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Sample GSM6893752 Query DataSets for GSM6893752
Status Public on Jun 25, 2023
Title nc_2
Sample type SRA
 
Source name cell line
Organism Homo sapiens
Characteristics tissue: cell line
cell line: SK-Hep1 cells
chip antibody: anti-polymerase II ((Abcam, ab26721)
treatment: nc
Growth protocol DMEM, 10% fetal bovine serum, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.
Extracted molecule genomic DNA
Extraction protocol For ChIP–seq analysis, briefly, reads from ChIP-seq data for polymerase II antibodies were aligned to the hg19 genome using bowtie2 (v2.3.5.1). Peaks were called using MACS2(v2.2.6) for polymerase II. Different peaks were generated using bdgdiff. The ChIP-seq pileup heatmaps were generated using plotHeatmap. GO/KEGG enrichment analysis was performed using the R package clusterProfiler(v4.0). Visualization was realized by IGV(v2.8.9). Motifs were found to analyze the DNA sequence of poly II protein binding through motifmatchr(v 1.20.0)[1].
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NovaSeq 6000
 
Data processing Reads from ChIP-seq data for polymerase II antibodies were aligned to the hg19 genome using bowtie2 (v2.3.5.1).
Peaks were called using MACS2(v2.2.6).
Different peaks were generated using bdgdiff.
Motifs were found to analyze the DNA sequence of poly II protein binding through motifmatchr(v 1.20.0).
Visualization was realized by IGV(v2.8.9).
Assembly: hg19
Supplementary files format and content: bigWig,
Supplementary files format and content: narrowPeak
 
Submission date Dec 24, 2022
Last update date Jun 25, 2023
Contact name zhenxi zhang
E-mail(s) liwei@ibms.pumc.edu.cn
Organization name PUMC
Street address Dongdan Santiao No. 5
City beijing
ZIP/Postal code 10005
Country China
 
Platform ID GPL24676
Series (1)
GSE221723 αKG-driven RNA polymerase II transcription of cyclin D1 licenses malic enzyme 2 to promote cell cycle progression
Relations
BioSample SAMN32398598
SRA SRX18847375

Supplementary file Size Download File type/resource
GSM6893752_IP_1.bw 117.1 Mb (ftp)(http) BW
GSM6893752_ip_1_peaks.xls.gz 812.7 Kb (ftp)(http) XLS
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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