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Sample GSM7990247 Query DataSets for GSM7990247
Status Public on Feb 01, 2024
Title ChIP_DLD1-NT_H3K27me3
Sample type SRA
 
Source name DLD1
Organism Homo sapiens
Characteristics cell line: DLD1
cell type: colorectal adenocarcinoma cell line
genotype: DNMT1-AID
chip antibody: H3K27me3 (Cell Signalling Technology, 9733S, RRID:AB_2616029)
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 ChIP assays were carried out as described previously (Scelfo et al., 2019). Briefly, 1% formaldehyde cross-linked chromatin was sonicated to an average size of 300–600 bp and quantified.
100 μg of sonicated chromatin was incubated overnight at 4°C with 2 μg of the indicated antibodies, and recovered by Sepharose protein A beads. DNA from washed beads was column-purified, quantified using the Qubit dsDNA HS, and used for library preparation with KAPA UDI Primer Mixes Kit.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NovaSeq 6000
 
Data processing ChIP-seq data, including data from (Rokavec et al., 2017) were processed following the steps of the ENCODE ChIP-seq pipeline (https://github.com/ENCODE-DCC/chip-seq-pipeline2) with slight modifications using a simplified custom snakemake workflow as described in (Spracklin et al., 2023).
Reads were mapped to hg38 using bwa mem (Li, 2013).
Alignment files (BAM format) were filtered for quality and duplicates using samtools (Li et al., 2009).
Cross-correlation analysis and fragment length estimation for single-ended datasets was performed using the phantompeakqualtools package (Landt et al., 2012).
Signal track (target over input) generation was performed using MACS2 (Y. Zhang et al., 2008).
ChIP-seq tracks were compared by aggregating bigwig signal at 10-kb resolution using pybbi and generating density scatter plots using the matplotlib extension for datashader.
Assembly: hg38
Supplementary files format and content: bigWig
 
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)
GSE251932 Tunable DNMT1 degradation reveals cooperation of DNMT1 and DNMT3B in regulating DNA methylation dynamics and genome organization (ChIP-Seq).
GSE251935 Tunable DNMT1 degradation reveals cooperation of DNMT1 and DNMT3B in regulating DNA methylation dynamics and genome organization
Relations
BioSample SAMN39083459
SRA SRX23007791

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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