{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Misbah Abbas"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-13558"],"description":["RNA-Seq experiment to detect transcriptional differences in mouse embryonic stem cells, and ES derived neural stem cells (NSCs)."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Growth Protocol - ES (2i/LIF) cells were grown on gelatin-coated culture plastic in embryonic stem cells medium in the presence of MEK inhibitor (PD0325901) and GSK3 inhibition (CHIR99021) with LIF to maintain ESCs in a naive ground state. Cells were split at 80% confluence with a density of 30000 cells/sq.cm. The medium was exchanged daily.","Growth Protocol - NS cells were grown on laminin-coated plates in neural differentiation medium containing N2 and B27 supplements along with recombinant murine EGF and bFGF to a final concentration of 10 ng/ml. Cells were split at 80% confluence with a density of 35000 cells/sq.cm. The medium was exchanged daily.","Sample Collection - Cells were detached with Accutase, counted and 500,000 cells were lysed with TRI-Reagent (Sigma).","Sequencing - Sequencing was performed using Illumina 6000 platform in paired-end, 100bp mode.","Sample Treatment - CTCF depletion was carried out in CTCF-AID-GFP ES and NS Cells by treating with 500uM of indole acetic acid (IAA) dissolved in culture media for 24h","Library Construction - 1 ug of RNA (RIN > 8) was used for library constructions. Libraries were prepared using KAPA HyperPrep Kit, according to manufacturer's instructions. UDI/UMI (itDNA) indexes were used. Library quality was assessed with 4200 TapeStation System, High Sensitivity D1000 ScreenTape (Agilent).","Nucleic Acid Extraction - RNA was isolated using Direct-Zol RNA Isolation kit (ZYMO), according to the manufacturer's instructions."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"pubmed_authors":["Bondita Dehingia","Małgorzata Milewska","Aleksandra Pękowska","Debadeep Chaudhury","Misbah Abbas"],"data_protocol":["Sequence Alignment - We aligned reads to reference mouse genome (mm10) using STAR with default options.","Data Transformation - We used the bamCoverage tool from the deeptools suite to generate bigwig tracks using the default parameters, and normalised using 'BPM'"],"additional_accession":[]},"is_claimable":false,"name":"RNA-seq from mouse embryonic stem cell and their derivative neural stem cells","description":"RNA-Seq experiment to detect transcriptional differences in mouse embryonic stem cells, and ES derived neural stem cells (NSCs).","dates":{"release":"2025-06-13T00:00:00Z","modification":"2025-06-13T14:01:09.509Z","creation":"2023-11-22T23:04:34.186Z"},"accession":"E-MTAB-13558","cross_references":{"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0004917","EFO_0003816","EFO_0005518","EFO_0003738","EFO_0004184","EFO_0003969"]}}