|
| Status |
Public on Aug 05, 2012 |
| Title |
nrpe1 BSseq |
| Sample type |
SRA |
| |
|
| Source name |
seedling tissue (10-day)
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype: nrpe1-12 mutant (eco. Columbia)
genetic background: Columbia
tissue: seedling
genotype: nrpe1-12
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 |
SRX159115 |
| BioSample |
SAMN01087302 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM958802_nrpe1_50bp_2mis_nosibs_Chr1_CG.wig.gz |
3.1 Mb |
(ftp)(http) |
WIG |
| GSM958802_nrpe1_50bp_2mis_nosibs_Chr1_CHG.wig.gz |
3.2 Mb |
(ftp)(http) |
WIG |
| GSM958802_nrpe1_50bp_2mis_nosibs_Chr1_CHH.wig.gz |
13.6 Mb |
(ftp)(http) |
WIG |
| GSM958802_nrpe1_50bp_2mis_nosibs_Chr2_CG.wig.gz |
2.1 Mb |
(ftp)(http) |
WIG |
| GSM958802_nrpe1_50bp_2mis_nosibs_Chr2_CHG.wig.gz |
2.2 Mb |
(ftp)(http) |
WIG |
| GSM958802_nrpe1_50bp_2mis_nosibs_Chr2_CHH.wig.gz |
9.1 Mb |
(ftp)(http) |
WIG |
| GSM958802_nrpe1_50bp_2mis_nosibs_Chr3_CG.wig.gz |
2.5 Mb |
(ftp)(http) |
WIG |
| GSM958802_nrpe1_50bp_2mis_nosibs_Chr3_CHG.wig.gz |
2.7 Mb |
(ftp)(http) |
WIG |
| GSM958802_nrpe1_50bp_2mis_nosibs_Chr3_CHH.wig.gz |
10.9 Mb |
(ftp)(http) |
WIG |
| GSM958802_nrpe1_50bp_2mis_nosibs_Chr4_CG.wig.gz |
2.0 Mb |
(ftp)(http) |
WIG |
| GSM958802_nrpe1_50bp_2mis_nosibs_Chr4_CHG.wig.gz |
2.1 Mb |
(ftp)(http) |
WIG |
| GSM958802_nrpe1_50bp_2mis_nosibs_Chr4_CHH.wig.gz |
8.5 Mb |
(ftp)(http) |
WIG |
| GSM958802_nrpe1_50bp_2mis_nosibs_Chr5_CG.wig.gz |
2.8 Mb |
(ftp)(http) |
WIG |
| GSM958802_nrpe1_50bp_2mis_nosibs_Chr5_CHG.wig.gz |
3.0 Mb |
(ftp)(http) |
WIG |
| GSM958802_nrpe1_50bp_2mis_nosibs_Chr5_CHH.wig.gz |
12.3 Mb |
(ftp)(http) |
WIG |
| GSM958802_nrpe1_50bp_2mis_nosibs_Chr6_CG.wig.gz |
14.5 Kb |
(ftp)(http) |
WIG |
| GSM958802_nrpe1_50bp_2mis_nosibs_Chr6_CHG.wig.gz |
12.5 Kb |
(ftp)(http) |
WIG |
| GSM958802_nrpe1_50bp_2mis_nosibs_Chr6_CHH.wig.gz |
64.0 Kb |
(ftp)(http) |
WIG |
| GSM958802_nrpe1_50bp_2mis_nosibs_Chr7_CG.wig.gz |
31.2 Kb |
(ftp)(http) |
WIG |
| GSM958802_nrpe1_50bp_2mis_nosibs_Chr7_CHG.wig.gz |
30.5 Kb |
(ftp)(http) |
WIG |
| GSM958802_nrpe1_50bp_2mis_nosibs_Chr7_CHH.wig.gz |
96.4 Kb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
