|
| Status |
Public on Jan 23, 2013 |
| Title |
PC3 [RRBS] |
| Sample type |
SRA |
| |
|
| Source name |
Prostate cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: PC3 (purchased from ATCC)
assay: RRBS
|
| Growth protocol |
ATCC complete growth medium
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
RRBS was performed by BaseClear (Leiden, NL) using their EpiQuest DNA Methylation Analysis Platform (http://www.baseclear.com/dna-sequencing/next-gen-sequencing/epiquest-5-mc-analysis/).
Easy DNA kit (Invitrogen K1800-01)
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Sample 18
|
| Data processing |
RRBS: Data preprocessing, including alignment, was performed by BaseClear's proprietary algorithms (http://www.baseclear.com/dna-sequencing/next-gen-sequencing/epiquest-5-mc-analysis/basic-service/)
RRBS: Data were summarized into file where for each CpG assessed by RRBS both the coverage (amount of alleles sequenced) and amount of methylated alleles for that specific CpG are mentioned. Amounts of alleles sequenced and methylated were summed for both strands.
Supplementary_files_format_and_content: RRBS .txt file with columns containing resp. line number, chromosome, start and end position CpG, amount of alleles methylated, amount of alleles assessed (= coverage for specific CpG). Txt file containing amounts of methylated alleles and total alleles measured per CpG that was assessed by RRBS (summed for both strands).
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 |
GPL11154 |
| Series (1) |
| GSE42790 |
Quality evaluation of Methyl Binding Domain based kits for enrichment DNA-methylation sequencing |
|
| Relations |
| SRA |
SRX209029 |
| BioSample |
SAMN01823779 |
