Spotted Oligonucleotide array

The oligonucleotides spotted onto the array were designed by MWG from the EMBL release (accession number AL645882) of the Streptomyces coelicolor genome and the SCP1 sequences.

Coverage

Genes with a

Chromosome

SCP1

Total

Unique probe

7563

195

7758

Non-unique probe*

60

77

137

Alternative probe**

64

75

121

Cross_hybridising probe***

120

8

128

No probe

33

3

36

 

*Probes that have matches of 35-50bp out of 50bp in multiple genes. **Genes that have not been assigned to any probe as they cross-hybridise to existing gene probes (these hybridise to probes in the non-unique probe list). ***Probes that have matches of 35-49bp out of 50bp in multiple genes.

Controls

Positives - Oligos for the 16s and 23s rRNA genes

Negatives - Oligos vs PA0079, PA3222 and MWG's Arabidopsis control mwgaracontrol#003. MWG have included at least one Arabidopsis control per plate.

Mismatch - mismatches of 5, 10 and 15 spread evenly across a probe and a stretch of 5 and 10 contiguous non-homology in the centre of a probe. The probe used as the basis for these mismatch oligos was the one for SCO4721. See table below for details (lower case sequence letters indicate mismatch).

 

Oligo

Sequence

Mismatch

mwgsco4548m5

CCTGcTGGCCAAGGcTGCCGTTCGgAAGAACAGCgTCGTCAAGGgCCTCG

mismatch at pos 5, 15, 25, 35 and 45 to SCO4721

mwgsco4548m10

CCaGGTGcCCAAcGGTGgCGTTgGCAAcAACAcCCTCcTCAAtGTCCaCG

mismatch at pos 3, 8, 13, 18, 23, 28, 33, 38, 43 and 48 to SCO4721

mwgsco4548m15

CCTGcTGcCCtAGcGTcCCcTTgGCtAGtACtGCgTCcTCtAGcTCgTCG

mismatch at pos 5, 8, 11, 14, 17, 20, 23, 26, 29, 32, 35, 38, 41, 44 and 47 to SCO4721

mwgsco4548s5

CCTGGTGGCCAAGGGTGCCGTTgcgttGAACAGCCTCGTCAAGGTCCTCG

mismatch at pos 23-28 to SCO4721

mwgsco4548s10

CCTGGTGGCCAAGGGTaaagcgttcttCAGCCTCGTCAAGGTCCTCG

mismatch at pos 18-28 to SCO4721

 

 

Grid Map

 

SCo3

Page Owner: bss2el
Page Created: Monday 27 July 2009 18:35:09 by t00345
Last Modified: Tuesday 12 December 2017 12:01:07 by t00345
Expiry Date: Wednesday 27 October 2010 10:55:20
Assembly date: Tue Dec 12 12:01:35 GMT 2017
Content ID: 10726
Revision: 1
Community: 1020

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