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Platform GPL6703 Query DataSets for GPL6703
Status Public on Apr 09, 2008
Title MERH03-S1-0003 (Rhodococcus sp. RHA1 11K)
Technology type spotted oligonucleotide
Distribution custom-commercial
Organism Rhodococcus jostii RHA1
Manufacturer The Microarray Facility of the Prostate Centre at Vancouver General Hospital
Manufacture protocol Oligonucleotides are consolidated into 384-well plates, lyophilized by speed-Vac, and resuspended in 3x SSC to a printing concentration of 30uM. Oligos are printed on aminosilane slides (Erie, Hudson, NH, USA) with a Biorobotics Microgrid II microarray printer (Genomic Solutions). Microspot 10K quill pins (Biorobotics) in a 48-pin tool were used to deposit <0.5 nL per spot onto the slide. The resulting microarrays have a 4 x12 subgrid layout with 392 spots per subgrid, each spot having approximate diameter and pitch of 90 µm and 190µm, respectively. A 280-bp GFP (green fluorescent protein) oligo was printed in subgrid corners to assist in placing on the grid. The slides were crosslinked in a UV Stratalinker 2400 (Stratagene) at 300mJ. Array quality was assessed by visual inspection and hybridization of representative slides from a print run by dye-labelled random 9-mer oligonucleotides. The quality control images were aquired via the ScanArray Express from Perkin Elmer at a 10 micron resolution and quantified with the Imagene 6.0 software suite.
Support glass
Coating aminosilane
 
 
Contributor(s) Anderson SA
Submission date Apr 07, 2008
Last update date Apr 20, 2008
Contact name Shawn Anderson
E-mail(s) shawn.anderson@vch.ca
Phone 604-875-4111 (63436)
Fax 604-875-5654
Organization name University of British Columbia
Department Urological Sciences
Lab Microarray Facility, Dr. Colleen Nelson
Street address The Prostate Centre at Vancouver General Hospital, 2660 Oak Street
City Vancouver
State/province B.C.
ZIP/Postal code V6H 3Z6
Country Canada
 
Samples (21) GSM281063, GSM282348, GSM282349, GSM282364, GSM282365, GSM282366 
Series (1)
GSE10378 Desiccation and control transcriptomes of Rhodococcus jostii RHA1

Data table header descriptions
ID
ORF_LIST locus tag(s)
SPOT_ID
manufID Microarray facility generated ID
METAROW Field row
METACOLUMN Field column
ROW Subgrid row
COLUMN Subgrid column
GENE_NAME
GENE_PRODUCT
SEQUENCE Oligo probe sequence
RO_ALIGN first base of the alignment of the probe to the sequence
OLIGO_ID
ELEMENT genetic element in the organism the probe is from
ORGANISM
manufPLATE Microarray facility generated plate ID
COMMENT

Data table
ID ORF_LIST SPOT_ID manufID METAROW METACOLUMN ROW COLUMN GENE_NAME GENE_PRODUCT SEQUENCE RO_ALIGN OLIGO_ID ELEMENT ORGANISM manufPLATE COMMENT
1 --CONTROL_GFP oligo GFP Oligo 1 1 1 1 CAATTGGCGATGGCCCTGTCCTTTTACCAGACAACCATTACCTGTCCACACAATCTGCCCTTTCGAAAGA GFP Oligo XX0001-P1-0035-DE037-001-A12 GFP
2 RHA1_ro04037 RHA1_03456__05412 1 1 1 2 possible PPE family protein CTGAAGAACTTCGAGCACTTCTCCGACGGGCGCACCGTCATTCCGTCGGTCATCGGCGCGAACCCCGACC chRHL_ro04037_1513 12074 Chromosome Rhodococcus sp. RHA1 MERH03-P1-0027-DE034-001-A12 Sample
3 RHA1_ro04517 RHA1_03464__04135 1 1 1 3 hydantoin racemase GAAGCGTAGGTCGACGAACGTGCACATCAAGATCATCAATCCCAACACCACCCAGTCGATGACCGACAAG 12076 Chromosome Rhodococcus sp. RHA1 MERH03-P1-0027-DE034-001-E12 Sample
4 RHA1_ro03143| RHA1_ro08544| RHA1_ro07028 RHA1_03507__06970 1 1 1 4 ABC Fe(3+)-transporter, permease protein SfuB CGTTCATCATGATCGTGCTGTCGCTGCCGATGACGTACGTGCTCTTCTCCCAGTCGAAAAAGGTAGCGGG pRHL1_ro08544_1490 12078 Chromosome Rhodococcus sp. RHA1 MERH03-P1-0027-DE034-001-I12 Sample
5 RHA1_ro11288 RHA1_03529__05169 1 1 1 5 conserved hypothetical protein GGCCGTGGAACATGCGTCCGGTCGGCAAGCAGCGCCGCTACATCCAGAACGAGGGCTTGGTCGTGGCGAA pRHL3_ro11288_443 12080 Plasmid3 Rhodococcus sp. RHA1 MERH03-P1-0027-DE034-001-M12 Sample
6 RHA1_ro04535 RHA1_04052__06086 1 1 1 6 hsaF 4-hydroxy-2-oxovalerate aldolase GAACTCATCTCGATCGCCGTCGACACGGCGAAGAACGCGAAGATCGCCTTCCTCATGCTGCCCGGGCTGG chRHL_ro04535_244 12122 Chromosome Rhodococcus sp. RHA1 MERH03-P1-0027-DE034-001-A24 Sample
7 RHA1_ro05415| RHA1_ro03847| RHA1_ro06254| RHA1_ro03317 RHA1_04065__04897 1 1 1 7 conserved hypothetical protein GCGCGAAAATCAAGTGATCGCCATCGAGGATCTGAGTGTGCGGAACATGGTCAAGAATCGGTCGTTGTCT chRHL_ro03847_876 12124 Chromosome Rhodococcus sp. RHA1 MERH03-P1-0027-DE034-001-E24 Sample
8 RHA1_ro05131 RHA1_04075__02674 1 1 1 8 metabolite transporter, MFS superfamily GCCGCGCGGTCCGACGCGCTACTGGCGTTCTCCTTCTGCCAGTTCTGCGCGATCTTCCTGGTCCTCGGAT chRHL_ro05131_835 12126 Chromosome Rhodococcus sp. RHA1 MERH03-P1-0027-DE034-001-I24 Sample
9 RHA1_ro10437 RHA1_04109__07185 1 1 1 9 conserved hypothetical protein CTCCGGCCAACTGCCGTTGCGAGACGGACAAATGCTCTCACCTGGAAAGGTGGGTGCCGAGATCAGCCTC pRHL2_ro10437_147 12128 Plasmid2 Rhodococcus sp. RHA1 MERH03-P1-0027-DE034-001-M24 Sample
10 --Buffer 3xSSC 1 1 1 10 3xSSC MERH03-P1-0028-DE034-001-A12 Buffer
11 --Buffer 3xSSC 1 1 1 11 3xSSC MERH03-P1-0028-DE034-001-E12 Buffer
12 --Buffer 3xSSC 1 1 1 12 3xSSC MERH03-P1-0028-DE034-001-I12 Buffer
13 --Buffer 3xSSC 1 1 1 13 3xSSC MERH03-P1-0028-DE034-001-M12 Buffer
14 --Buffer 3xSSC 1 1 1 14 3xSSC MERH03-P1-0028-DE034-001-A24 Buffer
15 --Buffer 3xSSC 1 1 1 15 3xSSC MERH03-P1-0028-DE034-001-E24 Buffer
16 --Buffer 3xSSC 1 1 1 16 3xSSC MERH03-P1-0028-DE034-001-I24 Buffer
17 --Buffer 3xSSC 1 1 1 17 3xSSC MERH03-P1-0028-DE034-001-M24 Buffer
18 --CONTROL_GFP oligo GFP Oligo 1 1 1 18 CAATTGGCGATGGCCCTGTCCTTTTACCAGACAACCATTACCTGTCCACACAATCTGCCCTTTCGAAAGA GFP Oligo XX0001-P1-0035-DE037-001-A12 GFP
19 RHA1_ro02018 RHA1_01672 1 1 2 1 probable amino acid transporter TTTCCGACGCCATCGCGCGTTCGTTCGCCACCGGCGAGCCCGAACGTCAG chRHL_ro02018_11 11306 Chromosome Rhodococcus sp. RHA1 MERH03-P1-0025-DE034-001-A12 Sample
20 RHA1_ro05388 RHA1_01712 1 1 2 2 amino acid transporter, APC family GCGAAGGGCCTCAACAGCGGGGCACTGGGATTGATCGGCAACACGGTGAT chRHL_ro05388_67 11308 Chromosome Rhodococcus sp. RHA1 MERH03-P1-0025-DE034-001-E12 Sample

Total number of rows: 11232

Table truncated, full table size 2269 Kbytes.




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