biostudies-arrayexpressHyun Jung KimHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-16296To explore the non-canonical functions of core clock proteins in ESCs, we generated CRISPR/Cas9-edited isogenic human ESC lines carrying targeted truncations of CLOCK, BMAL1, NR1D1, and/or NR1D2. Comprehensive characterization and transcriptomic analyses demonstrated changes in gene expression associated with pluripotency and differentiation, despite the absence of rhythmic activity.biostudies-arrayexpressLibrary Construction - cDNA libraries were prepared with the TruSeq™ Stranded Total RNA Prep Kit (Illumina) according to the manufacturer’s protocol.Sample Collection - Wild-type and mutant hESCs were maintained in mTeSR™ Plus medium (STEMCELL Technologies, Vancouver, Canada) on culture plates coated with diluted Matrigel (Corning Inc., Corning, NY, USA) in DMEM/F-12 medium (Thermo Fisher Scientific Inc., Waltham, MA, USA). Colonies were passaged every 5–7 days using ReLeSR™ (STEMCELL Technologies) and resuspended in medium supplemented with 10 μM Y-27632 (STEMCELL Technologies).Nucleic Acid Extraction - Total RNA was extracted from hESCs using the miRNeasy Mini Kit (Qiagen), and RNA integrity was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies). Ribosomal RNA was depleted using the Ribo-Zero™ reagent (Illumina).Sequencing - Sequencing was performed on the Illumina NovaSeq 6000 platform using paired-end reads.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Transcript abundance quantification and gene-level normalization were performed using RSEM (v1.3.3) with default parameters, producing TPM-normalized counts.Sequence Alignment - Raw sequencing reads (FASTQ files) were trimmed to remove adapter sequences using Cutadapt (v2.8). The trimmed reads were aligned to the human reference genome (GRCh38) using the STAR aligner (v2.7.10b) with default parameters.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000RNA-seq of coding RNAHomo sapiensHyun Jung KimfalseTranscriptomic characterization of circadian clock gene-mutated human pluripotent stem cell linesTo explore the non-canonical functions of core clock proteins in ESCs, we generated CRISPR/Cas9-edited isogenic human ESC lines carrying targeted truncations of CLOCK, BMAL1, NR1D1, and/or NR1D2. Comprehensive characterization and transcriptomic analyses demonstrated changes in gene expression associated with pluripotency and differentiation, despite the absence of rhythmic activity.2026-04-13T00:00:00Z2026-04-13T01:02:01.558Z2025-11-26T15:58:05.392ZE-MTAB-16296ERP185685EFO_0002944EFO_0004170EFO_0004917EFO_0005518EFO_0003816EFO_0003738EFO_0004184