biostudies-arrayexpressMisbah AbbasMus musculushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-13572Hi-C experiment was performed to map and compare potential changes in wildtype and Ddx5 Knockout neural stem cells.biostudies-arrayexpressSequencing - Sequencing was performed using Illumina NovaSeq X-Plus series paired-end, 150bp modeNucleic Acid Extraction - Hi-C experiments were performed as described as describer before (Rao et al., 2014)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 Treatment - Ddx5 depletion was carried out in Ddx5-FKBP NS Cells by treating with 500nM of dTAG13 dissolved in culture media for 24hLibrary Construction - Hi-C libraries were generated using NEBNext Ultra II DNA Library Kit, according to manufacturer's instructionsSequencing - Sequencing was performed using Illumina 6000 platform in paired-end, 100bp modeSample Collection - Cells were detached with Accutase, counted and crosslinked with 1% (final) formaldehyde in their medium. The reaction was quenched with 0.125M (final) glycine, and cell pellets were washed with PBS, snap-frozen, and stored in a -80 freezer. The pellet of 5 million cells was used for each Hi-C experiment.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesSequence Alignment - Reads were aligned to reference genome (mm10) using the juicer pipeline with default settings.Data Transformation - Normalisation of the data was done automatically as a part of the juicer pipelineMetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000Illumina NovaSeq XHi-CMus musculusBondita DehingiaMałgorzata MilewskaAleksandra PękowskaDebadeep ChaudhuryMisbah AbbasfalseHi-C from mouse embryonic stem cell derived neural stem cellsHi-C experiment was performed to map and compare potential changes in wildtype and Ddx5 Knockout neural stem cells.2025-07-30T00:00:00Z2025-08-08T11:22:08.106Z2023-11-27T14:27:36.282ZE-MTAB-13572ERP172942EFO_0007693EFO_0002944EFO_0004170EFO_0003789EFO_0004917EFO_0003816EFO_0005518EFO_0004184EFO_0003969