|
| Status |
Public on May 28, 2018 |
| Title |
H3122_H3K4me1_ChIP-seq |
| Sample type |
SRA |
| |
|
| Source name |
H3122 lung cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: H3122
treatment: None
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Standard DNA extraction protocol using Qiagen prep kit.
Libraries were prepared according to Illumina's instructions.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Base calling performed using CASAVA version 1.7
The sequencing reads were aligned to the reference sequence (hg 19) using the Bowtie2 (v.2.2.2) software.
Finding, estimation and annotation of ChIP-seq peaks were carried out by the Homer (v.4.8.2) platform.
ChIP-fragment density at each position in the genome was estimated by starting with each tag and extending it by the estimated fragment length determined by autocorrelation.
The ChIP-fragment density is then defined as the total number of overlapping fragments at each position in the genome.
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph files were generated by makeUCSCfile module in the Hommer software. Scores represent ChIP-seq density value as described in data processing step.
|
| |
|
| Submission date |
May 16, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Seon-Kyu Kim |
| E-mail(s) |
seonkyu@kribb.re.kr
|
| Phone |
+82-42-879-8107
|
| Organization name |
Korea Research Institutue of Bioscience & Biotechnology
|
| Department |
Personalized Genomic Medicine Research Center
|
| Street address |
125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Korea
|
| City |
Daejeon |
| ZIP/Postal code |
305-806 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE81482 |
ChIP-seq for identifying molecules associated with epithelial-mesenchymal transition and acquired resistance to ALK inhibitors |
| GSE81487 |
Epithelial-mesenchymal transition and acquired resistance to ALK inhibitors |
|
| Relations |
| BioSample |
SAMN05003672 |
| SRA |
SRX1769315 |
