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Sample GSM1886341 Query DataSets for GSM1886341
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
BioSample SAMN04090353
SRA SRX1250552

Supplementary file Size Download File type/resource
GSM1886341_ABA_tolerant_ONSEN_lines_6_16_1.xls.gz 150.3 Kb (ftp)(http) XLS
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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