|
Status |
Public on Jan 23, 2013 |
Title |
DU145 [MBD MethylMagnet] |
Sample type |
SRA |
|
|
Source name |
Prostate cancer cell line
|
Organism |
Homo sapiens |
Characteristics |
cell line: DU145 (purchased from ATCC) assay: MBD mbd-capturing by kit: MethylMagnet
|
Growth protocol |
ATCC complete growth medium
|
Extracted molecule |
genomic DNA |
Extraction protocol |
MBD-capturing by MethylCollector, MethylCollector Ultra, MethylCap, MethylMiner, or MethylMagnet. For MBD-seq, libraries were prepared using standard multiplexed paired-end Chip-seq protocol. Easy DNA kit (Invitrogen K1800-01)
|
|
|
Library strategy |
MBD-Seq |
Library source |
genomic |
Library selection |
MBD2 protein methyl-CpG binding domain |
Instrument model |
Illumina Genome Analyzer IIx |
|
|
Description |
Sample 2
|
Data processing |
MBD: Data were mapped using BOWTIE (--phred64-quals -a -X400 -n0 -m1 -p16) MBD: Data were summarized into file where each line includes the chromosome, the beginning and end position of a stretch of that chromosome with the same amount of mapped fragments, and the amount of mapped fragments Supplementary_files_format_and_content: MBD .txt file with columns containing resp. line number, chromosome, start and end position (nucleotide) and amount of mapped fragments. Txt file containing intensities per nucleotide (summarized). Genome_build: HG19
|
|
|
Submission date |
Dec 06, 2012 |
Last update date |
May 15, 2019 |
Contact name |
Tim De Meyer |
Organization name |
Ghent University
|
Department |
Dept. of Mathematical Modelling, Statistics and Bioinformatics
|
Lab |
BIOBIX lab of Bioinformatics and Computational Genomics
|
Street address |
Coupure Links 653
|
City |
Ghent |
ZIP/Postal code |
9000 |
Country |
Belgium |
|
|
Platform ID |
GPL10999 |
Series (1) |
GSE42790 |
Quality evaluation of Methyl Binding Domain based kits for enrichment DNA-methylation sequencing |
|
Relations |
SRA |
SRX209013 |
BioSample |
SAMN01823763 |