2025-08-08
ENA first public
ERC000011
ENA-CHECKLIST
Nuclear Dynamics Unit UMR3664 CNRS/IC Institut Curie - Centre de Recherche
INSDC center name
public
INSDC status
ERS20953402
SRA accession
E-MTAB-14431:HiC_KO_HIRA_H33
Submitter Id
ArrayExpress
broker name
HeLa
cell_line
epithelial cell
cell_type
not collected
collection date
human
common name
Protocols: We performed Hi-C using the Arima Hi-C+ kit following the manufacturer’s instructions. Briefly, 3-5 million asynchronous HeLa cells per condition were fixed in 4% formaldehyde for 10min before quenching the reaction with Stop Solution 1. Fixed cells were washed in PBS and snap-frozen in liquid nitrogen at 1 million cell aliquots.  We performed cell and nuclear lysis, restriction enzyme digestion, end repair, biotinylation, ligation and decrosslinking as per manufacturer’s instructions and proximally ligated DNA was isolated using AMPure XP beads. Arima QC1 was performed and was successful for all samples. We sonicated DNA using Covaris E220 Evolution (100μL sample, 7 degrees C, peak incident power: 105W, duty factor: 5%, cycles/burst: 200 for 100s), and fragmented DNA was size selected using AMPure XP beads. We verified that the mean size of selected DNA was 400bp using Tapestation. After biotin enrichment, we performed library preparation using the KAPA HyperPrep kit, following the modified protocol described in the Arima Hi-C+ kit instructions. After ligation of Illumina TruSeq sequencing adaptors, we performed Arima QC2 (library quantification) to determine the number of amplification cycles for the library PCR using the KAPA Library Quantification Sample kit following the manufacturer’s instructions.
description
adult
developmental stage
cervical adenocarcinoma
disease
H3.3-SNAP-HA HIRA CRISPR/Cas9 KO + HIRA
genotype
not collected
geographic location (country and/or sea)
not applicable
isolate
Homo sapiens
organism
Homo sapiens
organism
uterine cervix
organism part
Homo sapiens
scientific_name
HiC_KO_HIRA_H33
title