|
| Status |
Public on May 26, 2012 |
| Title |
Col_BSseq |
| Sample type |
SRA |
| |
|
| Source name |
WT (eco Columbia) leaves
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Columbia-0
genotype/variation: WT
tissue: 3 week old leaves
|
| Growth protocol |
Constant light
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Illumina PE library construction
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
50 bp reads were mapped to the Arabidopsis genome (TAIR8) using BSseeker wrapper for the short read aligner. Alignments passing the conversion filter were filtered to eliminate sibling reads and then using to calculate methylation percentages for individual cytosines.
Processed data file *mincoverage5-CG.cytosine:
methylated/unmethylated cytosine counts for CG context cytosines with at least 5X coverage in all libraries
Processed data file *mincoverage5-CHG.cytosine:
methylated/unmethylated cytosine counts for CHG context cytosines with at least 5X coverage in all libraries
Processed data file *mincoverage5-CHH.cytosine:
methylated/unmethylated cytosine counts for CHH context cytosines with at least 5X coverage in all libraries
Genome Build:
Col_nosibs_mincoverage5-CG_cytosine.txt: TAIR8
Col_nosibs_mincoverage5-CHG_cytosine.txt: TAIR8
Col_nosibs_mincoverage5-CHH_cytosine.txt: TAIR8
|
| |
|
| Submission date |
Feb 28, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Christopher Joel Hale |
| E-mail(s) |
chris.joel.hale@gmail.com
|
| Organization name |
University of Washington
|
| Department |
Pathology
|
| Lab |
Center for Precision Diagnostics
|
| Street address |
1959 NE Pacific St., HSC H-458
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98195 |
| Country |
USA |
| |
|
| Platform ID |
GPL13222 |
| Series (2) |
| GSE36143 |
An IDN2-containing complex involved in RNA-directed DNA methylation in Arabidopsis [BS-seq] |
| GSE36148 |
An IDN2-containing complex involved in RNA-directed DNA methylation in Arabidopsis |
|
| Relations |
| Reanalyzed by |
GSM1398759 |
| SRA |
SRX123895 |
| BioSample |
SAMN00793021 |
