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| Status |
Public on Feb 22, 2022 |
| Title |
PHF8 ChIPseq-replicate B2 |
| Sample type |
SRA |
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| Source name |
Melanoma cell line
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| Organism |
Homo sapiens |
| Characteristics |
cell type: SKMEL-147 melanoma cell line
chip antibody: anti-PHF8 antibody (Abcam, ab36068)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
SKMEL-147 cells were crosslinked with 1% PFA (in PBS 1X) for 10 min at RT. The reaction was quenched with 0.125 M glycine for 5 min at room temperature. After washing with PBS, cells were collected and the pellet was lysed in 50 mM Hepes pH7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% Igepal CA-630, and 0.25% Triton X-100, freshly supplemented with 1X Protease Inhibitors Cocktail (Sigma-Aldrich). After centrifugation, isolated nuclei were washed once in 10 mM Tris pH 8.0, 200 mM NaCl, 1 mM EDTA and 0.5 mM EGTA, 1X Protease Inhibitors Cocktail then resuspended in ChIP buffer (10 mM Tris pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% sodium deoxycholate, 0.5% N-Lauryl Sarcosine, 1X Protease Inhibitors Cocktail) prior sonication. After optimization for each cell line, sonication of SKMEL-147 nuclei was carried out for 30 cycles (30 seconds on, 30 seconds off), with high intensity at 4°C in a Bioruptor sonicator (Diagenode). Under these conditions, chromatin fragments have an average size of 200 bp.
Thruplex kit was used according to manufacturer's instructions.
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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 |
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
Reads were aligned to the human genome (build hg19/GRCh37) with Bowtie 2 using local alignment.
Likely PCR duplicates were removed with Picard MarkDuplicates tool.
MACS was utilized to perform peak calling for each replicate.
Genome_build: hg19
Supplementary_files_format_and_content: BED files of peaks
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| Submission date |
Feb 16, 2022 |
| Last update date |
Feb 22, 2022 |
| Contact name |
Igor Dolgalev |
| Organization name |
NYU Grossman School of Medicine
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| Street address |
550 1st Ave
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| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10016 |
| Country |
USA |
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| Platform ID |
GPL16791 |
| Series (2) |
| GSE196897 |
The histone demethylase PHF8 regulates TGFβ signaling and promotes melanoma metastasis [ChIP-seq] |
| GSE196906 |
The histone demethylase PHF8 regulates TGFβ signaling and promotes melanoma metastasis |
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| Relations |
| BioSample |
SAMN25998153 |
| SRA |
SRX14204994 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5904392_CH11-5_PHF8_scr.bw |
350.7 Mb |
(ftp)(http) |
BW |
| GSM5904392_CH11-5_PHF8_scr.narrowPeak.bed.gz |
472.8 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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