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Platform GPL8290 Query DataSets for GPL8290
Status Public on Mar 12, 2010
Title OSU Streptococcus pyogenes M1 and M18 microarray-SDHHbtail
Technology type spotted oligonucleotide
Distribution custom-commercial
Organism Streptococcus pyogenes
Manufacturer Pancholi Laboratory, OSU, Columbus; Public Health Res Institute-Newark
Manufacture protocol Sense strand oligonucleotides with mainly 55-mer, representing the 1,769 open reading frames (ORFs) in the genome of S. pyogenes Type M1, strain SF370 and 175 ORFs (those absent in SF370 strain) of Type M18 (Strain MGAS8232) were designed and produced by Illumina (http://www.illumina.com). They were obtained as 1.35 nmoles quantity at 50 uM concentration in 27 ul of water in shallow well plates.
Support glass
Coating polysine
 
Description The oligonucleotides were spotted onto poly-L-lysine microarray slides by a robotic microarrayer (Omni GRAD 100 microarrayer) using 12 pin spotter at the Center of Applied Genomics (CAGE) of the Public Health Research Institute, Newark, NJ. Arrays were distributed in 16 blocks each with 12 columns and 12 rows.
 
Contributor(s) Pancholi V, Jin H, Boel G
Submission date Mar 12, 2009
Last update date Mar 12, 2010
Contact name Vijay Pancholi
E-mail(s) vijay.pancholi@osumc.edu
Phone 614-688-8053
Organization name Ohio State University
Department Pathology
Lab Bacterial Pathogenesis
Street address 420W 12th Ave, TMRF-288
City Columbus
State/province OH
ZIP/Postal code 43210
Country USA
 
Samples (34) GSM380310, GSM380320, GSM380321, GSM380322, GSM380331, GSM380332 
Series (4)
GSE15231 Microarray analysis for differential gene expression in M1-SDHHbtail
GSE15546 Microarray analysis for Streptococcus pyogenes M1-CdhA (-) mutant
GSE15598 Microarray analysis of S. pyogenes Type M1-CdhA55(-) mutant

Data table header descriptions
ID
Name-Spot Spot reference numbaer
Block the position of an oligo-spot in a given Block
Column the position of an oligo-spot in a given column of the Block
Row the position of an oligo-spot in a given row of the Column and the block
Location Location of a gene in the M1SF370 genome
Strand Positive or negative orientation of the gene
Length Length of a gene product-aminoacid
Gene given gene name
Code One-letter abbreviations for the functional categories (Nucleic Acids Res, 28:33-36 (2000)
COG Clusters of Orthologous Groups of proteins
ORF Entrez Gene
SEQUENCE probe nucleotide sequence (5'-3')
SPOT_ID spot identifier
Main function Major functional categoty
subfunction specific function

Data table
ID Name-Spot Block Column Row Location Strand Length Gene Code COG ORF SEQUENCE SPOT_ID Main function subfunction
SPy0002 1039388-4-A11 9 3 6 232..1587 (+) 451 dnaA L COG0593 SPy0002 CATGCCTATAATAAAATCAAAAACATGATCAGCCAGGACGAAAGCCTTAGGATCGA DNA replication, recombination and repair Chromosomal initiator protein
SPy0003 1039388-4-B11 11 3 6 1742..2878 (+) 378 dnaN L COG0592 SPy0003 CTGAGGTTGGTAAGGTAAACGAGGATTTAGATATTGTTAGTCAGTCTGGTAGTGATTT DNA replication, recombination and repair beta subunit of DNA polymerase III
SPy0004 1039388-7-A08 5 5 4 2953..3150 (+) 65 SPy0004 CAGTGTACTAACTGTCAGCATGTGATTATGATGAGTCGTTATGATTTTGAGCGAA Function unknown conserved hypothetical protein
SPy0006 1039370-6-A04 6 7 2 3480..4595 (+) 371 R COG0012 SPy0006 TAAATTAACCAGAGCAGCTTATCATCTCTTAGGCCTTGGAACCTATTTTACAGCAG General function prediction only putative GTP-binding protein
SPy0007 1039361-4-A08 5 9 4 4665..5234 (+) 189 pth J COG0193 SPy0007 CCACATTGGAACTCAGGAATTTAACCGAATCAAAGTTGGTATTGGACGACCTTTAA Translation, ribosomal structure and biogenesis putative peptidyl-tRNA hydrolase
SPy0008 1039388-4-C11 9 3 12 5237..8740 (+) 1167 trcF L COG1197 SPy0008 TGAGCTTATGGATCGTTTTGGAGAGTATCCTGATCAAGTTGCCTATTTGTTAGAGA DNA replication, recombination and repair putative transcription-repair coupling factor
SPy0009 1039361-4-B08 7 9 4 8879..9175 (+) 98 J COG1188 SPy0009 CAGTAGCAAAAGAAGTTGCGGATAAGGGACGAATTAAAGTTAATGGGATACTTGC Translation, ribosomal structure and biogenesis conserved hypothetical proteins
SPy0010 1039388-7-B08 7 5 4 9162..9533 (+) 123 divIC SPy0010 GCTAGGGCAAAATACTATTTATCGCGTGAAGGAGAAATGATTTATCCTATTCCAGG Function unknown putative cell division protein (DivIC)
SPy0012 1039388-7-C08 5 5 10 9668..10954 (+) 428 SPy0012 GTGTTGAAGACCTACTGAAAGCTGTAGCACAACAATCGGATAATGTAGCAACTAATA Function unknown hypothetical protein
SPy0013 1039388-5-A11 14 3 6 10951..12237 (+) 428 D COG0037 SPy0013 GCTTTAGTAACAGCTCACCATTCAGATGATCAAGCAGAAACTATTTTGATGAGGC Cell division and chromosome partitioning putative cell-cycle protein
SPy0015 1039388-6-A09 10 3 5 12806..14785 (+) 659 ftsH O COG0465 SPy0015 CTCATAAATTGATTGCTGAAGCTCTTCTCAAATATGAAACTCTAGACGCTGCACA Posttranslational modification, protein turnover, chaperones putative cell division protein
SPy0016 1039388-3-A02 5 3 1 15110..16501 (+) 463 E COG0531 SPy0016 TCAAAATGCTACTCTTGTCACTGGACTACTTGCTATGATTTGTGCGGGAATATTTC Amino acid transport and metabolism putative amino acid permease
SPy0019 1039388-7-D08 7 5 10 30546..31742 (+) 398 SPy0019 CCGCTAATATGGCAATGGCTGAAGAAAACCAAAATACATTACGTACTCAACAAGCT Function unknown putative secreted protein
SPy0020 1039388-4-A03 9 3 2 31995..32957 (+) 320 prsA.2 F COG0462 SPy0020 AATTGCAGACTATTTTGATCGTCATGGTTTAGTGGGTGAAGATGTTGTCGTTGTTAGT Nucleotide transport and metabolism putative ribose-phosphate pyrophosphokinase
SPy0021 1039388-4-D11 11 3 12 33143..33898 (+) 251 L COG1381 SPy0021 GCACTGATTTACCGCTTGATTTTTCCCATCGTTTTTCAGCTGTACTTTGTTCTGAA DNA replication, recombination and repair conserved hypothetical protein
SPy0022 1039370-7-A10 1 1 5 34001..35008 (+) 335 plsX I COG0416 SPy0022 CGTGGTCGGACAATTAGTAGAAGAATTTGCTAAGGAGACTCAAGTAAATGACTAG Lipid metabolism putative fatty acid/phospholipid synthesis protein
SPy0023 1039370-7-B10 3 1 5 35001..35243 (+) 80 acpP.2 I COG0236 SPy0023 GACTAGACAGGAGATTTTTGAAAGGCTGATTAACTTAATTCAGAAGCAAAGAAGC Lipid metabolism putative acyl carrier protein
SPy0024 1039388-4-B03 11 3 2 35364..36098 (+) 244 purC F COG0152 SPy0024 ATGAACTCTTGAAAGGTTGGTTTGCTCAGATTGGGCTTAACTTGATTGACTTCAAG Nucleotide transport and metabolism putative phosphoribosylaminoimidazole - succinocarboxamide synthase (SAICAR synthetase)
SPy0025 1039388-4-C03 9 3 8 36174..39947 (+) 1257 SPy0025 ATCTGGAGCCAATATGTGGACTTTGACGGACAACCATCTATGGATTCTAAATACAAT Nucleotide transport and metabolism putative phosphoribosylformylglycinamidine synthase II
SPy0026 1039388-4-D03 11 3 8 40108..41562 (+) 484 purF F COG0034 SPy0026 AAGGATTGTCGGATTATTAAGAGAAGCAGGAGCTAGTGAAGTACATGTTGCTATAG Nucleotide transport and metabolism putative phosphoribosylpyrophosphate amidotransferase

Total number of rows: 1945

Table truncated, full table size 354 Kbytes.




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