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Sample GSM5899637 Query DataSets for GSM5899637
Status Public on Jul 28, 2023
Title ChIP-seq H3K4me3 siRad21
Sample type SRA
Source name RPE cells
Organism Homo sapiens
Characteristics cell type: RPE
type: Spike-in (mouse)
control sample: Input siRad21 rep2
treatment: siRad21
chip antibody: H3K4me3
Treatment protocol RNAi transfection was performed using Lipofectamine RNAiMAX (Thermo Fisher Scientific) in accordance with the manufacturer's protocol, using final RNA duplex concentration of 50 nM.
Growth protocol RPE cells were routinely cultured in DMEM supplemented with penicilline-streptomycin-L-glutamine solution (Wako) and 10% FBS.
Extracted molecule genomic DNA
Extraction protocol Chromatin immunoprecipitation was performed as previously described [Izumi, K. et al. Nat Genet, 2015, doi:10.1038/ng.3229]. In Brief, ~ 8 × 106 human cells were crosslinked with 1% formaldehyde for 10 min at room temperature, followed by an additional 5 min with glycine in PBS added at a final concentration of 125 mM. Fixed cells were lysed in LB1 (50 mM HEPES-KOH (pH 7.4); 140 mM NaCl; 1 mM EDTA; 10% glycerol; 0.5% NP-40; 0.25% Triton X-100; 10 mM dithiothreitol; 1 mM PMSF) on ice. The lysate was wash with LB2 (20 mM Tris-HCl (pH 8.0); 200 mM NaCl; 1 mM EDTA; 0.5 mM EGTA; 1mM PMSF) and LB3 (20 mM Tris-HCl (pH 7.5); 150 mM NaCl; 1 mM EDTA; 0.5 mM EGTA; 1% Triton X-100; 0.1% sodium deoxycholate; 0.1% SDS; 1 × cOmplete protease inhibitor cocktail (Roche)) on ice. The lysate was resuspended in LB3 and sonicated using Branson Sonifier 250D (Branson) for chromatin shearing (12 sec with amplitude setting at 17% of the maximum amplitude, 6 times). In addition, lysate containing fragmented chromatin was also prepared from ~ 2 × 106 C2C12 mouse cells with the same procedures. Human cell lysate and mouse cell lysate (as spike-in internal control) were combined (approximately 4:1 ratio) and incubated with protein A or G Dynabeads (Thermo Fisher Scientific) conjugated with antibodies for 14 h at 4℃. The beads were then washed 5 times with cold RIPA wash buffer (50 mM HEPES-KOH (pH 7.4); 500 mM LiCl, 1 mM EDTA; 0.5% sodium deoxycholate; 1% NP-40) and once with cold TE50 (50 mM Tris-HCl (pH 8.0); 10 mM EDTA). Material captured on the beads was eluted by TE50 containing 1% SDS. The eluted material and input were incubated for 6 h at 65℃ to reverse crosslinks and treated with 100 ng RNaseA (Roche) for 1 h at 37℃, followed by treatment with 100 ng Proteinase K (Merck) overnight at 50℃. The input and ChIP DNA were then purified by PCR purification kit (Qiagen) following manufacturer's instructions and further sheared to an average size of approximately 150 bp using Covaris S2 focused-ultrasnicator (settings: Duty Cycle, 10%; Intensity, 5; Cycle per Burst, 100; Duration, 300 sec). The sheared DNA was end-repaired, ligated to sequencing adaptors, amplified and size-selected using NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) and Agencourt AMPure XP (Beckman Coulter) following manufacturer's instructions.
Sequencing libraries were made using the NEBNext ChIP-Seq Library Prep Master Mix Set of Illumina (New England Biolabs).
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model NextSeq 2000
Data processing Sequenced reads were mapped to the human genome using bowtie2 version 2.4.1 with default parameters.
Genome_build: UCSC hg38
Supplementary_files_format_and_content: BigWig files were generated with the total read normaization and with the spike-in normaization for 100-bp bins by DROMPA+ verision 1.12.1.
Supplementary_files_format_and_content: Peak files (BED) with the spike-in normaization and the total read normalization were generated by DROMPA+ verision 1.12.1.
Submission date Feb 14, 2022
Last update date Jul 28, 2023
Contact name Ryuichiro Nakato
Phone +81-3-5841-1471
Organization name The University of Tokyo
Department Institute for Quantitative Biosciences
Lab Laboratory of Computational Genomics
Street address 1-1-1 Yayoi
City Bunkyo-ku
State/province Tokyo
ZIP/Postal code 113-0032
Country Japan
Platform ID GPL30173
Series (2)
GSE196450 Context-dependent perturbations in chromatin folding and the transcriptome by cohesin and related factors
GSE196727 Context-dependent perturbations in chromatin folding and the transcriptome by cohesin and related factors [ChIP-seq]
BioSample SAMN25945427
SRA SRX14178563

Supplementary file Size Download File type/resource 115.2 Mb (ftp)(http) BW
GSM5899637_spikein.100.2021_010_H3K4me3_IP_RAD21KD.peak.bed.gz 105.8 Kb (ftp)(http) BED 113.4 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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