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Platform GPL8189 Query DataSets for GPL8189
Status Public on Sep 22, 2009
Title Colorado State University Mycobacterium tuberculosis V20071007
Technology type spotted oligonucleotide
Distribution non-commercial
Organism Mycobacterium tuberculosis H37Rv
Manufacturer Colorado State University TB Vaccine Testing and Research NIH, NIAID Contract No. HHSN266200400091C
Manufacture protocol Oligonucleotide 70mers were generated from whole genome sequence within coding regions. Features were designed to have similar hybridization temperatures. Samples were spotted and pre-processed using standard procedures from the lab of Rocky Mountain Regional Center of Excellence.
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Coating other
 
Description The Tuberculosis Genome Oligo Set consists of 70mer probes representing 4,269 M. tuberculosis (H37Rv and CDC1551) genes, plus 26 controls. The probes were designed from the predicted genomic sequence of the best-characterized M. tuberculosis strain, H37Rv, obtained from the Sanger Center (Cambridge, UK) and The Institute for Genomic Research (Rockville, MD, USA). An additional 371 probes were designed from the CDC1551 strain. The probes are Tm normalized to 79°C.
 
Web link http://www.cvmbs.colostate.edu/mip/tb/microarray.htm
Contributor(s) Karakousis P, Rifat D
Submission date Feb 12, 2009
Last update date Sep 22, 2009
Contact name Petros Karakousis
E-mail(s) petros@jhmi.edu
Phone 4105028233
Fax 4106148173
Organization name John Hopkins University school of medicine
Department Medicine
Lab The center for tuberculosis research
Street address 1550 Orleans street
City Baltimore
State/province MD
ZIP/Postal code 21231
Country USA
 
Samples (6) GSM371007, GSM371278, GSM371280, GSM371282, GSM371284, GSM371285
Series (1)
GSE14840 Phosphate depletion: A novel trigger for Mycobacterium tuberculosis persistence

Data table header descriptions
ID
Block Master grouping of rows and columns during spotting coinciding with spotting pins
Row Horizontally aligned spots
Column Vertically aligned spots
type Feature type(ORF, Negative_Control, Oligonucleotide_Control, No spot)
Name Name of transcription product
ORF Gene number for NCBI Genome NC_000962
ORGANISM Non-control spots represent organism Mycobacterium Tuberculosis H37Rv
SPOT_ID

Data table
ID Block Row Column type Name ORF ORGANISM SPOT_ID
ID-1 1 1 1 ORF Rv0205 Rv0205 Mycobacterium Tuberculosis H37Rv
ID-2 1 1 2 ORF Rv0207c Rv0207c Mycobacterium Tuberculosis H37Rv
ID-3 1 1 3 ORF Rv0209 Rv0209 Mycobacterium Tuberculosis H37Rv
ID-4 1 1 4 ORF pckA Rv0211 Mycobacterium Tuberculosis H37Rv
ID-5 1 1 5 ORF Rv0213c Rv0213c Mycobacterium Tuberculosis H37Rv
ID-6 1 1 6 ORF fadE3 Rv0215c Mycobacterium Tuberculosis H37Rv
ID-7 1 1 7 ORF Rv0229c Rv0229c Mycobacterium Tuberculosis H37Rv
ID-8 1 1 8 ORF fadE4 Rv0231 Mycobacterium Tuberculosis H37Rv
ID-9 1 1 9 ORF nrdB Rv0233 Mycobacterium Tuberculosis H37Rv
ID-10 1 1 10 ORF Rv0235c Rv0235c Mycobacterium Tuberculosis H37Rv
ID-11 1 1 11 ORF lpqI Rv0237 Mycobacterium Tuberculosis H37Rv
ID-12 1 1 12 ORF Rv0239 Rv0239 Mycobacterium Tuberculosis H37Rv
ID-13 1 1 13 ORF nirD Rv0253 Mycobacterium Tuberculosis H37Rv
ID-14 1 1 14 ORF cobQ Rv0255c Mycobacterium Tuberculosis H37Rv
ID-15 1 1 15 ORF Rv0257c Rv0257c Mycobacterium Tuberculosis H37Rv
ID-16 1 1 16 ORF Rv0259c Rv0259c Mycobacterium Tuberculosis H37Rv
ID-17 1 1 17 ORF narK3 Rv0261c Mycobacterium Tuberculosis H37Rv
ID-18 1 1 18 ORF Rv0263c Rv0263c Mycobacterium Tuberculosis H37Rv
ID-19 1 1 19 ORF Rv0277c Rv0277c Mycobacterium Tuberculosis H37Rv
ID-20 1 2 1 ORF PE_PGRS Rv0279c Mycobacterium Tuberculosis H37Rv

Total number of rows: 5168

Table truncated, full table size 332 Kbytes.




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