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Status |
Public on Nov 01, 2015 |
Title |
nb005 |
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 |
SAMN04193756 |
SRA |
SRX1353210 |
Supplementary file |
Size |
Download |
File type/resource |
GSM1910908_nb005.cov.txt.gz |
2.4 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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