{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Valeria Fernandez Vallone"],"organism":["Homo sapiens"],"software":["STAR aligner (v.2.7.10b)."],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-17066"],"description":["This experiment aims to define DGE when hiPSC derived brain organoids are exposed for long (chronic) or short (pulse) time to T3. Additionally, a comparison regarding T3 responsive genes can be assessed for two different brain organoids systems: cerebral organoids (CO) and Neural Stem Cell derived Organoids (NSCO). CO correspond to unguided differentiation following Lancaster et al. 2013. NSCO are neurospheres derived as desribed in https://dx.doi.org/10.17504/protocols.io.3byl4j6kzlo5/v1"],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - In RNA lysis buffer from kit Aurum™ Total RNA Mini Kit (Bio-Rad, 732-6820), according to manufacturer instructions","Sample Treatment - T3 was added to indicated final concentration to culture medium.","Sequencing - For NSCO: The sequencing libraries were multiplexed and loaded on the flow cell on the Illumina NovaSeq 6000 instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150 Pair-End (PE) configuration v1.5.","Nucleic Acid Extraction - Used kit Aurum™ Total RNA Mini Kit (Bio-Rad, 732-6820), according to manufacturer instructions","Growth Protocol - For CO: According to kit STEMdiff™ Cerebral Organoid Kit (STEMCELL Technologies, 08570), following manufacturer instructions","Library Construction - For CO: bulk 3′ mRNA sequencing libraries Illumina sequencing libraries were prepared from 100 ng totalRNA using the QuantSeq 3’ mRNA-Seq V2 Library Prep Kit FWD with UDI 12 nt (Lexogen) according to the recommendations of the manufacturer.","Sequencing - For CO: after equimolar pooling libraries were sequenced paired-end 100 cycles on an illumina NovaSeq Xplus 10B flow cell (illumina), targeting ~30 million reads per sample.","Growth Protocol - For NSCO: follow protocol: https://dx.doi.org/10.17504/protocols.io.3byl4j6kzlo5/v1","Library Construction - For NSCO: bulk RNA-sequencing was performed by Brooks Life Sciences Genewiz® using poly(A) selection for mRNA enrichment targeting depth of ~30 million reads per sample. Sequenc-ing libraries were prepared using the NEBNext® Ultra™ RNA Library Prep Kit for Illu-mina (New England Biolabs, E7770)."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - RNA-sequencing reads were mapped to human genome (GRCh38.p14) using the STAR aligner (v.2.7.10b). Prior to model fitting, low-abundance transcripts were filtered to reduce noise by excluding genes with <10 total counts across all samples and retaining only genes with ≥5 counts in at least 3 samples."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["NA","Illumina NovaSeq X","Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA"],"species":["Homo sapiens"],"pubmed_title":["Comparative Evaluation of hiPSC-Derived Brain Organoids as Platforms for Assessing Thyroid Hormone System  Disrupting Chemicals"],"pubmed_authors":["Valeria Fernandez Vallone","Valeria Fernandez Vallone, Lina Hellwig, Eddy Rijntjes, Nicolai von Kügelgen, Rajas Sane,  Robert Opitz, Peter Kühnen, Josef Köhrle, Philipp Mergenthaler and Harald Stachelscheid"],"additional_accession":[]},"is_claimable":false,"name":"Bulk RNA-seq comparing brain organoids in vitro systems treated or not with 3,3’-5-triiodothyronine (T3)","description":"This experiment aims to define DGE when hiPSC derived brain organoids are exposed for long (chronic) or short (pulse) time to T3. Additionally, a comparison regarding T3 responsive genes can be assessed for two different brain organoids systems: cerebral organoids (CO) and Neural Stem Cell derived Organoids (NSCO). CO correspond to unguided differentiation following Lancaster et al. 2013. NSCO are neurospheres derived as desribed in https://dx.doi.org/10.17504/protocols.io.3byl4j6kzlo5/v1","dates":{"release":"2026-05-30T00:00:00Z","modification":"2026-05-30T01:01:28.521Z","creation":"2026-05-20T15:13:12.629Z"},"accession":"E-MTAB-17066","cross_references":{"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184","EFO_0003969"]}}