|
Status |
Public on May 28, 2018 |
Title |
H3122_LR_H3K4me1_ChIP-seq |
Sample type |
SRA |
|
|
Source name |
H3122 lung cancer cell line
|
Organism |
Homo sapiens |
Characteristics |
cell line: H3122 treatment: Certinib
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Standard DNA extraction protocol using Qiagen prep kit. Libraries were prepared according to Illumina's instructions.
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|
|
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.
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|
|
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 |
SAMN05003675 |
SRA |
SRX1769318 |