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Platform GPL4908 Query DataSets for GPL4908
Status Public on Jun 08, 2007
Title Scoelicolor_UMN_Def_v1.0
Technology type spotted DNA/cDNA
Distribution non-commercial
Organism Streptomyces coelicolor
Manufacturer University of Minnesota - Chemical Engineering and Materials Science - Hu lab
Manufacture protocol The following text is taken from the authors' previous publication - Mehra et al., "A framework to analyze multiple time series data: a case study with Streptomyces coelicolor", J Ind Microbiol Biotechnol, 2006 Feb;33(2):159-72.
"A whole genome cDNA microarray was constructed for
S. coelicolor. Gene-specific probes with an average
length of 500 bp were designed based on the genomic
sequence database at Sanger Center to represent the
7,825 genes. The primers to amplify these probes were
designed to be 20 bp in length with a melting temperature
around 62 deg C. An iterative primer/probe design
process was adopted. The primers were first Blasted
against the entire genome to check for the specificity to
the corresponding genes. The probe sequences resulting
from these primers were also blasted against the entire
genome to check for possible cross-hybridization with
sequences other than the corresponding gene. Any primer
pair that may give rise to a potentially croshybridizing
probe sequence was redesigned with alternate
coordinates. This probe checking-redesign process
minimized the possibility of cross-hybridization between
a probe and other cDNA species. For some highly
homologous genes, a unique probe was not attainable
and a multigene probe was used. A multigene probe was
designed in such cases. 7,581 genes were successfully
amplified and spotted on the microarray. The microarray
was fabricated on poly-L-lysine slides with duplicate
spots for each probe."
Support glass
Coating polysine
 
 
Web link http://hugroup.cems.umn.edu/Protocols/protocol.htm
Contributor(s) Lian W, Jayapal KP, Mehra S
Submission date Mar 01, 2007
Last update date Jun 08, 2007
Contact name Karthik P Jayapal
E-mail(s) [email protected]
Organization name University of Minnesota
Department Chemical Engineering and Materials Science
Lab Hu lab
Street address 421 Washington Ave SE
City Minneapolis
State/province MN
ZIP/Postal code 55414
Country USA
 
Samples (238) GSM172586, GSM172592, GSM172797, GSM172822, GSM172823, GSM172824 
Series (19)
GSE7167 S. lividans TK21 - S. coelicolor M145 Comparative Genomic Hybridizations
GSE7172 S. coelicolor Wild Type R5- Medium Time-course Study
GSE8084 S. coelicolor Wild Type Time-course Study in R5- medium (Culture#1)

Data table header descriptions
ID
SCO# Gene ID from primary annotation (http://streptomyces.org.uk)
Probe_Start Start location (in bp) of spotted probe from coding sequence start site
Probe_End End location (in bp) of spotted probe from coding sequence start site
Block Location id of block in printed array
Column_1 Column location id of printed spot in block (replicate 1)
Row_1 Row location id of printed spot in block (replicate 1)
Column_2 Column location id of printed spot in block (replicate 2)
Row_2 Row location id of printed spot in block (replicate 1)
ORF GenBank Identifier

Data table
ID SCO# Probe_Start Probe_End Block Column_1 Row_1 Column_2 Row_2 ORF
SCO0001 SCO0001 59 566 9 4 15 13 6 SCO0001
SCO0003 SCO0003 1237 1767 44 7 14 16 5 SCO0003
SCO0005 SCO0005 1446 1993 20 3 11 12 2 SCO0005
SCO0008 SCO0008 1 333 14 8 7 18 17 SCO0008
SCO0009-a SCO0009 109 162 40 7 12 16 3 SCO0009
SCO0009-long SCO0009 14 306 23 4 2 14 12 SCO0009
SCO0012 SCO0012 3 395 21 9 13 18 4 SCO0012
SCO0013 SCO0013 19 259 4 2 13 11 4 SCO0013
SCO0014 SCO0014 6 273 15 5 19 14 10 SCO0014
SCO0015 SCO0015 43 560 32 5 11 14 2 SCO0015
SCO0016 SCO0016 4 148 10 8 19 17 10 SCO0016
SCO0017 SCO0017 54 339 37 4 9 14 19 SCO0017
SCO0018 SCO0018 167 681 38 9 18 18 9 SCO0018
SCO0019 SCO0019 1 197 36 8 19 17 10 SCO0019
SCO0020 SCO0020 558 1086 22 2 11 11 2 SCO0020
SCO0021 SCO0021 81 589 39 1 8 11 18 SCO0021
SCO0022 SCO0022 10 508 35 1 11 10 2 SCO0022
SCO0025 SCO0025 4 214 19 6 2 16 12 SCO0025
SCO0026 SCO0026 60 495 4 2 9 12 19 SCO0026
SCO0027 SCO0027 19 298 11 1 19 10 10 SCO0027

Total number of rows: 7629

Table truncated, full table size 332 Kbytes.






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Supplementary file Size Download File type/resource
GPL4908.gal.gz 94.0 Kb (ftp)(http) GAL

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