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Sample GSM822107 Query DataSets for GSM822107
Status Public on Oct 26, 2011
Title HH1-JxoI, biological replicate 2
Sample type RNA
 
Source name HH1 seedlings
Organism Oryza sativa
Characteristics tissue: leaves
age: 75-day
cultivar: Minghui 63
genotype/variation: HH1
agent: rice leaf blight disease pathogen of Xanthomonas oryzae pv. oryzae JxoI
Treatment protocol At the age of 30-day, 60-day, 75-day and 90-day old, seedling samples were collected; seedlings, at the age of 30-day old, were treated with high-temperature (45°C) and low-temperature (12°C) respectively at climate chambers, and samples were collected 6 hours after treatment; Seedlings were inoculated respectively with rice leaf blight disease pathogen of Xanthomonas oryzae pv. oryzae JxoI and Pxo99 strains, rice leaf streak disease pathogen of Xanthomonas oryzae pv. oryzicola Rs105 strain and rice non-host pathogen of Xanthomonas compestris pv. vesicatoria Xv5 strain at the age of 75-day old.
Growth protocol Rice seeds were surface-disinfected and then soaked in distilled sterile water for germination at 28°C for 2 days. Rice seedlings were grown in pots fertilized with half-strength of basal macro- and micro-salt nutrition components of MS medium (Murashige and Skoog, 1962) in a controlled climate chamber at 16-h-light (30°C)/8-h-dark (26°C) cycle.
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
 
Hybridization protocol Following fragmentation, 10 ug of cRNA were hybridized for 16 h at 45°C using an Affymetrix GeneChip Hybridization Oven 640. GeneChips were washed and stained at Affymetrix GeneChip Fluidics Station 450.
Scan protocol GeneChips were scanned with Affymetrix GeneChip® Scanner 3000 7G.
Description Gene expression data from HH1 inoculated with rice leaf blight disease pathogen of Xanthomonas oryzae pv. oryzae JxoI
Data processing The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
 
Submission date Oct 25, 2011
Last update date Oct 26, 2011
Contact name Jie Zhao
E-mail(s) [email protected]
Phone 15901108454
Organization name Institute of Plant Protection, Chinese Academe of Agricultural Sciences
Street address No. 2 Yuan Ming Yuan West Street
City Beijing
ZIP/Postal code 100193
Country China
 
Platform ID GPL2025
Series (1)
GSE33204 DNA microarray data from transgenic rice Huahui 1 (HH1) and its parent Minghui 63 (MH63)

Data table header descriptions
ID_REF
VALUE MAS5.0 signal intensity.

Data table
ID_REF VALUE
AFFX-BioB-3_at 157.153447
AFFX-BioB-5_at 168.4044371
AFFX-BioB-M_at 121.7766558
AFFX-BioC-3_at 462.6188403
AFFX-BioC-5_at 435.9128569
AFFX-BioDn-3_at 3206.300014
AFFX-BioDn-5_at 1347.342585
AFFX-CreX-3_at 7838.296622
AFFX-CreX-5_at 6704.439234
AFFX-DapX-3_at 604.8911337
AFFX-DapX-5_at 157.0248889
AFFX-DapX-M_at 306.7114261
AFFX-LysX-3_at 130.8508689
AFFX-LysX-5_at 44.13706032
AFFX-LysX-M_at 54.79708088
AFFX-Mgr-actin-3_at 21.39731537
AFFX-Mgr-actin-5_at 24.09239993
AFFX-Mgr-actin-M_at 17.08525295
AFFX-Mgr-ef1a-3_at 28.01094685
AFFX-Mgr-ef1a-3_x_at 16.07682572

Total number of rows: 57381

Table truncated, full table size 1728 Kbytes.




Supplementary file Size Download File type/resource
GSM822107.CEL.gz 4.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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