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| Status |
Public on Mar 26, 2013 |
| Title |
WT2003 BS-seq |
| Sample type |
SRA |
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| Source name |
3wk-old leaf tissue
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| Organism |
Oryza sativa |
| Characteristics |
ecotype: Nipponbare
genotype/variation: Wild type
tissue: 3wk-old leaf tissue
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| Treatment protocol |
Genomic DNA was extracted using Qiagen Plant DNeasy Maxi Kit.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Fragmented genomic DNA library as described in Cokus et al., Nature 2008, except directly with pre-methylated final adapters (see Feng et al., Methods Mol. Biol. 2011;733:223-38 for further information)
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Bisulfite-treated genomic DNA_Sample 1
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| Data processing |
BS-Seq reads were mapped with BS seeker (Chen et al., 2010 BMC Bioinformatics) to MSU6.1 chr1..12, allowing up to 2 mismatches and retaining only uniquely-mapping reads. Identical reads were collapsed into single reads.
Genome_build: MSU 6.1
Supplementary_files_format_and_content: Column 1 is chromosome (1..12). Column 2 is the coordinate of the genomic cytosine. Column 3 is genomic strand (+/-) of the cytosine. Column 4 is context (CG, CHG, or CHH) of the genomic cytosine. Column 5 is #Cs. Column 6 is #Ts.
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| Submission date |
Nov 20, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Hume Stroud |
| Organization name |
UT Southwestern
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| Street address |
5323 Harry Hines Blvd
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| City |
Dallas |
| State/province |
TX |
| ZIP/Postal code |
75390 |
| Country |
USA |
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| Platform ID |
GPL13160 |
| Series (1) |
| GSE42410 |
Plants regenerated from tissue culture contain stable epigenome changes in rice |
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| Relations |
| SRA |
SRX205347 |
| BioSample |
SAMN01817930 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1039487_sample01_BSseq.txt.gz |
450.2 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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