{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Misbah Abbas"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-13572"],"description":["Hi-C experiment was performed to map and compare potential changes in wildtype and Ddx5 Knockout neural stem cells."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - Sequencing was performed using Illumina NovaSeq X-Plus series paired-end, 150bp mode","Nucleic 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 24h","Library Construction - Hi-C libraries were generated using NEBNext Ultra II DNA Library Kit, according to manufacturer's instructions","Sequencing - Sequencing was performed using Illumina 6000 platform in paired-end, 100bp mode","Sample 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."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Sequence 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 pipeline"],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000","Illumina NovaSeq X"],"study_type":["Hi-C"],"species":["Mus musculus"],"pubmed_authors":["Bondita Dehingia","Małgorzata Milewska","Aleksandra Pękowska","Debadeep Chaudhury","Misbah Abbas"],"additional_accession":[]},"is_claimable":false,"name":"Hi-C from mouse embryonic stem cell derived neural stem cells","description":"Hi-C experiment was performed to map and compare potential changes in wildtype and Ddx5 Knockout neural stem cells.","dates":{"release":"2025-07-30T00:00:00Z","modification":"2025-08-08T11:22:08.106Z","creation":"2023-11-27T14:27:36.282Z"},"accession":"E-MTAB-13572","cross_references":{"ENA":["ERP172942"],"EFO":["EFO_0007693","EFO_0002944","EFO_0004170","EFO_0003789","EFO_0004917","EFO_0003816","EFO_0005518","EFO_0004184","EFO_0003969"]}}