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| Status |
Public on Apr 12, 2021 |
| Title |
H3K4me3 Hi-CHIP in USP22 wild type (shLuc), untreated cells, replicate 1 |
| Sample type |
SRA |
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| Source name |
HCT116 colorectal cancer cells
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| Organism |
Homo sapiens |
| Characteristics |
antibody: anti-H3K4me3 Millipore Sigma #07-473
genotype: wt
shRNA: shLuc
treatment: u
replicate: 1
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
HCT116 cells were fixed in 1% formaldehyde for 10 minutes at room temperature, followed by quenching with 0.125 M Glycine for 5 minutes. Cells were harvested and crosslinked chromatin was extracted, MboI-digested, biotin-labeled, and ligated as described. Chromatin was sheared to 100-300 bp fragments using the Q800R2 Sonicator with circulating chiller (QSonica), for 25 minutes at 50% amplitude, 20 sec on/20 sec off. Sheared chromatin was incubated with anti-H3K4me3 (Sigma #: 07-473) for 2 hours at 4°C against indicated proteins followed by wash, elution, reverse-crosslinking, biotin purification, and Tn5 tagmentation steps.
Libraries were constructed using Nextera XT Index Kit (Illumina) and size selected using Ampure XP beads (Beckman-Coulter).
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Library strategy: Hi-CHIP
Raw Hi-CHIP data was aligned using bowtie2 (v2.2.4) algorithm against hg19 genome version and processed using HiC-Pro (v2.11.3) software with default parameters. Loops across all samples were identified based on HiC-Pro output using hichipper (v0.7.7) R package (Ref3) and sloops that passed FDR<1% threshold were considered significant
Genome_build: hg19
Supplementary_files_format_and_content: CHIP-seq signal in bigwig format
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| Submission date |
Sep 17, 2020 |
| Last update date |
Apr 12, 2021 |
| Contact name |
Priyankara J Wickramasinghe |
| E-mail(s) |
priyaw@wistar.org
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| Phone |
2154956837
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| Organization name |
The Wistar Institute
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| Department |
Bioinformatics
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| Lab |
Genomics
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| Street address |
3601 Spruce Street
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| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE158108 |
The SAGA complex regulates early steps in transcription via its deubiquitylase module subunit USP22 |
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| Relations |
| BioSample |
SAMN16191945 |
| SRA |
SRX9140638 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4792288_HICHIP.wt.u.1.bb |
2.6 Mb |
(ftp)(http) |
BB |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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