{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Alessia Valenti"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-17184"],"description":["To investigate the impact of hormonal modulation on neurodevelopmental processes, we performed single-cell RNA sequencing (ScRNA-seq) on neural organoids derived from two genetically validated human induced pluripotent stem cell (hiPSC) control lines (CTL08, male; CTL04, female). Organoids were chronically exposed to agonists and inhibitors targeting seven hormone signaling pathways known to regulate human brain development: androgen (AND), estrogen (EST), glucocorticoid (GC), thyroid (THY), retinoic acid (RA), liver X (LX), and aryl hydrocarbon (AH). Appropriate negative controls were included, consisting of vehicle-treated (DMSO) and/or untreated samples depending on the experimental condition.  GitHub: https://github.com/GiuseppeTestaLab/noha Cellxgene: https://cellxgene.cziscience.com/"],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - Neural organoids were collected at DIV 50 (+/- 3 days). For each scRNA seq run, 2 exposure conditions were processed, using 3 organoids per condition to obtain technical replicates which were univocally labelled with Cell Multiplexing Oligos (CMOs) (10X Genomics). After rinsing organoids in PBS twice, dissociation was performed following the Stemcell Neural Organoids dissociation protoco","Library Construction - After completing the washing steps, 1x 105 cells per replicate were pooled together, subsequently adjusting the cell concentration to be within 1.2-1.6 x 106 cells/ml to obtain an estimated target recovery of 30000 cells/sample. Droplet-based single-cell partitioning and single-cell RNA-Seq libraries were generated using the Chromium Next GEM Single Cell 3’ v3.1 kit (10X Genomics)","Sequencing - Two indexed libraries were equimolarly pooled and sequenced on Illumina NOVAseq 6000 platform using the v3 Kit (Illumina, San Diego, CA) with a customized paired end, dual indexing (26/8/0/98-bp) format according to the recommendation by 10× Genomics. Using proper cluster density, a coverage of around 750 M reads per sample (30000 cells) was obtained for the gene expression, corresponding to at least 25,000 reads/cell whereas for CellPlex Multiplexing Oligos a sequencing depth of 5000 reads/cell was used as recommended by 10X Genomics.","Nucleic Acid Extraction - Droplet-based single-cell partitioning and single-cell RNA-Seq libraries were generated using the Chromium Next GEM Single Cell 3’ v3.1 kit (10X Genomics)"],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Fastq files are partially processed. Due to legal constraints associated with one of the multiplexed human cell line (CTL08A), read pairs mapping to chromosome Y were removed prior to public submission. Reads were aligned to the human reference genome to identify chromosome Y-associated reads, and the remaining mapped reads were exported back to FASTQ format."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000","Illumina NOVAseq 6000"],"pubmed_abstract":["Hormonal signalling shapes the development of the human brain and its disruption is implicated in various neuropsychiatric conditions. However, a comprehensive and mechanistic understanding of how hormonal pathways orchestrate human neurodevelopment remains elusive. Here we present a multi-scale high resolution atlas of endocrine signalling in human neural organoids through systematic perturbations with agonists and inhibitors of seven key hormonal pathways: androgen (AND), estrogen (EST), glucocorticoid (GC), thyroid (THY), retinoic acid (RA), liver X (LX), and aryl hydrocarbon (AH). By integrating bulk and single-cell transcriptomics, high-throughput imaging and targeted steroidomics, we mapped the molecular and cellular consequences of their physiologically relevant perturbations. Retin"],"study_type":["RNA-seq of coding RNA from single cells"],"species":["Homo sapiens"],"pubmed_title":["A molecular cell atlas of endocrine signalling in human neural organoids"],"pubmed_authors":["Alessia Valenti","Gaja Matassa, Marco Tullio Rigoli, Davide Castaldi, Alessia Valenti, Manuel Lessi, Nicolò Caporale, Sarah Stucchi, Benedetta Muda, Riccardo Nagni, Lisa Mainardi, Alessandro Melon, Amaia Tintori, Davide Bulgheresi, Michal Kubacki, Sebastiano Trattaro, Sara Evangelista, Pim Leonards, Human Cell Atlas Organoid Biological Network, Carlo Emanuele Villa, Cristina Cheroni, Giuseppe Testa"],"additional_accession":[]},"is_claimable":false,"name":"scRNAseq NOHA","description":"To investigate the impact of hormonal modulation on neurodevelopmental processes, we performed single-cell RNA sequencing (ScRNA-seq) on neural organoids derived from two genetically validated human induced pluripotent stem cell (hiPSC) control lines (CTL08, male; CTL04, female). Organoids were chronically exposed to agonists and inhibitors targeting seven hormone signaling pathways known to regulate human brain development: androgen (AND), estrogen (EST), glucocorticoid (GC), thyroid (THY), retinoic acid (RA), liver X (LX), and aryl hydrocarbon (AH). Appropriate negative controls were included, consisting of vehicle-treated (DMSO) and/or untreated samples depending on the experimental condition.  GitHub: https://github.com/GiuseppeTestaLab/noha Cellxgene: https://cellxgene.cziscience.com/","dates":{"release":"2026-07-22T00:00:00Z","modification":"2026-07-22T01:01:03.362Z","creation":"2026-06-19T13:52:02.108Z"},"accession":"E-MTAB-17184","cross_references":{"EFO":["EFO_0002944","EFO_0004170","EFO_0005684","EFO_0005518","EFO_0003816","EFO_0004184"],"doi":["10.1101/2025.08.14.669814"]}}