|
| Status |
Public on Feb 01, 2024 |
| Title |
HiC_DLD1-NT |
| Sample type |
SRA |
| |
|
| Source name |
DLD1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: DLD1
cell type: colorectal adenocarcinoma cell line
genotype: DNMT1-AID
treatment: None
|
| 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 |
SAMN39082791 |
| SRA |
SRX23007250 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7990272_DLD1.360.NT.50000.E0-E128.trans.eigvals.pq.gz |
2.5 Kb |
(ftp)(http) |
PQ |
| GSM7990272_DLD1.360.NT.50000.E0-E128.trans.eigvecs.pq.gz |
54.7 Mb |
(ftp)(http) |
PQ |
| GSM7990272_DLD1.360.NT.50000.E1-E128.comp_10.kmeans9_5.bed.gz |
71.5 Kb |
(ftp)(http) |
BED |
| GSM7990272_DLD1.360.NT.50000.E1-E128.comp_10.kmeans_sm.tsv.gz |
2.8 Mb |
(ftp)(http) |
TSV |
| GSM7990272_DLD1.360.NT.R1-T1T2.50000.expected.cis.tsv.gz |
1.9 Mb |
(ftp)(http) |
TSV |
| GSM7990272_DLD1.360.NT.R1-T1T2.50000.expected.cisarm.tsv.gz |
1.8 Mb |
(ftp)(http) |
TSV |
| GSM7990272_DLD1.360.NT.R1-T1T2.50000.expected.interarm.tsv.gz |
1.5 Mb |
(ftp)(http) |
TSV |
| GSM7990272_DLD1.360.NT.R1-T1T2.50000.expected.trs.tsv.gz |
12.1 Kb |
(ftp)(http) |
TSV |
| GSM7990272_DLD1.360.NT.R1-T1T2.hg38.mapq_30.1000.mcool |
1.0 Gb |
(ftp)(http) |
MCOOL |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
