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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Nov 01, 2015 |
| Title |
nb001 |
| Sample type |
SRA |
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| Source name |
Breast
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| Organism |
Homo sapiens |
| Characteristics |
tissue: normal breast
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was purified using standard phenol-chloroform extraction method after treatment with PrK.
XmaI-RRBS
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Ion Torrent PGM |
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| Data processing |
Basecalls performed using Ion Torrent Suite 4.0
XmaI-RRBS reads were aligned to the hg19 genome assembly using Bismark v0.12.2 with bowtie2 v2.2.3 with settings --non_directional -L 24 --rdg 0,3 --rfg 0,3.
Data were filtered to remove artificial methylation using custom script
Methylation state called using bismark_methylation_extractor
Genome_build: hg19
Supplementary_files_format_and_content: .cov files were generated using bismark_methylation_extractor
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| Submission date |
Oct 19, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Alexander S. Tanas |
| Organization name |
Research Centre for Medical Genetics
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| Lab |
Epigenetics
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| Street address |
Moskvorechie St., 1
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| City |
Moscow |
| ZIP/Postal code |
115478 |
| Country |
Russia |
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| Platform ID |
GPL17301 |
| Series (1) |
| GSE74126 |
Rapid and affordable genome-wide bisulfite DNA sequencing by XmaI-RRBS |
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| Relations |
| BioSample |
SAMN04193752 |
| SRA |
SRX1353206 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1910904_nb001.cov.txt.gz |
1.9 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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