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Sample GSM850477 Query DataSets for GSM850477
Status Public on Dec 18, 2011
Title Arabidopsis thaliana leaf mRNA 24 hr after Botrytis cinerea infection Rep 1
Sample type SRA
 
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.
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
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina Genome Analyzer
 
Data processing aligned_24hRep1_cdna.txt; genome build: TAIR10
aligned_24hRep1_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
 
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 SRX112185
BioSample SAMN00766458

Supplementary file Size Download File type/resource
GSM850477_aligned_24hRep1_cdna.txt.gz 598.2 Mb (ftp)(http) TXT
GSM850477_aligned_24hRep1_repcdna.txt.gz 253.2 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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