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| Status |
Public on Feb 26, 2024 |
| Title |
HCT-116 cells, DAC300_EM_1 |
| Sample type |
SRA |
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| Source name |
HCT-116
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HCT-116
cell type: colorectal carcinoma
passages: 4-5 passages
treatment: 5'aza-2'deoxycytidine (300 nM)
time: 3 days
chip antibody: Cell Signaling H3K27me3 (CST#9733, clone C36B11, lot 14)
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| Treatment protocol |
5-aza-2’-deoxycytidine (DAC, Sigma A3656) was dissolved in DMSO:PBS at a ratio of 1:150 and stored at -80°C. Each drug or % vehicle equivalent was applied to attached cells for a period of 72 hours.
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| Growth protocol |
HCT116 colon cancer cell lines was purchased from ATCC and maintained according to ATCC recommendations in McCoy's (Gibco 16600-082) media supplemented with 10% Fetal Bovine Serum (Millipore Sigma F0926) and 1% penicillin/streptomycin (Life Technologies, 15140-122) at 5% CO2 and 37C.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells exposed to drugs for 72 hours were fixed in buffer (1% formaldehyde, 50 mM HEPES-KOH pH 7.6, 100 mM NaCl, 1 mM EDTA pH 8.0, 0.5 mM EGTA pH 8.0) for 10 min at room temp with shaking and then quenched with 125 mM glycine 5 min at room temp. Cells were scraped into cold PBS, washed 2X with cold PBS, flash frozen in liquid N2, and stored at -80°C until use. Thawed pellets were lysed in LB1 (50 mM HEPES-KOH pH 7.6, 140 mM NaCl, 1 mM EDTA, 10% Glycerol, 0.5% NP-40, 0.25% Triton X-100, Roche protease inhibitor cocktail) for 20 min with rotation at 4°C and cleared by centrifugation at 300 x g for 5 min at 4°C. Supernatant with intact nuclei was set aside. Cell pellets were lysed again in 4x LB1 (LB1 with 2% NP-40 and 1% Triton X-100) for 20 min. Intact nuclei from this and the saved supernatant were collected by centrifugation at 1,700 x g for 5 min at 4°C, resuspended and washed in LB2 (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 200 mM NaCl, protease cocktail inhibitor) for 10 min with rotation at 4°C, and collected again by centrifugation at 1,700 x g for 5 min at 4°C. Nuclei were gently rinsed 2x with LB3 (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 0.01% NP-40, protease cocktail inhibitor) without disturbing the pellet. Nuclei were resuspended in 1 mL LB3 and transferred to a 1 ml milliTUBE (Covaris). Chromatin was sheared to a range of 300-600 base-pair fragments using a Covaris E220 evolution Focused ultrasonicator with the following parameters: Peak power (140.0), Duty Factor (5.0), Cycles/Burst (200), Duration (600 seconds), Temperature (4°C). Sheared chromatin was quantified by Bradford Assay, and 450 µg of chromatin was brought to 500 µL in LB3 and 500 µL of ChIP Cocktail Mix (40 mM Tris-HCl pH 7.6, 150 mM NaCl, 1 mM EDTA pH 8.0, 1% Triton X-100, 0.5% NP-40, Protease inhibitor cocktail) was added. Prepared chromatin was pre-cleared by incubation with 20 µL of pre-washed Dynabeads Protein G magnetic beads (Invitrogen, 10004D) for 3 hours at 4°C with rotation. After bead removal, 10% input (100 µL) of pre-cleared chromatin was removed and set aside. Pre-cleared chromatin was immunoprecipitated with 5 µL of H3K27me3 antibody (Cell Signaling 9733) overnight at 4°C with constant rotation. Protein G magnetic beads (35 µL/IP) were blocked in buffer containing PBS, 0.5% BSA, and 20 µg Herring Sperm DNA (Sigma, D7290) with rotation at 4°C overnight. Blocked beads were washed 3X with PBS and 0.5% BSA and 2X with WB1 (50 mM Tris-HCl pH 7.6, 150 mM NaCl, 5 mM EDTA pH 8.0, 0.5% NP-40, 1% Triton X-100). Immuno-chromatin complexes were incubated with blocked beads for 3 hours with rotation at 4°C. Bead-immuno-chromatin complexes were then washed 3X for 5 min with rotation at 4°C with WB1, 3X with WB2 (50 mM Tris-HCl pH 7.6, 500 mM NaCl, 5 mM EDTA pH 8.0, 0.5% NP-40, 1% Triton X-100), 2X with WB1, and 1X with Low Salt TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0, 50 mM NaCl). Beads were incubated in 50 µl of Elution Buffer (10 mM Tris-HCl pH 8.0, 10 mM EDTA, 150 mM NaCl, 5 mM DTT, 1% SDS) at 65°C for 15 min in 50 µL volume to elute immuno-chromatin complexes. The elution step was repeated, and eluates combined. Eluents and input were incubated overnight at 65°C with constant shaking to reverse crosslinks, followed by incubation at 37°C for 1 hour with DNase-free RNase A, then at 37°C for 2 hours with 10 µL of Proteinase K (20 mg/mL stock). DNA was isolated with a 1.5x ratio of KAPA Pure Beads (KAPA Biosystems KK8000) to DNA volume.
Libraries were prepared by the Van Andel Institute Genomics Core from an input of 41 ng to 51 ng of ChIP DNA using the NEBNext Enzymatic Methyl-seq Kit (New England Biolabs, Cat. #E7120L). Denaturation method used was 0.1 N sodium hydroxide, according to the protocol, and 8 cycles of PCR amplification were performed. Quality and quantity of the finished libraries were assessed using a combination of Agilent High Sensitivity DNA chip (Agilent Technologies, Inc., Cat. # 5067-4626) and QuantiFluor® dsDNA System (Promega Corp., Cat. # E2670). 150 bp paired-end sequencing was performed on an Illumina NovaSeq6000 sequencer using an S4, 300 bp sequencing kit (Illumina Inc., San Diego, CA, USA), with 10% PhiX to a minimum read depth of 100M read pairs per library. Base calling was done by Illumina RTA3 and output of NCS was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v1.9.0.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
2x150 bp
DAC300_IP_rep1
All_samples_mergeCG_output.bed
DAC300.combined.8.betas.bw
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| Data processing |
Base calling was done by Illumina RTA3 and output of NCS was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v1.9.0.
EM-seq reads were aligned to human genome build hg38, duplicate marked (samblaster), and sorted (samtools) using the ‘biscuitBlaster’ pipeline from BISCUIT (v0.3.16) (https://huishenlab.github.io/biscuit/). Cytosine retention and callable SNP mutations were computed with ‘biscuit pileup’ and output into a VCF file. Cytosine beta values and coverage were extracted with ‘biscuit vcf2bed’ and CpG methylation status was merged with ‘biscuit mergecg’.
Integrated siQ-ChIP-seq and EM-seq analysis was conducted with deeptools (v3.2.0) (148) by constructing matrices with ‘computeMatrix’ across queried genomic coordinates with the respective bigwig data and visualizing the summarized integration with ‘plotProfile’ and ‘plotHeatmap’.
Assembly: hg38
Supplementary files format and content: tab delimited bed file of Biscuit output for determining b-values
Supplementary files format and content: bigwig file
Library strategy: Enzymatic-Methyl(EM)-seq
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| Submission date |
Jul 18, 2023 |
| Last update date |
Feb 26, 2024 |
| Contact name |
Scott Rothbart |
| E-mail(s) |
scott.rothbart@vai.org
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| Organization name |
Van Andel Research Institute
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| Street address |
333 Bostwick Avenue NE
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| City |
Grand Rapids |
| State/province |
MI |
| ZIP/Postal code |
49503 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (2) |
| GSE237662 |
Select EZH2 inhibitors enhance the viral mimicry effects of DNMT inhibition through a mechanism involving Calcium-Calcineurin-NFAT signaling [EM-seq] |
| GSE237665 |
Select EZH2 inhibitors enhance the viral mimicry effects of DNMT inhibition through a mechanism involving Calcium-Calcineurin-NFAT signaling |
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| Relations |
| BioSample |
SAMN36531453 |
| SRA |
SRX21064465 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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