{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Haxiaoyu Liu"],"instrument_platform":["Illumina HiSeq 4000"],"study_type":["RNA-seq of coding RNA"],"organism":["Homo sapiens"],"species":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16792"],"description":["Human cortical organoids (hCOs) were employed to examine the developmental neurotoxic effects of ciprofloxacin (CPFX). Organoids were subjected to chronic exposure to low doses of CPFX for two weeks, while untreated organoids served as controls. Assessments included mitochondrial function, reactive oxygen species (ROS) production, and the expression of key neurodevelopmental regulators, including FOXG1, as well as genes associated with excitatory and inhibitory neuronal network formation. This study establishes a human-relevant model to investigate the molecular and functional consequences of CPFX exposure on cortical development."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - Total RNA was extracted from cortical organoids with four biological replicates set for each sample (n = 4 per sample).","Sequencing - Libraries were sequenced on an Illumina HiSeq 4000 platform using 150 bp paired-end reads with NovaSeq chemistry. Raw reads were subjected to quality filtering, aligned to the human reference genome GRCh38.p10 using HISAT2 v2.2.1, and quantified as transcripts per million (TPM) with RSEM v1.3.3.","Nucleic Acid Extraction - Total RNA was extracted from cortical organoids using TRIzol™ reagent (Thermo Fisher).","Library Construction - The extracted total RNA was used to construct mRNA sequencing libraries with the TruSeq™ mRNA Library Kit (Illumina)."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"pubmed_authors":["Haxiaoyu Liu"],"additional_accession":[]},"is_claimable":false,"name":"RNA-seq of Human Cortical Organoids Treated with Ciprofloxacin versus Untreated Controls","description":"Human cortical organoids (hCOs) were employed to examine the developmental neurotoxic effects of ciprofloxacin (CPFX). Organoids were subjected to chronic exposure to low doses of CPFX for two weeks, while untreated organoids served as controls. Assessments included mitochondrial function, reactive oxygen species (ROS) production, and the expression of key neurodevelopmental regulators, including FOXG1, as well as genes associated with excitatory and inhibitory neuronal network formation. This study establishes a human-relevant model to investigate the molecular and functional consequences of CPFX exposure on cortical development.","dates":{"release":"2026-03-31T00:00:00Z","modification":"2026-03-31T01:03:46.752Z","creation":"2026-03-20T16:33:02.55Z"},"accession":"E-MTAB-16792","cross_references":{"ENA":["ERP191111"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003738","EFO_0004184"]}}