biostudies-arrayexpressValeria Fernandez ValloneHomo sapiensSTAR aligner (v.2.7.10b).https://www.ebi.ac.uk/biostudies/studies/E-MTAB-17066This 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/v1biostudies-arrayexpressSample Collection - In RNA lysis buffer from kit Aurum™ Total RNA Mini Kit (Bio-Rad, 732-6820), according to manufacturer instructionsSample 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 instructionsGrowth Protocol - For CO: According to kit STEMdiff™ Cerebral Organoid Kit (STEMCELL Technologies, 08570), following manufacturer instructionsLibrary 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/v1Library 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).OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData 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.UnknownTranscriptomicsGenomicsProteomicsNAIllumina NovaSeq XIllumina NovaSeq 6000RNA-seq of coding RNAHomo sapiensComparative Evaluation of hiPSC-Derived Brain Organoids as Platforms for Assessing Thyroid Hormone System Disrupting ChemicalsValeria Fernandez ValloneValeria Fernandez Vallone, Lina Hellwig, Eddy Rijntjes, Nicolai von Kügelgen, Rajas Sane, Robert Opitz, Peter Kühnen, Josef Köhrle, Philipp Mergenthaler and Harald StachelscheidfalseBulk RNA-seq comparing brain organoids in vitro systems treated or not with 3,3’-5-triiodothyronine (T3)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/v12026-05-30T00:00:00Z2026-05-30T01:01:28.521Z2026-05-20T15:13:12.629ZE-MTAB-17066EFO_0002944EFO_0004170EFO_0003789EFO_0005518EFO_0003816EFO_0003738EFO_0004184EFO_0003969