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| Status |
Public on Dec 14, 2017 |
| Title |
Rat_R2_Sperm BS-seq |
| Sample type |
SRA |
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| Source name |
Sperm
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| Organism |
Rattus norvegicus |
| Characteristics |
individual: 2
library: L1
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| Treatment protocol |
Bisulfite treated genomic DNA
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Standard Illumina genomic library
PE Illumina adaptors were used, ligated libraires were amplified according the maunfacturers instruction.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Bisulfite-Seq reads were mapped to reference genome by rmapbs with default parameters
Methylation levels at all cytosine sites and hmr calls were made by methpipe with default parameters
Genome_build: gorGor3; rn5; canFam3
Supplementary_files_format_and_content: .meth files contain 6 columns: chromosome, start position, strand, base context, methylation level, coverage
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| Submission date |
Mar 24, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Andrew D Smith |
| E-mail(s) |
andrewds@usc.edu
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| Organization name |
University of Southern California
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| Street address |
1050 Childs way
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| City |
Los Angeles |
| State/province |
California |
| ZIP/Postal code |
90089 |
| Country |
USA |
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| Platform ID |
GPL18694 |
| Series (1) |
| GSE79566 |
Whole genome DNA methylation profile of sperm cells in mammalian species |
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| Relations |
| BioSample |
SAMN04578000 |
| SRA |
SRX1659591 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2098424_Rat_Sperm_R2.meth.txt.gz |
116.0 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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