|
| Status |
Public on Mar 28, 2015 |
| Title |
6918_16C |
| Sample type |
SRA |
| |
|
| Source name |
aerial seedling
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
accession number: 6918
accession name: Fäb-4
growth temperature: 16C
tissue: whole rosette
developmental stage: 9-true -leaf stage
|
| Growth protocol |
Accessions were sown on soil and stratified for 3 days at 4 C in the dark. They were then transferred to environmentally controlled growth chambers set at 10C or 16C under long day conditions (04:00-20:00) and individual seedlings were transplanted to single pots after one week. When plants attained the 9-true -leaf stage of development, whole rosettes were collected between 15:00 and 16:00 hours and flash frozen in liquid nitrogen.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For each sample two individual plants were pooled and total DNA was extracted using CTAB and phenol-chloroform
Approximately two micrograms of genomic DNA was sent for BS-seq library construction and sequencing (preformed under contract by Beijing Genomics Institute)
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
base calling and de-muiltiplexing done under contract by Beijing Genomics Institute
Reads were aligned to the pseudo-reference genome (TAIR10 with the SNPs from the relevent accession) using using NexGenMap version 0.4.3 with the following settings -p -i 0.90 -R 45 --bs-mapping --silent-clip
Genome_build: TAIR10 (incorporating relevant SNV's)
Supplementary_files_format_and_content: A TSV (tab separated values) detailing the methylation levels at each cytosine was generated using the methratio.py script from the BSMAP (version 2.73) using the -z and -u flags
|
| |
|
| Submission date |
Jan 22, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Manu Dubin |
| E-mail(s) |
manu.dubin@gmi.oeaw.ac.at
|
| Organization name |
Gregor Mendel Institute, Austrian Academy of Sciences
|
| Street address |
Dr. Bohr-Gasse 3
|
| City |
Vienna |
| ZIP/Postal code |
1030 |
| Country |
Austria |
| |
|
| Platform ID |
GPL13222 |
| Series (1) |
| GSE54292 |
DNA methylation variation in Arabidopsis has a genetic basis and appears to be involved in local adaptation |
|
| Relations |
| BioSample |
SAMN02594735 |
| SRA |
SRX446043 |
