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Status
Public on Dec 25, 2010
Title
Affymetrix Rice Genome Array (custom CDF)
Technology type
in situ oligonucleotide
Distribution
custom-commercial
Organism
Oryza sativa Manufacturer
Affymetrix
Manufacture protocol
see manufacturer's web site
Description
The custom CDF was built by uniquely mapping 442,810 probe sequences to 35,161 rice gene-based probe sets in the following manner: (i) probes that have perfect sequence identity with a single target gene were selected, (ii) probes mapping to reverse complements of genes were annotated separately as antisense probes (not used in the above counts), and finally, (iii) probes were grouped into probe sets, each corresponding to a single gene, and probe sets having at least 3 unique sequences were retained (>98% probe sets have >=5 probes). Note that these stringent criteria used to construct the CDF make it possible to reliably measure expression values of members of multigene families (free from cross-hybridization between paralogs showing high sequence similarity).
Submission date
Dec 15, 2010
Last update date
May 25, 2012
Contact name
Andy Pereira
E-mail(s)
[email protected] Phone
540-231-3784
Organization name
Virginia Tech
Department
Virginia Bioinformatics Institute
Lab
Plant Stress Systems Biology
Street address
Washington Street MC0477
City
Blacksburg
State/province
VA
ZIP/Postal code
24061
Country
USA
Samples (22)
GSM640584 , GSM640585 , GSM640586 , GSM640587 , GSM1493943 , GSM1493944
GSM1493945 ,
GSM1493946 ,
GSM2147527 ,
GSM2147528 ,
GSM2147529 ,
GSM2147530 ,
GSM2147531 ,
GSM2147532 ,
GSM2147533 ,
GSM2147534 ,
GSM2147535 ,
GSM2147536 ,
GSM2147537 ,
GSM2147538 ,
GSM2147539 ,
GSM2147540 Series (3)
GSE26092 Coordinated activation of cellulose and repression of lignin biosynthesis pathways in rice
GSE60936 Coordinated regulation of photosynthesis in rice increases yield and tolerance to environmental stress.
GSE81253 A resource for systems analysis of transcriptional modules involved in drought response in rice
Relations Affiliated with
GPL2025
Data table header descriptions ID Gene DESCRIPTION SPOT_ID
Data table ID Gene DESCRIPTION SPOT_ID AFFX-BioB-3_at
AFFX-BioB-3
Control
AFFX-BioB-5_at
AFFX-BioB-5
Control
AFFX-BioB-M_at
AFFX-BioB-M
Control
AFFX-BioC-3_at
AFFX-BioC-3
Control
AFFX-BioC-5_at
AFFX-BioC-5
Control
AFFX-BioDn-3_at
AFFX-BioDn-3
Control
AFFX-BioDn-5_at
AFFX-BioDn-5
Control
AFFX-CreX-3_at
AFFX-CreX-3
Control
AFFX-CreX-5_at
AFFX-CreX-5
Control
AFFX-DapX-3_at
AFFX-DapX-3
Control
AFFX-DapX-5_at
AFFX-DapX-5
Control
AFFX-DapX-M_at
AFFX-DapX-M
Control
AFFX-LysX-3_at
AFFX-LysX-3
Control
AFFX-LysX-5_at
AFFX-LysX-5
Control
AFFX-LysX-M_at
AFFX-LysX-M
Control
AFFX-Mgr-actin-3_at
AFFX-Mgr-actin-3
Control
AFFX-Mgr-actin-5_at
AFFX-Mgr-actin-5
Control
AFFX-Mgr-actin-M_at
AFFX-Mgr-actin-M
Control
AFFX-Mgr-ef1a-3_at
AFFX-Mgr-ef1a-3
Control
AFFX-Mgr-ef1a-3_x_at
AFFX-Mgr-ef1a-3_x
Control
37407 2717 Kbytes .Supplementary file Size Download File type/resource GPL11322_Rice_Affymetrix_Genome_Array.MSUv6.1.custom.CDF.gz
13.4 Mb
(ftp) (http) CDF
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