|
| Status |
Public on Dec 07, 2017 |
| Title |
150H rep 2 [Bisulfite-Seq] |
| Sample type |
SRA |
| |
|
| Source name |
Aerial rosette tissue
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: Aerial rosette tissue at 21/22 DAS (days after sowing)
line: epiHybrid 150
|
| Treatment protocol |
Aerial rosette tissue 21/22 days after sowing (DAS) was harvested.
|
| Growth protocol |
Arabidopsis lines (epiRILs 92, 150, 193, 232 and epiHybrids 92H, 150H, 193H, 232H and Col-wt) were grown in a climate-controlled growth chamber in long day (16h light, 8h dark) conditions.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Plant tissues were ground in liquid nitrogen and DNA was extracted using a CTAB-based extraction protocol.
Approximately 5000 ng of total DNA was submitted to the Beijing Genome Institute (BGI) for BS-treatment, library construction and sequencing on an Illumina HiSeq4000 instrument.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
meth_levels_windows_qtl_intervals_w_100_s_50_c_3.txt
|
| Data processing |
Basecalls performed using Illumina’s real-time analysis software (RTA).
Quality filtering and adapter trimming of BS-seq reads were done using Cutadapt (Q20). Reads with less than 40 bps were discarded.
Read alignment and methylation calling were performed using BS-Seeker2 and Bowtie2.
Average methylation were calculated for 100 bp windows with 50 bp step size.
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab-delimited file containing methylation levels (absolute, mid-parents value, absolute difference and fold change) for each genomic window
|
| |
|
| Submission date |
May 30, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Maike Stam |
| Organization name |
University of Amsterdam
|
| Department |
Swammerdam Institute for Life Sciences
|
| Street address |
Science Park 904
|
| City |
Amsterdam |
| ZIP/Postal code |
1098XH |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL21785 |
| Series (2) |
| GSE99404 |
Genome-wide DNA methylation profiles from Arabidopsis epiRILs, epiHybrids and Colombia wild type |
| GSE99482 |
Arabidopsis epiRILs, epiHybrids and Colombia wild type |
|
| Relations |
| BioSample |
SAMN07179284 |
| SRA |
SRX2871278 |
