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Sample GSM3132598 Query DataSets for GSM3132598
Status Public on May 07, 2021
Title APOC2_OV_PHF8_ChIP
Sample type SRA
 
Source name RKO cell line
Organism Homo sapiens
Characteristics treatment: APOC2 overexpression
cell line: RKO cell line
chip antibody: PHF8 (abcam, ab36068, lot: GR3195675-1)
Treatment protocol RKO cells were transfected with vector or APOC2 overexpression plasmid.
Growth protocol RKO cells were cultured in Dulbecco's Modified Eagle Medium (DMEM; Gibco) supplemented with 10% (v/v) fetal bovine serum (FBS; Gibco), L-glutamine, and appropriate antibiotics. Cell cultures were maintained in a 5% CO2 humidified incubator at 37℃.
Extracted molecule genomic DNA
Extraction protocol ChIP was performed using the ChIP-IT High Sensitivity (HS) Kit (Active Motif 53040) according to the manufacturer’s recommended protocol.
ChIP-seq libraries were prepared using MicroPlex Library Preparation Kit v2 (Diagenode C05010014) and the Agencourt AMPure XP system (Beckman Coulter A63880) was used to select 350–550 bp libraries. Sequencing was carried out on the Illumina HiSeq Xten platform.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model HiSeq X Ten
 
Data processing All ChIP-seq reads were aligned to the hg38 reference human genome by Bowtie 2 (version 2.2.9)
Enriched PHF8 occupancies were called using MACS (version 2.0) with default settings. And the -B --trackline settings were used for generating the bedGraph files.
The enriched regions were annotated using the annotatePeaks package from the HOMER suite
Supplementary_files_format_and_content: bedGraph, peaks bed
 
Submission date May 07, 2018
Last update date May 07, 2021
Contact name Jian Chen
E-mail(s) yufuchenjian@163.com
Organization name Shanghai pulmonary Hospital
Department Department of thoracic Surgery
Street address 507 Zhengmin Road
City Shanghai
ZIP/Postal code 200000
Country China
 
Platform ID GPL20795
Series (1)
GSE114089 APOC2 increase PHF8 binding on chromatin
Relations
BioSample SAMN09080692
SRA SRX4047134

Supplementary file Size Download File type/resource
GSM3132598_APOC2_peaks.txt.gz 224.2 Kb (ftp)(http) TXT
GSM3132598_RKO_treat_pileup.bedGraph.gz 103.5 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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