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Platform GPL15488 Query DataSets for GPL15488
Status Public on Jul 01, 2012
Title IBBA/CCG_Common bean_90K_v1.0 [condensed]
Technology type in situ oligonucleotide
Distribution custom-commercial
Organisms Glycine max; Phaseolus vulgaris
Manufacturer University of Verona - Scientific and Technological Department - Plant Functional Genomics Centre
Manufacture protocol Probes are directly synthesized on a 90k Combimatrix array by an in situ oligo synthesis system developed by CombiMatrix Corporation (Mukilteo, USA) using the CombiMatrix CustomArray synthesizer. Standard synthesis protocol provided by CombiMatrix was used.
Support silicon
Coating unknown
 
Description 18,883 specific oligos (35-40mer) were designed on Bean Gene Index Version 3 (Release 3.0. May 22, 2009) tentative consensus (TC) sequences and 11,205 specific oligos (35-40mer) were designed on Soybean UniGene Built #38 by using the program design OligoArray 2.1 (Rouillard et al. 2003). 141 oligonucleotides sequences provided by the manufacturer were used as quality and negative controls. The 90K BeanArrayTM 1.0 was designed with three replicates of each probe randomly distributed across the array to allow measurement of the variability within the array. All the procedures provided were performed as indicated by CombiMatrix protocols available at the CombiMatrix website (www.combimatrix.com).
 
Web link http://www.ibba.cnr.it
Contributor(s) Ferrarini R, Sparvoli F, Castiglioni B, Cremonesi P, Panzeri D, Hernández G, Ramírez M
Submission date Apr 24, 2012
Last update date Jul 01, 2012
Contact name Mario Ramírez
E-mail(s) mario@ccg.unam.mx
Phone +52 777 3115164
Organization name Centro de Ciencias Genomicas-UNAM
Department Functional Genomics of Eukaryotes
Lab IV
Street address Avenida Universidad S/N
City Cuernavaca
State/province Morelos
ZIP/Postal code 62210
Country Mexico
 
Samples (17) GSM923542, GSM923543, GSM1005290, GSM1005291, GSM1005292, GSM1005293 
Series (3)
GSE37638 Transcript Profiling of the Common Bean - Rhizobium Symbiosis under Oxidative Stress
GSE40935 Common bean (Phaseolus vulgaris) PvTIFY orchestrates global changes in transcript profile response to phosphorus deficiency
GSE83324 Transcriptional analysis of oxidative-stressed bean nodules elicited by Rhizobium etli expressing an heterologous globin (VHb)

Data table header descriptions
ID identifier
GB_ACC GenBank Accession number
ORGANISM
SPOT_ID TC_id#, control etc.
SEQUENCE

Data table
ID GB_ACC ORGANISM SPOT_ID SEQUENCE
QC-oligoB-AS-3 QC-oligoB-AS-3 GAGTTGCTGTTACATCAGCGAATGTGCATGGAACACACTT
QC-3prime QC-3prime TGACTGACTGGACTGTGGGTGTGCGATACGTGTCC
QC-5prime QC-5prime TGGGTGTGCGATACGTGTCCGACTGACTGACTGAC
QC-LLD-1 QC-LLD-1 AGATTTCTTCGGTTTCCCGTGGTTGGCGTCTGA
QC-LLD-2 QC-LLD-2 GGAGTATGTTCGGCTGCGCGAGAGCTATGATGCCG
QC-LLD-3 QC-LLD-3 GTGGCGATGTTAACCTCGGCTTATGGCGTCACCGG
QC-LLD-4 QC-LLD-4 CGAACATCCCAGGGTAACACGCA
QC-LLD-5 QC-LLD-5 ATCGCTTCGAATGATGTTACTCCGG
NC-SP-phage-03-3 NC-SP-phage-03-3 CACCGTAATTACTGTGAGCCATCATGACGCCGATG
NC-SP-phage-03-7 NC-SP-phage-03-7 GACGGTGATCGCATCGGTGCTGTTAACAAGTTCAT
NC-SP-phage-03-8 NC-SP-phage-03-8 AGTGGCTGAAACAGTTGTTGATTGAGTCTCTTTGG
NC-SP-phage-05-2 NC-SP-phage-05-2 CCATGATTACGCCAGTTGTACGGACACGAACTCAT
NC-SP-phage-05-1 NC-SP-phage-05-1 GGAGACGGGCAATCAGTTCATCTTTCGTCATGGAC
NC-SP-phage-05-16 NC-SP-phage-05-16 CCTGTCCGGCATAGCTGATATTTTCAGGGTCATCA
NC-SP-phage-06-1 NC-SP-phage-06-1 GACTCTCCGGATTAACTGGCGGTGACGGTAATTTC
NC-SP-phage-06-8 NC-SP-phage-06-8 TCATACATACCAGACAGCCGGTACACCACGTTTTC
NC-SP-phage-06-14 NC-SP-phage-06-14 GTCACACCGTTATGTTCAAATGATTCGGTTTTCAG
NC-SP-phage-08-9 NC-SP-phage-08-9 GTGACCATACCGTACAGGTTAGAAACCGTCAGCGT
NC-SP-phage-08-10 NC-SP-phage-08-10 GGATCGGCGTAACTGTTTCCGTTGACGAAGTTCAC
NC-SP-phage-08-13 NC-SP-phage-08-13 GGACAGAAAGCGTCACGCTGTACGTTTTCAGGTTG

Total number of rows: 30229

Table truncated, full table size 2411 Kbytes.




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Supplementary data files not provided
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