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Status |
Public on Dec 18, 2011 |
Title |
Arabidopsis thaliana leaf mRNA 24 hr after Botrytis cinerea infection Rep 2 |
Sample type |
SRA |
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|
Source name |
Infected leaves
|
Organism |
Arabidopsis thaliana |
Characteristics |
strain: Columbia-0 wild type tissue: leaf infection: Botrytis cinerea
|
Treatment protocol |
Leaves from 4 week old plants were detached and infected with Botrytis cinerea as described in Denby et al. (2004) Plant Journal 38(3):473-86, with 5 droplets per leaf.
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Growth protocol |
Plants were grown under a 16:8 hr light:dark cycle at 20°C, 60% humidity and light intensity of 100 μmol photons.m-2.s-1. Arabidopsis seed was stratified for three days in 0.1% agar at 4°C before sowing onto Arabidopsis soil mix (Scotts Levingtons F2 compost:sand:fine grade vermiculite in a ratio of 6:1:1)
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was extracted from 10 pooled infected Arabidopsis leaves using Invitrogen TRIzol reagent according to the manufacturer's procedure. The total RNA was purified using Qiagen RNeasy columns according to the manufacturer's procedure. Libraries were constructed using the Illumina mRNA-seq Library Prep Kit (Illumina part number RS-100-0801) according to the manufacturer’s procedure
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
size fractionation |
Instrument model |
Illumina Genome Analyzer |
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Data processing |
aligned_24hRep2_cdna.txt; genome build: TAIR10 aligned_24hRep2_repcdna.txt; genome build: TAIR10 For 24hRep2 Illumina Pipeline software Casava version 1.7.0 was used using default parameters. For 24hRep1 Illumina Pipeline software Casava version 1.5.1 was used using default parameters. Alignment: The first 34 base-pairs of the paired end illumina sequences were aligned to the full TAIR10 cDNA sequence files using bowtie using -m 1 to reject non-unique mappings and the default -n 2 to allow up to two mismatches. The sequences were first matched to the TAIR10 cDNA sequences TAIR10_cdna_20101214, and those that did not match were matched to the TAIR10_cdna_20110103_representative_gene_model cDNA sequences
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Submission date |
Dec 17, 2011 |
Last update date |
May 15, 2019 |
Contact name |
Nigel Paul Dyer |
E-mail(s) |
nigel.dyer@warwick.ac.uk
|
Organization name |
University of Warwick
|
Street address |
Gibbet Hill Road
|
City |
Coventry |
ZIP/Postal code |
CV4 7AL |
Country |
United Kingdom |
|
|
Platform ID |
GPL9062 |
Series (1) |
GSE34521 |
Two replicates of mRNA from Arabidopsis thaliana leaves 24 hours post infection with Botrytis cinerea |
|
Relations |
SRA |
SRX112186 |
BioSample |
SAMN00766459 |