biostudies-arrayexpressMetabolomicsUnknownTranscriptomicsGenomicsProteomicsMisbah AbbasIllumina NovaSeq 6000RNA-seq of coding RNAhttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-13558RNA-Seq experiment to detect transcriptional differences in mouse embryonic stem cells, and ES derived neural stem cells (NSCs).biostudies-arrayexpressGrowth 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 24hLibrary 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.OrganizationMINSEQE ScoreAssays and DataMAGE-TAB FilesBondita DehingiaMałgorzata MilewskaAleksandra PękowskaDebadeep ChaudhuryMisbah AbbasSequence 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'falseRNA-seq from mouse embryonic stem cell and their derivative neural stem cellsRNA-Seq experiment to detect transcriptional differences in mouse embryonic stem cells, and ES derived neural stem cells (NSCs).2025-06-13T00:00:00Z2025-06-13T14:01:09.509Z2023-11-22T23:04:34.186ZE-MTAB-13558EFO_0002944EFO_0004170EFO_0003789EFO_0004917EFO_0003816EFO_0005518EFO_0003738EFO_0004184EFO_0003969