|
| Status |
Public on Feb 10, 2017 |
| Title |
ABA_tolerant_ONSEN_lines_6_16_1 |
| Sample type |
SRA |
| |
|
| Source name |
Plant
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
developmental stage: 1 week old
genotype: nrpd1-3
ecotype: Col-0
treatment: A progeny of a heat-stressed parent
|
| Treatment protocol |
A parent plant was shift to 37C for 24h.
|
| Growth protocol |
for two weeks at 21C on MS medium agar plate. Light:24h.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Qiagen plant DNA purification kit
pair-endo sequencing libraries using SOLiD fragment library construction kit (Life Technologies)
50bp-35bp pair-end sequencing for SOLiD4 sequencer (accoding to manufacturers instructions)
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
AB SOLiD 4 System |
| |
|
| Description |
ABA_tolerant_ONSEN_lines
|
| Data processing |
Basecalls were performed using standard tools equipped with ABI SOLiD4 sequencer.
Each sequences were aligned on TAIR9 genome using bowtie (version 0.12.8).
Sequences mapped on a subtype of retrotransposon (ONSEN) were collected and mapped regions of their pairs were evaluated.
Genome_build: TAIR9
Supplementary_files_format_and_content: An Excel file containing sequence IDs and their inserted positions and a file having summerized genomic locations where the retrotransposon were inserted.
|
| |
|
| Submission date |
Sep 16, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
motoaki seki |
| Organization name |
RIKEN
|
| Department |
CSRS
|
| Lab |
Plant Genomic Network Research Team
|
| Street address |
Suehiro-cho 1-7-22, Tsurumi-ku
|
| City |
Yokohama |
| State/province |
Kanagawa |
| ZIP/Postal code |
230-0045 |
| Country |
Japan |
| |
|
| Platform ID |
GPL14599 |
| Series (1) |
| GSE73097 |
ONSEN insertion site on Arabidopsis thaliana genome subjected to heat treatment |
|
| Relations |
| BioSample |
SAMN04090353 |
| SRA |
SRX1250552 |
