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| Status |
Public on Nov 01, 2013 |
| Title |
Col BS-seq |
| Sample type |
SRA |
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| Source name |
3 week leaf tissue
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| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype: Wild type
ecotype: Columbia
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| Growth protocol |
All plants were grown at 22 degrees celsius in constant light.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
phenol-chloroform extraction followed by bisulfite treatment
converted and fragmented genomic DNA library as described in Stroud et al., Cell 2013
genomic DNA isolated by phenol/chloroform and bisulfite treated
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Raw file content: quality scores in _qseq files are Phred scale with +64 ASCII offset... non-multiplexed: 1 lane
BS-seq reads were mapped with BS seeker (Chen et al., 2010 BMC Bioinformatics), allowing up to 2 mismatches and retaining only uniquely mapping reads. The drm2 and nrpe1 libraries used in this study were previously published (GSE39901), as were the 3 other Col replicates used (GSE39901 - WT replicate 2 ; GSE38286 ; GSE36129).
Genome_build: TAIR10
Supplementary_files_format_and_content: Variable step UCSC Genome Browser wiggle format files for each chromosome for each cytosine context (CG, CHG, or CHH where H=A,T,C) with following tab-separated information: Chromosome, start coordinate, stop coordinate, and methylation level (#methylated cytosines sequenced/#total cytosines sequenced).
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| Submission date |
Jul 22, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Christopher Joel Hale |
| E-mail(s) |
chris.joel.hale@gmail.com
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| Organization name |
University of Washington
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| Department |
Pathology
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| Lab |
Center for Precision Diagnostics
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| Street address |
1959 NE Pacific St., HSC H-458
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| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98195 |
| Country |
USA |
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| Platform ID |
GPL13222 |
| Series (1) |
| GSE49090 |
Interplay Between Active Chromatin Marks and RNA-directed DNA Methylation in Arabidopsis thaliana |
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| Relations |
| BioSample |
SAMN02261597 |
| SRA |
SRX326961 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1193638_Col_2_CG.wig.gz |
14.2 Mb |
(ftp)(http) |
WIG |
| GSM1193638_Col_2_CHG.wig.gz |
14.7 Mb |
(ftp)(http) |
WIG |
| GSM1193638_Col_2_CHH.wig.gz |
59.5 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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