation, coupled with a sustained upregulation of neurogenesis transcriptional programs, including key transcription factors normally repressed by AKG. This work suggests that the AKG complex acts as the relevant ADNP unit in the molecular onset of HVDAS."],"study_type":["RNA-seq of coding RNA from single cells"],"species":["Homo sapiens"],"pubmed_title":["Disruption of ADNP-KDM1A-GTF2I complex drives neural differentiation imbalance in Helsmoortel-Van der Aa syndrome"],"pubmed_authors":["Rizzuti, Vitriolo, Pelicano de Almeida, et al.","Alessandro Vitriolo"],"additional_accession":[]},"is_claimable":false,"name":"Disruption of ADNP-KDM1A-GTF2I complex drives neural differentiation imbalance in Helsmoortel-Van der Aa syndrome [multi-omic]","description":"Here, to characterize HVDAS in a developmental setting, we generated cortical brain organoids of 5 control and 5 HVDAS lines and profiled them by single-cell RNA- and ATAC-seq. Organoids were grown for 30 days using the protocol 10.1016/j.stem.2019.08.002. To reduce batch effects and costs, and maximize coverage in terms of cell number and detected genes, we performed 3 downstream multiplexing 10.1038/s41592-024-02555-5. We grew each line independently, then single-cell dissociated 3 organoids per line, than mixed the cells and performed multiomic (10x GEX+ATAC) on 3 pools of multiple individuals. In silico sample deconvolution was performed by using ScanSNP on bulk RNA-seq from E-MTAB-15963.","dates":{"release":"2026-01-27T00:00:00Z","modification":"2026-05-26T16:03:53.438Z","creation":"2025-12-19T12:41:04.186Z"},"accession":"E-MTAB-16422","cross_references":{"ENA":["ERP186830"],"Biostudies":["E-MTAB-15963"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0005684","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0004184"],"doi":["10.1101/2025.03.06.641037"]}}