|
Status |
Public on Aug 05, 2012 |
Title |
Col BSseq |
Sample type |
SRA |
|
|
Source name |
seedling tissue (10-day)
|
Organism |
Arabidopsis thaliana |
Characteristics |
genotype: Wild type (eco. Columbia) genetic background: Columbia tissue: seedling genotype: wild type sample type: Bisulfite-treated genomic DNA
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Samples 1..7 / 8..11 / 12..13 / are by NEBNext DNA sample preparation protocol using Illumina PE adapters / Illumina TruSeq small RNA / converted and fragmented genomic DNA library as described in Cokus et al., Nature 2008 /
|
|
|
Library strategy |
Bisulfite-Seq |
Library source |
genomic |
Library selection |
RANDOM |
Instrument model |
Illumina HiSeq 2000 |
|
|
Description |
genomic DNA isolated by phenol/chloroform and bisulfite treated; quality scores in _qseq files are Phred scale with +64 ASCII offset... non-multiplexed: 1 lane
|
Data processing |
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. Only cytosines covered with at least 5 reads in both libraries (Col and nrpe1) were considered. genome build: TAIR8 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).
|
|
|
Submission date |
Jul 10, 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 (1) |
GSE39247 |
The DDR complex facilitates the genome-wide association of RNA Polymerase V to promoters and evolutionarily young transposons |
|
Relations |
SRA |
SRX159114 |
BioSample |
SAMN01087301 |
Supplementary file |
Size |
Download |
File type/resource |
GSM958801_Col_50bp_2mis_nosibs_Chr1_CG.wig.gz |
2.6 Mb |
(ftp)(http) |
WIG |
GSM958801_Col_50bp_2mis_nosibs_Chr1_CHG.wig.gz |
2.7 Mb |
(ftp)(http) |
WIG |
GSM958801_Col_50bp_2mis_nosibs_Chr1_CHH.wig.gz |
10.5 Mb |
(ftp)(http) |
WIG |
GSM958801_Col_50bp_2mis_nosibs_Chr2_CG.wig.gz |
1.7 Mb |
(ftp)(http) |
WIG |
GSM958801_Col_50bp_2mis_nosibs_Chr2_CHG.wig.gz |
1.8 Mb |
(ftp)(http) |
WIG |
GSM958801_Col_50bp_2mis_nosibs_Chr2_CHH.wig.gz |
6.9 Mb |
(ftp)(http) |
WIG |
GSM958801_Col_50bp_2mis_nosibs_Chr3_CG.wig.gz |
2.1 Mb |
(ftp)(http) |
WIG |
GSM958801_Col_50bp_2mis_nosibs_Chr3_CHG.wig.gz |
2.2 Mb |
(ftp)(http) |
WIG |
GSM958801_Col_50bp_2mis_nosibs_Chr3_CHH.wig.gz |
8.3 Mb |
(ftp)(http) |
WIG |
GSM958801_Col_50bp_2mis_nosibs_Chr4_CG.wig.gz |
1.6 Mb |
(ftp)(http) |
WIG |
GSM958801_Col_50bp_2mis_nosibs_Chr4_CHG.wig.gz |
1.7 Mb |
(ftp)(http) |
WIG |
GSM958801_Col_50bp_2mis_nosibs_Chr4_CHH.wig.gz |
6.5 Mb |
(ftp)(http) |
WIG |
GSM958801_Col_50bp_2mis_nosibs_Chr5_CG.wig.gz |
2.3 Mb |
(ftp)(http) |
WIG |
GSM958801_Col_50bp_2mis_nosibs_Chr5_CHG.wig.gz |
2.4 Mb |
(ftp)(http) |
WIG |
GSM958801_Col_50bp_2mis_nosibs_Chr5_CHH.wig.gz |
9.4 Mb |
(ftp)(http) |
WIG |
GSM958801_Col_50bp_2mis_nosibs_Chr6_CG.wig.gz |
14.1 Kb |
(ftp)(http) |
WIG |
GSM958801_Col_50bp_2mis_nosibs_Chr6_CHG.wig.gz |
12.1 Kb |
(ftp)(http) |
WIG |
GSM958801_Col_50bp_2mis_nosibs_Chr6_CHH.wig.gz |
62.5 Kb |
(ftp)(http) |
WIG |
GSM958801_Col_50bp_2mis_nosibs_Chr7_CG.wig.gz |
30.7 Kb |
(ftp)(http) |
WIG |
GSM958801_Col_50bp_2mis_nosibs_Chr7_CHG.wig.gz |
29.2 Kb |
(ftp)(http) |
WIG |
GSM958801_Col_50bp_2mis_nosibs_Chr7_CHH.wig.gz |
90.1 Kb |
(ftp)(http) |
WIG |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |