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| Status |
Public on May 24, 2023 |
| Title |
CT26 Phf8 KO1, PHF8 |
| Sample type |
SRA |
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| Source name |
CT26
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| Organism |
Mus musculus |
| Characteristics |
cell line: CT26
cell type: colorectal cancer
genotype: Phf8 knockout
chip antibody: anti-PHF8 (ab280887, abcam)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for INPUT and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC mm10 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Assembly: mm10
Supplementary files format and content: bigWig
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| Submission date |
Sep 06, 2022 |
| Last update date |
May 25, 2023 |
| Contact name |
Yanan Liu |
| E-mail(s) |
Lyn19950902@outlook.com
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| Organization name |
East China Normal University
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| Department |
School of Life Sciences
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| Street address |
500 Dongchuan Road, Minhang District, Shanghai, China
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| City |
China |
| ZIP/Postal code |
200241 |
| Country |
China |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE212778 |
PHF8 enables immune evasion by silencing endogenous retroelements [ChIP-seq] |
| GSE212779 |
PHF8 enables immune evasion by silencing endogenous retroelements |
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| Relations |
| BioSample |
SAMN30687392 |
| SRA |
SRX17447809 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6547603_CT26_Phf8_KO1_PHF8.bw |
236.9 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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