|
| Status |
Public on Oct 04, 2016 |
| Title |
H3K4me3 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: H3K4me3 (Abcam,ab8580)
|
| 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 |
SAMN03247755 |
| SRA |
SRX792168 |
