{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["George Kassiotis"],"instrument_platform":["n/a","Illumina NovaSeq 6000"],"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-16688"],"description":["H9 human embryonic stem cells (ESCs cells) were modified by CRISPR/Cas9 in order to inactivate the CALB1 gene. Wild-type (wt) and targeted (em) clones, were resset into a naive state and sequenced in triplicate."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - H9 cells were grown in, stimulated and collected from culture dishes","Sequencing - RNA-seq libraries were sequenced on a NovaSeq 6000 (Illumina)","Library Construction - Library prep was performed with NEBNext Ultra II Directional PolyA mRNA kit (NEB, Cat #E7760)","Nucleic Acid Extraction - RNA from cultured H9 cells was extracted using RNeasy kit (Qiagen, Cat #74104)","Growth Protocol - H9 cells were chemically reset to naïve cells as previously described (29). DR4 MEFs, irradiated, were seeded onto 6-well plates coated with 0.1% gelatine 1-2 days before the conversion at a density of approximately 2×105 cells/well. The H9 cells were then passaged using TyplETM Select Enzyme and seeded at 5×105 cells/well in mTESRTM1 with 10 µM ROCKi for 24 h and a further 24 h in mTESTTM1 without ROCKi until medium sized colonies had formed. Chemical resetting medium was then applied at hypoxia 5% O2 for 3 days with the chemical resetting medium being replenished every 24 h. The cells were then maintained in PXGL at hypoxia, fed every day and passaged twice a week using StemPro™ Accutase™ Cell Dissociation Reagent and 10 µM ROCKi and Matrigel® hESC-Qualified Matrix for "],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"pubmed_authors":["George Kassiotis"],"additional_accession":[]},"is_claimable":false,"name":"RNA-Seq from naive CALB1wt and CALB1em H9 ESC clones","description":"H9 human embryonic stem cells (ESCs cells) were modified by CRISPR/Cas9 in order to inactivate the CALB1 gene. Wild-type (wt) and targeted (em) clones, were resset into a naive state and sequenced in triplicate.","dates":{"release":"2026-09-04T00:00:00Z","modification":"2026-09-04T08:34:28.323Z","creation":"2026-02-26T14:04:16.43Z"},"accession":"E-MTAB-16688","cross_references":{"ENA":["ERP189675"],"Biostudies":["E-MTAB-15900"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0005518","EFO_0003738","EFO_0004184"]}}