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Sample GSM1556821 Query DataSets for GSM1556821
Status Public on Oct 04, 2016
Title WDR5 KO_ChIPSeq
Sample type SRA
 
Source name BGC823 cells
Organism Homo sapiens
Characteristics cell line: BGC823
cell type: human gastric cancer cells
passages: 16-19
transfected with: shRNA adenovirus against human lncRNA PRLG
chip antibody: WDR5 (CST,13105)
Treatment protocol The shRNA adenovirus against human lncRNA PRLGC were introduced into the BGC823 gastric cells, while nonspecific shRNA virus was used as negative controls.
Growth protocol The human gastric cancer cells BGC823 were cultured in RPMI-1640 medium (Gibco, USA) supplemented with 10 % fetal bovine serum at 37 °C in an atmosphere of 5 % CO2.
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Data processing Basecalls performed using HOMER v4.7.2
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie 1.0.1
Data were filtered with a FDR value cutoff 0.05
peaks were called using HOMER v.4.7.2.
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph files were generated and compressed by IGV
 
Submission date Dec 02, 2014
Last update date May 15, 2019
Contact name Haoyan Chen
Organization name Renji Hospital
Street address 145 Shandong Road
City Shanghai
State/province Shanghai
ZIP/Postal code 200001
Country China
 
Platform ID GPL11154
Series (2)
GSE63763 Genome-wide maps of chromatin state of WDR5 and KAT2A in gastric cancer BGC823 cells [ChIP-seq]
GSE63765 ChIP-seq and RNA-seq in BGC823 cells after downregulation of GAS1 expression
Relations
BioSample SAMN03247756
SRA SRX792164

Supplementary file Size Download File type/resource
GSM1556821_WDR5_KO.bedGraph.tdf 84.1 Mb (ftp)(http) TDF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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