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Platform GPL7627 Query DataSets for GPL7627
Status Public on Nov 14, 2008
Title Rhodococcus sp. RHA1 13.8K MERH03-S1-0004
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 Nov 12, 2008
Last update date Nov 17, 2008
Contact name Jacques Mathieu
E-mail(s) mathieu@rice.edu
Phone 703-307-5802
Organization name Rice University
Department Civil and Environmental Engineering
Street address 6100 Main St. MS-317
City Houston
State/province TX
ZIP/Postal code 77005
Country USA
 
Samples (17) GSM552937, GSM552938, GSM552939, GSM553692, GSM553693, GSM553694 
Series (5)
GSE22214 Transition phase, Rhododoccus jostii RHA1 was grown in W minimal liquid medium with biphenyl
GSE22238 stationary phase, Rhododoccus jostii RHA1 was grown in W minimal liquid medium with biphenyl
GSE22239 solid-support dependent genes, Rhododoccus jostii RHA1 cells were grown on membrane filter placed on W minimal 2%-agar solid medium with vapor of biphenyl

Data table header descriptions
ID
ORF
SPOT_ID
manufID Microarray facility generated ID
METAROW Field row
METACOLUMN Field column
ROW Subgrid row
COLUMN Subgrid column
GENENAME
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 SPOT_ID manufID METAROW METACOLUMN ROW COLUMN GENENAME GENE_PRODUCT SEQUENCE RO_ALIGN OLIGO_ID ELEMENT ORGANISM manufPLATE COMMENT
1 --CONTROL_GFP oligo GFP Oligo 1 1 1 1 null GFP Oligo XX0001-P1-0035-DE037-001-A12 GFP
2 RHA1_ro10279 RHA10435_61 1 1 1 2 possible transposase CCCATCGAATCGATCTTCGCGACTGTACGTTTGAGGACCAGAGTGACGAAGGGCCCAGGCTCGCGAACAG pRHL2_ro10279_61 6644 Plasmid2 Rhodococcus jostii RHA1 MERH03-P1-0005-GA001-001-E12 Sample
3 RHA1_ro10441 RHA10469_71 1 1 1 3 conserved hypothetical protein ATCCGGACCCGGTTGATCCGAACCTCGTGCGTTATTGGGATGGCGCTCAGTGGACCGGGGACACCCGGCC pRHL2_ro10441_71 6668 Plasmid2 Rhodococcus jostii RHA1 MERH03-P1-0005-GA001-001-I12 Sample
4 RHA1_ro11091 RHA10537_1161 1 1 1 4 conserved hypothetical protein CAACGCCGCAATTTGTATGGGACGACGGGACGCACACCTGCTCCTGGCAGGCACAGACCAGCCACCCTGG pRHL3_ro11091_1161 6692 Plasmid3 Rhodococcus jostii RHA1 MERH03-P1-0005-GA001-001-M12 Sample
5 RHA1_ro10152 RHA10411_91 1 1 1 5 hypothetical protein CTGCAGTCGGATTCACAAAGAGCGGATTCGAGAGATGGTCATACGGGTGGTCATCAGAATGACTATATGA pRHL2_ro10152_91 6626 Plasmid2 Rhodococcus jostii RHA1 MERH03-P1-0005-GA001-001-A24 Sample
6 RHA1_ro10348 RHA10445_121 1 1 1 6 conserved hypothetical protein TTTACGGTGGCTACCGTGATCTCTACGCTTGGATACGCCATCGTGGGTTGGTACATTTTGATTGCCTGGC pRHL2_ro10348_121 6650 Plasmid2 Rhodococcus jostii RHA1 MERH03-P1-0005-GA001-001-E24 Sample
7 RHA1_ro11035 RHA10502_481 1 1 1 7 probable 3-hydroxybutyryl-CoA dehydratase CTACTTCTGACCGGACGTACCGTCAACGCATCCGAGGCGCTACACCTCGGACTTGTCAATGAAGTTGCCC pRHL3_ro11035_481 6674 Plasmid3 Rhodococcus jostii RHA1 MERH03-P1-0005-GA001-001-I24 Sample
8 RHA1_ro11117 RHA10556_231 1 1 1 8 conserved hypothetical protein GGTGCGTAGTTGGTTCCTCGCGGTCGCGGTCACGACGGGTGTGGATGTGGCGGTGCCGAGGACAACGGAG pRHL3_ro11117_231 6698 Plasmid3 Rhodococcus jostii RHA1 MERH03-P1-0005-GA001-001-M24 Sample
9 RHA1_ro05468 RHA08187_6361 1 1 1 9 non-ribosomal peptide synthetase GAGCGGATCGCGTACGTCGTGGCAACCGCCGGTCCAATCGTCGTTCTCACCATGACCGCCGATCGCGTCG chRHL_ro05468_6361 7000 Chromosome Rhodococcus jostii RHA1 MERH03-P1-0006-GA001-001-A12 Sample
10 RHA1_ro04715 RHA05952_14421 1 1 1 10 non-ribosomal peptide synthetase ACTCACCGATTTCATGGCCGCACACGCCGTGACGCACGCGATCATTCCGCCGTCCCTGCTGGCTGCTCTG chRHL_ro04715_14421 7024 Chromosome Rhodococcus jostii RHA1 MERH03-P1-0006-GA001-001-E12 Sample
11 RHA1_ro05452 RHA08037_19411 1 1 1 11 non-ribosomal peptide synthetase ACCAACACAGCAAAATTCGATCTCCACGTGACAGTGCGCGAGCGATGGGACGGTAACGATCCCGCAGGGA chRHL_ro05452_19411 7048 Chromosome Rhodococcus jostii RHA1 MERH03-P1-0006-GA001-001-I12 Sample
12 RHA1_ro08187 RHA09138_1 1 1 1 12 conserved hypothetical protein ATGCACCATCTGATCGTCTGTTACGGCCACCCGGACGAACCCGCGTCCTTCGACCAGTACTACAGCACCA pRHL1_ro08187_1 7072 Plasmid1 Rhodococcus jostii RHA1 MERH03-P1-0006-GA001-001-M12 Sample
13 RHA1_ro01426 RHA03504_9041 1 1 1 13 probable fatty-acyl-CoA synthase AGCAGTTCCCCCTGAAGGCCGGTCTGCTCACGAGCCTGGGCTTCGGTCACGTCTCCGGACTGATCGCCGT chRHL_ro01426_9041 7006 Chromosome Rhodococcus jostii RHA1 MERH03-P1-0006-GA001-001-A24 Sample
14 RHA1_ro05468 RHA08187_12421 1 1 1 14 non-ribosomal peptide synthetase GCGGCGATGGATCGATGGAATGCCACAGCCGTGGTTGTCGAGGGCGGGACACTCGTGCAGCTCTTCGACG chRHL_ro05468_12421 7030 Chromosome Rhodococcus jostii RHA1 MERH03-P1-0006-GA001-001-E24 Sample
15 RHA1_ro00141 RHA07392_23931 1 1 1 15 non-ribosomal peptide synthetase CGAGAACCCGACGCTGGAACTGCCGGATCTGCGGGTCGAGAACGTGGACCTCGAAACCAAGGTGGTGAAA chRHL_ro00141_23931 7054 Chromosome Rhodococcus jostii RHA1 MERH03-P1-0006-GA001-001-I24 Sample
16 RHA1_ro00393 RHA02853_435 1 1 1 16 cytochrome P450 CYP255 GCTGCCGACTCGGATCTTCCTTGCGCTCATGGGATGGCCACTGAGCGACGCACCACAGTTCACGGAGTGG chRHL_ro00393_435 7078 Chromosome Rhodococcus jostii RHA1 MERH03-P1-0006-GA001-001-M24 Sample
17 Empty Empty 1 1 1 17 Empty null null 0
18 --CONTROL_GFP oligo GFP Oligo 1 1 1 18 null GFP Oligo XX0001-P1-0035-DE037-001-A12 GFP
19 RHA1_ro00205 RHA07151_231 1 1 2 1 gas vesicle synthesis protein CGGCAGTGGCGAGCCGAAAGGCCTGACGGATCTGGTCGGGGACGTCACCGAGGGAGGCGCCAAATCGAAG chRHL_ro00205_231 5908 Chromosome Rhodococcus jostii RHA1 MERH03-P1-0003-GA001-001-I12 Sample
20 RHA1_ro00557 RHA07347_141 1 1 2 2 possible transcriptional regulator GGTCGCCTCGACTCTCGGCTACGCATCTCCCGCAGCCTTCTCCTTCGCCTTCAGCCGCGAGTTCGGAATG chRHL_ro00557_141 5932 Chromosome Rhodococcus jostii RHA1 MERH03-P1-0003-GA001-001-M12 Sample

Total number of rows: 13824

Table truncated, full table size 2688 Kbytes.




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