|
| Status |
Public on Mar 04, 2013 |
| Title |
G9a Input |
| Sample type |
SRA |
| |
|
| Source name |
Epithelial cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Embryonic epithelial kidney cell
passage: 5-8
cell line: HEK293T
enrichment: none
|
| Growth protocol |
HEK293T cells were routinely seeded into CellBIND surface T75 flask (Corning) and cultured in DMEM medium supplimented with 10% FBS and maintained in a humidified incubator at 37 °C and 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The cells were harvested and lysed in ice-cold RIPA buffer (Sigma) containing 1×Complete EDTA-free protease inhibitor cocktail (Roche).
Libraries were prepared using Illumina TruSeq DNA Sample Preparation Kit according to the standard preparation protocol (http://www.illumina.com/) with some modifications. In brief, after adding a single adenine nucleotide overhang to the ChIP/CliEn DNA or ~5ng of the input DNA, a 1:10 dilution of the DNA adapters were ligated. DNA fragments were then amplified with PCR Primer Cocktail (8 cycles) and 1/10 of the PCR product was checked on the Agilent Bioanalyzer. The purified DNA libraries were diluted to 10 nM for loading on the flow cell. Sequencing service was performed on an Illumina Hiseq 2000 sequencer according to the standard Illumina protocol resulting in ~ 15 million quality-filtered sequences of length 75/75 per sample.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
G9a Y1154A input
|
| Data processing |
Basecalls performed using CASAVA version 1.8.1
CliEn-seq reads were aligned to the hg19 genome assembly using BWA with default parameters
Data were filtered using the following specifications: only uniquely mapping reads were conserved.
Genome_build: hg19
|
| |
|
| Submission date |
Dec 06, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Rui Wang |
| E-mail(s) |
ruw2007@med.cornell.edu
|
| Organization name |
MSKCC
|
| Street address |
1275 York Avenue
|
| City |
new york |
| State/province |
new york |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE42792 |
Profiling Genome-wide Chromatin Methylation with Engineered Posttranslation Apparatus within Living Cells |
|
| Relations |
| SRA |
SRX209132 |
| BioSample |
SAMN01827966 |
