|
| Status |
Public on Jan 23, 2013 |
| Title |
DU145 [MBD MethylCollector Ultra] |
| 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: MethylCollector Ultra
|
| 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 8
|
| 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 |
SRX209019 |
| BioSample |
SAMN01823769 |
