biostudies-arrayexpressSagar SenguptaHomo sapiensBWAhttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-14629DREAM 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.biostudies-arrayexpressNucleic 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 mediaOrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData 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 BWAMetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000ChIP-seqHomo sapiensSagar SenguptafalseE2F4-p53 Re-ChIP seq in HCT116 p21-/- cells & HCT116 p53-/- TAD mutant cellsDREAM 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.2025-08-23T00:00:00Z2024-11-22T14:48:55.17Z2024-11-22T14:42:24.766ZE-MTAB-14629ERP166451E-MTAB-13359EFO_0002944EFO_0004170EFO_0003789EFO_0002692EFO_0004917EFO_0005518EFO_0003816EFO_0004184EFO_0003969