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Sample GSM2154746 Query DataSets for GSM2154746
Status Public on May 28, 2018
Title H3122_LR-2_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 SAMN05003682
SRA SRX1769325

Supplementary file Size Download File type/resource
GSM2154746_H3122_LR-2.wig.gz 16.2 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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