|
| Status |
Public on May 28, 2018 |
| Title |
H3122_LR-1_MBD-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.
|
| |
|
| Library strategy |
MBD-Seq |
| Library source |
genomic |
| Library selection |
MBD2 protein methyl-CpG binding domain |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Base calling performed using CASAVA version 1.7
Single-end reads (75 bp) were aligned against the human reference genome 19 with the BWA aligner (v.0.7.8).
The MEDIPS R package (v. 1.18.0) was used for data process and estimating methylation levels of MBD-seq data.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a standard protocol. The rpkm values are on log2 scale.
Genome_build: hg19
Supplementary_files_format_and_content: wig files were generated using MEDIPS package. Scores represent log2 transformed RPKM values.
|
| |
|
| 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) |
| GSE81483 |
Methylation profiling study by MBD-seq for identifying genes associated with epithelial-mesenchymal transition and acquired resistance to ALK inhibitors |
| GSE81487 |
Epithelial-mesenchymal transition and acquired resistance to ALK inhibitors |
|
| Relations |
| BioSample |
SAMN05003679 |
| SRA |
SRX1769322 |
