{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Sagar Sengupta"],"organism":["Homo sapiens"],"software":["BWA"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-14629"],"description":["DREAM complex is known to regulate DNA repair and cell cycle-regulated genes in a p53-p21 dependent axis. This experiment identified an alternate pathway of DREAM target regulation."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - Cells were lysed using a nuclear lysis buffer. Followed by sonication of genomic DNA. 1ng of DNA used for library preparation.","Sequencing - Next-generation sequencing oflibraries was performed using the NovaSeq 6000 S4 Reagent Kit v1.5 for the paired-end, 30 million reads.","Sample Collection - Cells were harvested from 6 well-plate, followed by trypsinization, crosslinking and fixaton.","Library Construction - The Re-ChIP DNA libraries were constructed using the Kapa Hyperprep Kit with sample purification beads according to the manufacturer’s instructions.","Sample Treatment - HCT116 p21-/- cell were grown in 6 well plate, without any treatment.  HCT116 p53-/- p53 TAD mutant grown in 6 well in presence of Doxycycline.","Growth Protocol - Cells were grown under asynchronous condition in McCoy media"],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Peaks were detected using MACS2 and annotated with ChIPseeker R package.","Sequence Alignment - Bases with a high Phred score (more than 30) were aligned to the current human genome (hg38 assembly) using BWA"],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["ChIP-seq"],"species":["Homo sapiens"],"pubmed_authors":["Sagar Sengupta"],"additional_accession":[]},"is_claimable":false,"name":"E2F4-p53 Re-ChIP seq in HCT116 p21-/- cells & HCT116 p53-/- TAD mutant cells","description":"DREAM complex is known to regulate DNA repair and cell cycle-regulated genes in a p53-p21 dependent axis. This experiment identified an alternate pathway of DREAM target regulation.","dates":{"release":"2025-08-23T00:00:00Z","modification":"2024-11-22T14:48:55.17Z","creation":"2024-11-22T14:42:24.766Z"},"accession":"E-MTAB-14629","cross_references":{"ENA":["ERP166451"],"Biostudies":["E-MTAB-13359"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0002692","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0004184","EFO_0003969"]}}