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Sample GSM7990267 Query DataSets for GSM7990267
Status Public on Feb 01, 2024
Title HiC_3BKO-IAA10d
Sample type SRA
 
Source name DLD1
Organism Homo sapiens
Characteristics cell line: DLD1
cell type: colorectal adenocarcinoma cell line
genotype: DNMT1-AID;DNMT3b -/-
treatment: Auxin 10 days
Treatment protocol Auxin indole-3-acetic acid sodium salt (IAA) (I5148, Sigma-Aldric) was used at 500 nM dissolved in water. 2'-deoxy-5-azacytidine (DAC) (A3656, Sigma-Aldrich) was used at 2.5 µM for 96h. GSK-3685032 (HY-139664, MedChemExpress) was used at the indicated time and concentrations. All cell lines were tested negative for mycoplasma contamination. IAA washout was performed by five gentle washes in PBS. Cells were then analyzed at the indicated time points.
Growth protocol Cells were cultured at 37 °C in a 5% CO2 atmosphere. DLD-1 cells were maintained in DMEM-GlutaMAX media, supplemented with 10% fetal bovine serum, 100 U/mL penicillin-streptomycin, 0.13% sodium bicarbonate (RPE-1).
Extracted molecule genomic DNA
Extraction protocol Hi-C assays were performed with an Arima Hi-C plus kit (Arima Genomics #A510008) according to manufacturer's Instructions starting from 2*106 cells/reaction.
ibraries preparation were performed with a Kapa Hyper Prep Kits with KAPA Library Amplification Primer Mix (Roche, 07962347001), quantified by Qubit (Invitrogen), checked on a Tapestation device (Agilent) and Pair-End sequenced on a NovaSeq platform (Illumina).
 
Library strategy Hi-C
Library source genomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Data processing Hi-C libraries were processed using the distiller pipeline (https://github. com/open2c/distiller-nf).
Briefly, Hi-C sequencing reads were mapped to the hg38 assembly using bwa mem, and alignments were processed, deduplicated and classified into contact pairs using pairtools (https://github.com/open2c/pairtools).
Hi-C pairs were aggregated into multiresolution contact matrices, filtered and normalized by iterative correction using the cooler package.
Genome browser plots were generated using HiGlass and coolbox. Contact frequency vs distance profiles were calculated using cooltools.
Spectral clustering and analysis were performed on Hi-C from untreated NADNMT1 cells using the inspectro package as described in (Spracklin et al., 2023) applied to the first 10 eigenvectors of the contact matrix at 50kb resolution. We compared the results of k-means with several functional and epigenomic tracks, including H3K9me3 and DNAme (this study), H3K27me3 and RNA-seq (Rokavec et al., 2017), as well as GC content and distance from centromere. Based on cluster metrics and interpretability, we selected k=9 clusters and combined two pairs and one triple of clusters whose functional profiles were largely similar but differed in overall proximity to the centromere to yield 5 IPGs. Comparison of IPGs with labels from SNIPER was generated using bioframe. Summaries of IPG-level observed/expected contact frequency were generated using cooltools.
Assembly: hg38
Supplementary files format and content: mcool
 
Submission date Dec 22, 2023
Last update date Feb 01, 2024
Contact name Nezar Abdennur
E-mail(s) nezar.abdennur@umassmed.edu
Organization name UMass Chan Medical School
Department Genomics and Computational Biology
Street address 368 Plantation Street
City Worcester
State/province MA
ZIP/Postal code 01605
Country USA
 
Platform ID GPL24676
Series (2)
GSE251934 Tunable DNMT1 degradation reveals cooperation of DNMT1 and DNMT3B in regulating DNA methylation dynamics and genome organization (Hi-C).
GSE251935 Tunable DNMT1 degradation reveals cooperation of DNMT1 and DNMT3B in regulating DNA methylation dynamics and genome organization
Relations
BioSample SAMN39082796
SRA SRX23007245

Supplementary file Size Download File type/resource
GSM7990267_3bKO.377.IAA10d.R1-T1T2.50000.expected.cis.tsv.gz 1.9 Mb (ftp)(http) TSV
GSM7990267_3bKO.377.IAA10d.R1-T1T2.50000.expected.cisarm.tsv.gz 1.8 Mb (ftp)(http) TSV
GSM7990267_3bKO.377.IAA10d.R1-T1T2.50000.expected.interarm.tsv.gz 1.5 Mb (ftp)(http) TSV
GSM7990267_3bKO.377.IAA10d.R1-T1T2.50000.expected.trs.tsv.gz 12.1 Kb (ftp)(http) TSV
GSM7990267_3bKO.377.IAA10d.R1-T1T2.hg38.mapq_30.1000.mcool 1.2 Gb (ftp)(http) MCOOL
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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