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| Status |
Public on Apr 05, 2016 |
| Title |
K562-H3K9me3-ATRX_KO-Native_ChIP |
| Sample type |
SRA |
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| Source name |
K562
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| Organism |
Homo sapiens |
| Characteristics |
cell line: K562
protocol: Native ChIP
fixation: none
phenotype: ATRX KO
chip antibody: H3K9me3 (Abcam, ab8898, 5ug)
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| Growth protocol |
K562 cells were growth in T-75 flasks at maximum confluency of 1x10^6 cells per ml in RPMI + 10%FBS + 1x Antibiotic-Antimycotic (gibco). 40-60 million cells were used per ChIP
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Native ChIP: Native ChIP was performed essentially as described (Hasson et al., Nat Struct Mol. Biol, 2013) with minor changes. Briefly: 60 million cells were collected and resuspended in 2 ml of ice-cold buffer I (0.32 M sucrose, 60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA, 15 mM Tris, pH 7.5, 0.5 mM DTT, 0.1 mM PMSF and 1:1,000 protease inhibitor cocktail (Sigma)). Ice-cold buffer I supplemented with 0.1% IGEPAL (2 ml) was added, and samples were placed on ice for 8 min. The resulting 4 ml of nuclei was gently layered on top of 8 ml of ice-cold buffer III (1.2 M sucrose, 60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA, 15 mM Tris, pH 7.5, 0.5 mM DTT, 0.1 mM PMSF and 1:1,000 protease inhibitor cocktail) and centrifuged at 10,000g for 20 min at 4°C. Pelleted nuclei were resuspended in Native buffer A (0.34 M sucrose, 15 mM HEPES, pH 7.4, 15 mM NaCl, 60 mM KCl, 4 mM MgCl2, 1 mM DTT and 1:1,000 protease inhibitor cocktail (Sigma)) to 400 ng/μl. MNase (Affymetrix) digestion reactions were carried out on chromatin (100 μg or more), using 0.1 U/μg chromatin in Native buffer A supplemented with 3 mM CaCl2 for 10 min at 37 °C. The reaction was quenched with 5 mM EGTA. The chromatin was resuspended in 10 mM EDTA, pH 8.0, 1 mM PMSF and 1:1,000 protease inhibitor cocktail and rotated at 4 °C for 2–4 h. The mixture was adjusted to 500 mM NaCl, allowed to rotate for another 45 min and then centrifuged at 13,500g for 10 min, yielding nucleosomes in the supernatant. Chromatin (80 μg per ChIP) was diluted to 100 ng/μl with Native buffer B (20 mM Tris, pH 8.0, 5 mM EDTA, 500 mM NaCl and 0.2% Tween 20). 1% was took as Input and the rest incubated overnight at 4 °C with specific antibodies. The chromatin was incubated for 3 h at 4 °C with 80 ul of ChIP-grade Magna ChIP protein A/G magnetic beads. The beads were washed three times with Native buffer B and once with Native buffer B without Tween. 100 ul of pK buffer (1x TE, 1mM CaCl2, 50mM NaCl, 0.5% SDS, 0.1ug/ul RNAse A) were added to the Input samples and the beads and incubated in a Thermomixer at 37°C for 1 hour, 2000 rpm. 3ul of Proteinase K were added and incubated for 3h at 56 °C, 2000 rpm. The DNA was purified using the MinElute PCR purification kit from Qiagen following the kit’s instructions, eluted in 30ul of Qiagen’s elution buffer and its concentration determined with an Agilent 2100 Bionanalyzer High Sensitivity Kit.
25ng of ChIPed or Input DNA were processed for library preparation from each sample. All enzymes used are from NEB unless stated otherwise. 1. DNA was End Repaired in 50ul reaction containing 40ul of DNA, 5ul T4 DNA ligase buffer with 10mM ATP, 2ul 10mM dNTP, 1ul Klenow DNA pol (1u/ul), 1ul T4 DNA pol and 1ul T4 PNK. The reaction was incubated for 30min at 20C. Products were purified in Qiagen PCR purification column in 35ul. 2. Adding over-hang A to the 3’ end in 50ul reaction containing 34ul DNA, 5ul 10X NEB buffer 2, 10ul 1mM dATP and 1ul Klenow exo-. The reaction was incubated for 30min at 37C. Products were purified in Qiagen PCR Mini elute purification column in 14ul. 3. Adapter ligation in 30ul reaction containing 13ul DNA, 15ul 2X T4 DNA ligase buffer, 1ul of 1:200 dilution of Illumina true seq DNA sample prep kit and 1ul quick T4 DNA ligase. The reaction was incubated for 15min at 25C. Products were purified in Qiagen Mini elute PCR purification column in 15ul. 4. Size selection. Ligated products were loaded onto 2% Agarose gel (1XTAE), and run for 1 hour at 120V. DNA was viewed on low-wave trans illuminator and size selected at the 300-400bp range using the Kb+ invitrogen DNA ladder. Products were purified in Qiagen PCR purification column in 25ul. 5. PCR amplification was done in 50ul reaction containing 25ul 2X master mix (2X Phusion HF, FINZYMES), 2ul PCR primers (illumina) and 23ul DNA. PCR program according to the illumina protocol. Products were purified in Qiagen Mini elute PCR purification column in 15ul. PCR products were then run on an Agilent DNA 1000 chip for quantification and submitted for sequencing on the Hi-Seq 2500 illumina platform.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Basecalls performed using Illumina's Real-Time Analysis (RTA) Software version 1.18.64.
Sequence reads were aligned to the GRCh37 (hg19) assembly using Bowtie v1.0.0 with the following parameters: For 100nt reads: -M 10 -k 1 -n 2 --trim5 5 -l 80 --best. For 50nt reads: -M 10 -k 1 -n 2 --trim5 3 -l 45 --best
Redundant reads were eliminated using the macs2 (v2.1.0) filterdup option with default parameters.
The optimal normalization factor between ChIP and Input samples was calculated with the R NCIS package v1.0.1 using a shift size of 75bp.
Peak calling was performed with macs2 callpeak using the following options: --ratio X --broad --bdg -q 0.0005 --broad-cutoff 0.0005, where X is the normalization factor estimated by NCIS
ChIP/Input fold enrichment pileups were created with the macs2 bdgcmp tool using the -m FE option and converted to bigWig files using the bedGraphToBigWig program (v4) from the UCSC binaries.
A second peak calling was performed using SICER v1.1 using a window of 200bp, allowing gaps of 400pb and filtering for q-values < 1x10^-8.
All peaks overlapping with the Encode blacklisted regions were eliminated.
The final peak list was generated overlaping the macs2 and SICER peaks with the intersectBed program from bedtools v2.17.0. All SICER peaks overlaping at least one macs2 peak were kept
Genome_build: GRCh37
Supplementary_files_format_and_content:
- ChIP/Input fold enrichment bigWig file obtained with macs2 bdgcmp, as described.
- Bed file with significant peaks from macs2 and SICER
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| Submission date |
Jul 14, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Emily Bernstein |
| E-mail(s) |
[email protected]
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| Phone |
(212) 824-9335
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| Organization name |
Mount Sinai School of Medicine
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| Department |
Oncological Sciences
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| Lab |
Bernstein Lab
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| Street address |
1470 Madison Avenue, 6th floor Rm 302
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10029 |
| Country |
USA |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE70920 |
The chromatin remodeler ATRX binds to atypical chromatin domains at the 3’ exons of ZNF genes to preserve H3K9me3 enrichment |
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| Relations |
| BioSample |
SAMN03859888 |
| SRA |
SRX1097316 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1821908_hg19-K562-H3K9me3_ATRX_KO-enrichment_over_input.bigWig |
703.2 Mb |
(ftp)(http) |
BIGWIG |
| GSM1821908_hg19-K562-H3K9me3_ATRX_KO-peaks.bed.gz |
59.0 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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