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Sample GSM278444 Query DataSets for GSM278444
Status Public on Jul 18, 2008
Title LW05set1_Col-0_Psm_24h
Sample type RNA
 
Source name Arabidopsis thaliana Col-0, leaves, 1x10E8 cfu/ml Pseudomonas syringae ES4326-infiltrated, 24h
Organism Arabidopsis thaliana
Characteristics Genotype: Col-0
Tissue: leaves
Age: 4 week-old
Treatment: 1x10E8 cfu/ml Pseudomonas syringae ES4326
Time point: 24h
Biomaterial provider Lin Wang
Treatment protocol Individual leaves were infiltrated in the morning using a needle-less syringe with 1x10E8 cfu/ml Pseudomonas syringae ES4326 and harvested 24h later.
Growth protocol Plants were grown in pots with BM-2 soil (Berger Peat Moss Ltd, Quebec, Canada) at a density of 9 plants per pot and kept at 22 degrees Celsius and 75% humidity with a 12 hour day length.
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Label Alexa555
Label protocol Following procedure was performed with Amino Allyl MessageAmp aRNA Amplification Kit II (Ambion).First, cDNA was synthesized from 1ug of total RNA. Next, RNA was in vitro transcribed. The RNA was then labeled with Alexa555 in coupling reaction.
 
Hybridization protocol Labeled RNA was suspended in hybridization buffer (50% Formamide, 5xSSC, 0.1% SDS, 10 ug Sheared Salmon Sperm DNA (Eppendorf), 50pg calbation oligo)
Scan protocol Slide was scaned using Genepix4000B with low and high voltages of photomultiplier at 532nm and constant voltage at 635nm.
Description Col-0 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae ES4326, harvested 24h after infiltration in set1 experiment.
Data processing Note that each Sample corresponds to two GPR files (we use low PMT and high PMT, then combine them).

The median of ratios for each spot was processed by the following linear model: Sij = mu + Ai + Bj + Eij where Sij denotes the log2-transformed, median of ratios for the spot, mu denotes a constant, Ai and Bj denote the effects of i-th gene and j-th subarray. The residual Eij is assumed to be independent and normally distributed. Stable genes-based quantile normalization was applied for slide-to-slide comparisons. LW01_set1_Col-0_Psm_24h, LW01_set1_eds5_Psm_24h, LW01_set1_mpk3_Psm_24h, LW01_set1_mpk6_Psm_24h, LW01_set1_npr_Psm_24h, LW01_set1_pad4_Psm_24h, LW01_set1_sid2_Psm_24h, LW01_set1_tga_Psm_24h, LW01_set2_Col-0_Psm_24h, LW01_set2_eds5_Psm_24h, LW01_set2_mpk3_Psm_24h, LW01_set2_mpk6_Psm_24h, LW01_set2_npr_Psm_24h, LW01_set2_pad4_Psm_24h, LW01_set2_sid2_Psm_24h, LW01_set2_tga_Psm_24h, LW01_set3_Col-0_Psm_24h, LW01_set3_eds5_Psm_24h, LW01_set3_mpk3_Psm_24h, LW01_set3_mpk6_Psm_24h, LW01_set3_npr_Psm_24h, LW01_set3_pad4_Psm_24h, LW01_set3_sid2_Psm_24h, LW01_set3_tga_Psm_24h, LW02_set1_Col-0_Psm_24h, LW02_set1_SALK023199_Psm_24h, LW02_set1_SALK066990_Psm_24h, LW02_set1_coi1_Psm_24h, LW02_set1_dde2_Psm_24h, LW02_set1_ein2_Psm_24h, LW02_set1_jai1_Psm_24h, LW02_set1_jar1_Psm_24h, LW02_set2_Col-0_Psm_24h, LW02_set2_SALK023199_Psm_24h, LW02_set2_SALK066990_Psm_24h, LW02_set2_coi1_Psm_24h, LW02_set2_dde2_Psm_24h, LW02_set2_ein2_Psm_24h, LW02_set2_jai1_Psm_24h, LW02_set2_jar1_Psm_24h, LW02_set3_Col-0_Psm_24h, LW02_set3_SALK023199_Psm_24h, LW02_set3_SALK066990_Psm_24h, LW02_set3_coi1_Psm_24h, LW02_set3_dde2_Psm_24h, LW02_set3_ein2_Psm_24h, LW02_set3_jai1_Psm_24h, LW02_set3_jar1_Psm_24h, LW03_set1_Col-0_Psm_24h, LW03_set1_Col-0_mock_24h, LW03_set1_SALK018487_Psm_24h, LW03_set1_SALK052422_Psm_24h, LW03_set1_SALK084141_Psm_24h, LW03_set1_SALK143063_Psm_24h, LW03_set1_eds1_Psm_24h, LW03_set1_fmo1_Psm_24h, LW03_set2_Col-0_Psm_24h, LW03_set2_Col-0_mock_24h, LW03_set2_SALK018487_Psm_24h, LW03_set2_SALK052422_Psm_24h, LW03_set2_SALK084141_Psm_24h, LW03_set2_SALK143063_Psm_24h, LW03_set2_eds1_Psm_24h, LW03_set2_fmo1_Psm_24h, LW03_set3_Col-0_Psm_24h, LW03_set3_Col-0_mock_24h, LW03_set3_SALK018487_Psm_24h, LW03_set3_SALK052422_Psm_24h, LW03_set3_SALK084141_Psm_24h, LW03_set3_SALK143063_Psm_24h, LW03_set3_eds1_Psm_24h, LW03_set3_fmo1_Psm_24h, LW05_set1_Col-0_Psm-cor-_24h, LW05_set1_Col-0_Psm_24h, LW05_set1_Col-0_mock_24h, LW05_set1_coi1_Psm-cor-_24h, LW05_set1_coi1_Psm_24h, LW05_set1_coi1_mock_24h, LW05_set1_ndr1_Psm_24h, LW05_set1_pbs3_Psm_24h, LW05_set2_Col-0_Psm-cor-_24h, LW05_set2_Col-0_Psm_24h, LW05_set2_Col-0_mock_24h, LW05_set2_coi1_Psm-cor-_24h, LW05_set2_coi1_Psm_24h, LW05_set2_coi1_mock_24h, LW05_set2_ndr1_Psm_24h, LW05_set2_pbs3_Psm_24h, LW05_set3_Col-0_Psm-cor-_24h, LW05_set3_Col-0_Psm_24h, LW05_set3_Col-0_mock_24h, LW05_set3_coi1_Psm-cor-_24h, LW05_set3_coi1_Psm_24h, LW05_set3_coi1_mock_24h, LW05_set3_ndr1_Psm_24h, and LW05_set3_pbs3_Psm_24h were normalized together. Perl scripts for the linear model and the normalization are available for non-commercial research conducted upon request (Fumiaki Katagiri, katagiri@umn.edu). Spots with bad quality (missing, lints, and high background) were flagged as indicated in Flag in the attached .gpr file for this sample.
 
Submission date Mar 31, 2008
Last update date Jul 18, 2008
Contact name lin wang
E-mail(s) wang0602@umn.edu
Organization name University of Minnesota
Department Plant Biology
Lab Jane Glazebrook
Street address 350 Cargill building, 1500 Gortner Ave
City St Paul
State/province MN
ZIP/Postal code 55108
Country USA
 
Platform ID GPL3638
Series (1)
GSE11009 The Genetic Network Controlling the Arabidopsis Transcriptional Response to Pseudomonas syringae pv. maculicola

Data table header descriptions
ID_REF
EST_VALUE Estimated expression values after combining signals measured at high and low PMT
STD_ERR Standard error for the estimated expression values
VALUE Normalized expression values

Data table
ID_REF EST_VALUE STD_ERR VALUE
1 15.03541375 1.265e-01 5.25107515367258
2 14.69541375 1.284e-01 4.79558197786691
3 15.02541375 1.285e-01 5.2375091578298
4 13.60541375 1.290e-01 3.07052557593551
5 13.00541375 1.261e-01 1.75103351400084
6 17.41541375 1.282e-01 8.14314582001974
7 17.97541375 1.299e-01 8.83432071854746
8 14.80541375 1.258e-01 5.05122616778193
9 14.88541375 1.273e-01 5.11626663259391
10 13.73541375 1.262e-01 3.33668857959851
11 13.84541375 1.262e-01 3.5262391748366
12 15.23541375 1.419e-01 5.61049975684719
13 13.51541375 1.270e-01 2.96034743376517
14 18.73541375 1.265e-01 9.77234379512078
15 14.26541375 1.277e-01 4.04576383470055
16 17.04541375 1.276e-01 7.49130773744684
17 15.50541375 1.316e-01 5.83999795822802
18 14.42541375 1.295e-01 4.21416838402028
19 12.98541375 1.285e-01 1.72744289203777
20 15.15541375 1.267e-01 5.46380867763773

Total number of rows: 576

Table truncated, full table size 24 Kbytes.




Supplementary file Size Download File type/resource
GSM278444_high.gpr.gz 473.8 Kb (ftp)(http) GPR
GSM278444_low.gpr.gz 417.6 Kb (ftp)(http) GPR
Processed data included within Sample table

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