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Sample GSM818248 Query DataSets for GSM818248
Status Public on Oct 01, 2013
Title Stem from healthy plant 4, biological rep3
Sample type RNA
 
Source name Citrus stems from non-infected plants
Organism Citrus sinensis
Characteristics tissue: young stem tissues and bark peels with phloem
age: 3 year old plants
infection: none
Treatment protocol Valencia sweet orange (C. sinensis) plants were graft inoculated with budwood from Ca. L. asiaticus-infected citrus plants
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from freshly obtained stems and roots using RNeasy Plant Mini kit and treated with DNase (Qiagen, Valencia, CA) according to the manufacturer's instructions.
Label biotin
Label protocol Four micrograms of total RNA was used to generate biotinylated cRNA using one-cycle target labelling kit (Affymetrix, Santa Clara, CA).
 
Hybridization protocol Following fragmentation, cRNA were hybridized for 16 hr at 450C on GeneChip Citrus Genome Array. GeneChips were washed and stained in the Affymetrix Model 450 Fluidics Station.
Scan protocol GeneChips were scanned using Affymetrics Model 3000 7G scanner according to the manufacture's recommended protocols.
Description Valencia sweet orange
Gene expression data from stems of healthy 3 year old plants
Data processing Raw data collected using Microarray Suite version 5.0 (MAS 5.0). Statistical tests were performed using the BioConductor statistical software, Version 2.5.
Normalsied log2 fold change (stems from Ca. L. asiaticus infected plants/healthy, roots from Ca. L. asiaticus infected plants/healthy); False discovery rate; P-values; MAS5.0 signal intensity
 
Submission date Oct 14, 2011
Last update date Oct 01, 2013
Contact name Valente Aritua
E-mail(s) varitua@ufl.edu
Phone 863-956-1151
Organization name University of Florida
Department Plant Pathology
Street address 700 Experiment Staion Road
City Lake Alfred
State/province Florida
ZIP/Postal code 33850
Country USA
 
Platform ID GPL5731
Series (1)
GSE33004 Regulation of gene expression by Candidatus Liberibacter asiaticus in stem and root of Sweet orange (Citrus Sinensis)

Data table header descriptions
ID_REF
VALUE log2 MAS 5.0 signal
ABS_CALL

Data table
ID_REF VALUE ABS_CALL
Cit.100.1.S1_x_at 12.62 P
Cit.1000.1.S1_s_at 7.75 P
Cit.10001.1.S1_at 3.28 A
Cit.10005.1.S1_s_at 11.63 P
Cit.10006.1.S1_at 6.77 P
Cit.10007.1.S1_s_at 10.77 P
Cit.10009.1.S1_s_at 10.80 P
Cit.1001.1.S1_at 5.03 P
Cit.1001.1.S1_s_at 8.51 P
Cit.10010.1.S1_at 6.18 P
Cit.10011.1.S1_s_at 9.46 P
Cit.10012.1.S1_at 4.21 A
Cit.10014.1.S1_s_at 10.58 P
Cit.10017.1.S1_s_at 10.12 P
Cit.1002.1.S1_s_at 2.49 A
Cit.10021.1.S1_s_at 10.21 P
Cit.10024.1.S1_s_at 8.64 P
Cit.10025.1.S1_at 6.40 P
Cit.10026.1.S1_at 3.30 A
Cit.10028.1.S1_at 8.90 P

Total number of rows: 30277

Table truncated, full table size 751 Kbytes.




Supplementary file Size Download File type/resource
GSM818248_8167_Wang_STH4_2.CEL.gz 3.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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