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Sample GSM1355078 Query DataSets for GSM1355078
Status Public on Jun 02, 2015
Title P. syringae pv tomato DC3000 hrpA- mutant 12 hours biorep D
Sample type RNA
 
Source name P. syringae pv tomato DC3000 hrpA- mutant 12 hours biorep D
Organism Arabidopsis thaliana
Characteristics strain: Col0
treatment: Infected P. syringae pv tomato DC3000 hrpA- mutant
hours_since_infection: 12
tissue: leaf
Growth protocol Arabidopsis plants Col-0 were grown under a 16:8 hr light:dark cycle (lights on 04:00 to 20:00) 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 F2s compost:sand:fine grade vermiculite in a ratio of 6:1:1).
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from four individual leaves from each sampled time point (arbitrarily labelled as biological replicates A, B, C and D) using TRIzol reagent (Invitrogen), purified with RNeasy columns (Qiagen) and amplified using the MessageAmp II aRNA Amplification kit (Ambion) in accordance with the kit protocol with a single round of amplification.
Label Cy3 or Cy5
Label protocol Cy3 and Cy5 labelled cDNA probes were prepared by reverse transcribing 5µg of aRNA with Cy3- or Cy5- dCTP (GE Healthcare) and a modified dNTP mix (10mM each dATP, dGTP and dTTP; 2mM dCTP) using random primers (Invitrogen) and SuperScript II reverse transcriptase (Invitrogen), with the inclusion of RNase inhibitor (RNaseOUT, Invitrogen) and DTT. Labelled probes were purified using QiaQuick PCR Purification columns (Qiagen), freeze-dried, and resuspended in 50µl hybridization buffer (25% formamide, 5xSSC, 0.1% SDS, 0.5µg/µl yeast tRNA [Invitrogen]).
 
Hybridization protocol The order in which the 288 slides were hybridized and scanned was randomised to minimise the impact on differences between samples of any potential variation in the processing conditions. According to this randomised experimental design combinations of labelled samples were hybridized to slides overnight at 42oC.
Scan protocol Following hybridization, slides were washed and scanned using an Affymetrix 428 array scanner at 532nm (Cy3) and 635nm (Cy5).
Scanned data were quantified using Imagene 7.5.0 software (BioDiscovery, Inc.).
Description Randomised loop design providing dye-swaps between treatments, time points and bioreps
Data processing Quantified microarray data were Lowess normalized within pintip groups and within arrays, then variation due to arrays and dyes was removed by a random effects model, and averaged, in log space, using R/MAANOVA (MicroArray ANalysis Of VAriance) (Wu et al. 2003). Oligo sequences of CATMA array probes were mapped to individual mRNA sequences of transcripts from the TAIR9 genome assembly using BLASTn with e-value cutoff of 0.01. Additionally, alignments were filtered to exclude alignments shorter than 30bp or with less than 80% sequence identity.
 
Submission date Mar 21, 2014
Last update date Jun 03, 2015
Contact name Jonathan David Moore
E-mail(s) jonathan.moore@tgac.ac.uk
Organization name The Genome Analysis Centre
Department Platforms and Pipelines
Street address Norwich Research Park
City Norwich
ZIP/Postal code NR4 7UH
Country United Kingdom
 
Platform ID GPL10840
Series (1)
GSE56094 Transcriptional dynamics driving MAMP-triggered immunity and pathogen effector-mediated immunosuppression in Arabidopsis leaves following infection with Pseudomonas syringae pv. tomato DC3000.

Data table header descriptions
ID_REF
VALUE Lowess normalized averaged signals in log space

Data table
ID_REF VALUE
CATMA1a00010 10.72731511
CATMA1a00020 7.95555817
CATMA1a00030 8.141007164
CATMA1a00035 10.29643028
CATMA1a00040 11.72404944
CATMA1a00045 14.47313156
CATMA1a00050 10.1989678
CATMA1a00060 11.44846095
CATMA1a00070 13.80331117
CATMA1a00080 15.0346959
CATMA1a00090 9.692639269
CATMA1a00100 8.40388997
CATMA1a00110 11.03919043
CATMA1a00130 10.71259465
CATMA1a00140 8.273335079
CATMA1a00150 11.3609987
CATMA1a00160 11.4832891
CATMA1a00170 12.26135054
CATMA1a00180 9.006610499
CATMA1a00190 8.170572148

Total number of rows: 30336

Table truncated, full table size 737 Kbytes.




Supplementary file Size Download File type/resource
GSM1355078_LB_13628144_Cy5.txt.gz 1.5 Mb (ftp)(http) TXT
GSM1355078_LB_13757187_Cy3.txt.gz 1.7 Mb (ftp)(http) TXT
GSM1355078_LB_13757325_Cy3.txt.gz 1.7 Mb (ftp)(http) TXT
GSM1355078_LB_13781865_Cy5.txt.gz 1.6 Mb (ftp)(http) TXT
Processed data included within Sample table

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