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Platform GPL7620 Query DataSets for GPL7620
Status Public on Sep 01, 2009
Title JCVI Pseudomonas fluorescens Pf-5 23k v1.0
Technology type mixed spotted oligonucleotide/cDNA
Distribution non-commercial
Organism Pseudomonas protegens Pf-5
Manufacturer J. Craig Venter Institute
Manufacture protocol Unique 70-mer oligonucleotides were designed for 6147 genes of the Pseudomonas fluorescens Pf-5 genome. Oligonucleotides were suspended in 50% DMSO and spotted onto Corning UltraGAPS slides using an Intelligent Automation Systems arrayer. Each gene is represented three times on the array. Negative controls include 50% DMSO / 50% DI water and air. Arabidopsis spike-in controls and Arabidopsis 70-mer oligonucleotides were used as positive controls. Slides were air dried for at least 30 minutes after printing. DNA was irreversibly cross-linked to the slides with 250 mJ/cm^2 UV energy by using a Stratagene Stratalinker. Slides were stored at room temperature in a dessicator.
Support glass
Coating aminosilane
 
 
Contributor(s) Paulsen IT, Loper J, Phillippy KH, Johnson DA
Submission date Nov 10, 2008
Last update date Sep 01, 2009
Contact name Ian Paulsen
E-mail(s) ipaulsen@cbms.mq.edu.au
Organization name Macquarie University
Department Department of Chemistry and Biomolecular Sciences
Street address Macquarie University
City Sydney
State/province NSW
ZIP/Postal code 2109
Country Australia
 
Samples (18) GSM406443, GSM406444, GSM406445, GSM406446, GSM406447, GSM406448 
Series (3)
GSE16898 Inactivation of the GacA response regulator in Pseudomonas fluorescens Pf-5 has far-reaching transcriptomic consequences
GSE38632 The rpoS transcriptome of Pseudomonas protegens Pf-5 grown in rich medium
GSE38633 Genes expressed by the biological control bacterium Pseudomonas protegens Pf-5 on seed surfaces under the control of the global regulators GacA and RpoS

Data table header descriptions
ID
row feature coordinate within tiff image
column feature coordinate within tiff image
meta_row feature coordinate within tiff image
meta_column feature coordinate within tiff image
sub_row feature coordinate within tiff image
sub_column feature coordinate within tiff image
block feature coordinate within tiff image
feat_name feature name
ORF_ID Open reading frame identifier
ORF locus tag
SPOT_ID alternative spot identifier
description gene product or control feature description
GENOME_ACC Genome accession number
SEQUENCE sequence of spotted 70mer oligonucleotide if applicable

Data table
ID row column meta_row meta_column sub_row sub_column block feat_name ORF_ID ORF SPOT_ID description GENOME_ACC SEQUENCE
1 1 1 1 1 1 1 1 A12g14610a_219 NULL --positional_control positional_control NC_003071 TTGTCCTTACACACATTTTTCCTAATATTGTTTCGTATCGGTAGCTTTGCCATTGTTGATATATTTTTTT
2 1 2 1 1 1 2 1 orf00956 PFL1532 PFL_1532 3-oxoacyl-(acyl-carrier-protein) synthase III NC_004129 [AminoC6]GGCGGATCGGAATAAAGCGATGCCAGAAACGGCTCCCTTGGCGGGAGTCGTCCCTTTACGGTTTGGCACG
3 1 3 1 1 1 3 1 orf02370 PFL2503 PFL_2503 conserved hypothetical protein NC_004129 [AminoC6]GCGCGGGGGCCGAAAGGCACCGCTGCCTATTATTCAATGAACCAGGGACAGGTGATGGACAAGATCATGC
4 1 4 1 1 1 4 1 orf04440 PFL3841 PFL_3841 hypothetical protein NC_004129 [AminoC6]ATTATCGCCTGGCGGAGTCGGATGGCCGGCTGTGGTGCTCGCCCTCTCAGTACTACCTGTACAACCGTGA
5 1 5 1 1 1 5 1 orf05846 PFL4834 PFL_4834 conserved hypothetical protein NC_004129 [AminoC6]ATCGTTTTGTGTTACCGGCGGCCACGGTCGAAGAAGAATTCAGGCAAGCCGGCTTTCGTGTCCAGGAGCA
6 1 6 1 1 1 6 1 orf07284 PFL5843 PFL_5843 metW protein NC_004129 [AminoC6]CCGGTCTCGGAGTTCCTCCCGTACACCTGGTACAACACGCCGAACATCCACTTCTGCACCTTCGAGGACT
7 1 7 1 1 1 7 1 orf08733 PFL0585 PFL_0585 hypothetical protein NC_004129 [AminoC6]CTGACCCAGGTTCTTGCCCGCCAACGGATCGAAAGCCAGATAAACCTGCCGCGTCTGTTTGCCGCCATCG
8 1 8 1 1 1 8 1 orf00386 PFL1132 PFL_1132 CheW domain protein NC_004129 [AminoC6]ACCGCATCGGTATCCATGGCGACAAGTCCTGCCCGTTGCTGGTCGAGCACATTCATTGCCGCAACTGCTC
9 1 9 1 1 1 9 1 orf01754 PFL2105 PFL_2105 ribokinase NC_004129 [AminoC6]CAGTGGTATGGCGCGATCGACTACCTGATTCCCAACGAGAGCGAGGCTTCGGCCTTGAGCGGGGTAGCGG
10 1 10 1 1 1 10 1 orf03288 PFL3082 PFL_3082 polysaccharide biosynthesis/export protein NC_004129 [AminoC6]GCTGGCGGACGTGATCATGTTCCAGGGTGTCGGGTTCAGCTTCGGCTACCGCGTCGACAACAAAGAAACG
11 1 11 1 1 1 11 1 orf04751 PFL4048 PFL_4048 hypothetical protein NC_004129 [AminoC6]GGCGCGGATAAAAATTTCATTTGCCCGCGACGGATTCCCCGCCCATCTATCGTTGAACCCATCAGCTGCG
12 1 12 1 1 1 12 1 orf06696 PFL5427 PFL_5427 phosphomethylpyrimidine kinase NC_004129 [AminoC6]TCGCCGCCCATGAATATCTACAGCTCTCGCCCCGTTGTCCTCTGTCTCTCCGGCCACGACCCCAGTGGTG
13 1 13 1 1 1 13 1 orf08130 PFL0185 PFL_0185 succinate-semialdehyde dehydrogenase NC_004129 [AminoC6]GGGCCGTGAAGGTTCCAAGTACGGGATCGAGGATTACCTGGAAATCAAATACCTCTGCCTGGGTATCTGA
14 1 14 1 1 1 14 1 NULL NULL blank blank NULL
15 1 15 1 1 1 15 1 orf00660 PFL1338 PFL_1338 conserved hypothetical protein NC_004129 [AminoC6]AGGCGTTACGCCGGCATCGTCATCGACGTGTTCTTCGACCATTGCCTGGCCCGGGATTGGCAGCATTACG
16 1 16 1 1 1 16 1 orf02656 PFL2683 PFL_2683 transporter, LysE family NC_004129 [AminoC6]CTGGCGGTGGTGCTGCAAGCCTCGGAGCTGTTGTTCTACGGGATCAAGATTCTCGGCGCGGGCTACCTGC
17 1 17 1 1 1 17 1 orf04163 PFL3648 PFL_3648 aldehyde dehydrogenase family protein NC_004129 [AminoC6]CCCGGGACGGTGCGCGTCAGTTGCGCATGGCTCACAAGCTGCGCTGTGGCCAGGTGTTCATCAACAACTA
18 1 18 1 1 1 18 1 orf05610 PFL4638 PFL_4638 conserved hypothetical protein NC_004129 [AminoC6]TACAACCTGTGCATTGACTACGAAGTGGCCCACGACCCCAAGGAGGGCAAGGGCATGCTGTTCACCCTGC
19 1 19 1 1 1 19 1 orf06976 PFL5648 PFL_5648 4-hydroxythreonine-4-phosphate dehydrogenase NC_004129 [AminoC6]ACCACGACCAAGGCTTGCCTGTGCTGAAATACAAAGGCTTCGGCGCGGCCGTCAACGTGACGCTCGGCTT
20 1 20 1 1 1 20 1 orf09009 PFL0770 PFL_0770 transcriptional regulator, LysR family NC_004129 [AminoC6]TGCCGCCAGAGGACTCATGTGAAAGCCCGATCCGACGAGTTGCAAGTCTTCGTCTGTGTCATCGAGTGCG

Total number of rows: 23232

Table truncated, full table size 3500 Kbytes.




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