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Status
Public on Sep 01, 2004
Title
UBEC Array2
Technology type
spotted oligonucleotide
Distribution
non-commercial
Organism
Escherichia coli
Description
The 70-mer oligonucleotide array was constructed, containing 6112 oligonucleotides that sampled chromosomal genes identified in the genome sequences of E. coli strains K-12 MG1655, O157:H7 VT2 Sakai, and O157:H7 EDL933 and plasmid genes from the two genome-sequenced O157:H7 strains (the Operon Array Ready E. coli Oligonucleotide set 1.0, Qiagen- Operon, Hilden, Germany). 12 positive and 12 negative control oligonucleotides were also included. The oligonucleotides were resuspended in 3 X SSC buffer and printed on to Corning GAPS II slides (Corning B.V Life Sciences, Schiphol-Rijk, Netherlands ) using a Biorobotics Microgrid TAS array printer. Amersham Lucidea array controls (Amersham Biosciences Ltd, Little Chalfont, UK) were printed in each subarray. After printing, slides were briefly rehydrated in steam, dried at 100oC, and UV-cross-linked according to the manufacturer's instructions. Slides were stored desiccated and in the dark until use.
Contributor(s)
Constantinidou C , Hobman JL , Penn CW , Patel M , Jones A Submission date
May 21, 2004
Last update date
May 26, 2005
Contact name
Chrystala Constantinidou
E-mail(s)
[email protected] Phone
+44 (0)121 414 5564
Organization name
University of Birmingham
Department
School of Biosciences
Lab
UBEC
Street address
City
Birmingham
ZIP/Postal code
B15 2TT
Country
United Kingdom
Samples (39)
GSM23459 , GSM23465 , GSM23467 , GSM30815 , GSM30816 , GSM30817
GSM30818 ,
GSM30819 ,
GSM30820 ,
GSM30821 ,
GSM30822 ,
GSM30823 ,
GSM82542 ,
GSM82543 ,
GSM82544 ,
GSM82545 ,
GSM82546 ,
GSM82547 ,
GSM82548 ,
GSM82549 ,
GSM82550 ,
GSM82551 ,
GSM82552 ,
GSM82553 ,
GSM82598 ,
GSM82600 ,
GSM82603 ,
GSM82604 ,
GSM82605 ,
GSM82606 ,
GSM82608 ,
GSM82610 ,
GSM82613 ,
GSM82616 ,
GSM82620 ,
GSM82621 ,
GSM116749 ,
GSM116750 ,
GSM116751 Series (4)
GSE1421 MelR experiment 1
GSE1780 The expression profile of Escherichia coli K-12 in response to minimal, optimal and excess copper concentrations
GSE3591 A reassesment of the FNR regulon and the effects of nitrate,nitrite, narXL and narQP
GSE5177 The role of multi-copper oxidase CueO
Data table header descriptions ID ARRAY_BLOCK Block (subarray) number
ARRAY_COL Column number (within subarray)
ARRAY_ROW Row number (within subarray)
GENE_SYMBOL Gene Name
GENE_DESC Gene description
K12_ORF_name E. coli K12 ORF name
O157H7_EDL933_ORF_name E. coli O157:H7 (EDL933) ORF name
O157H7_Sakai_ORF_name E.coli O157:H57 (Sakai) ORF name
Operon oligo_ID ID of Operon Array-Ready oligo
Source Plate Source Plate Column Source Plate Row ORF ORF name
SPOT_ID Column added by GEO staff to facilitate sequence tracking in Entrez GEO
Data table ID ARRAY_BLOCK ARRAY_COL ARRAY_ROW GENE_SYMBOL GENE_DESC K12_ORF_name O157H7_EDL933_ORF_name O157H7_Sakai_ORF_name Operon oligo_ID Source Plate Source Plate Column Source Plate Row ORF SPOT_ID 1
1
1
1
Cntrl:dnaK
Landing Light
b0014
Z0014
ECs0014
E100000014
1
12
a
b0014
2
1
2
1
Cntrl:dnaK
Landing Light
b0014
Z0014
ECs0014
E100000014
1
12
a
b0014
3
1
3
1
3x SSC
3x SSC
n/a
n/a
n/a
n/a
1
12
e
3x SSC
4
1
4
1
Ratio01
Ratio 1 (100 : 300)
n/a
n/a
n/a
n/a
1
12
I
Ratio 1 (100 : 300)
5
1
5
1
Ratio01
Ratio 1 (100 : 300)
n/a
n/a
n/a
n/a
1
12
I
Ratio 1 (100 : 300)
6
1
6
1
Ratio01
Ratio 1 (100 : 300)
n/a
n/a
n/a
n/a
1
12
I
Ratio 1 (100 : 300)
7
1
7
1
Ratio01
Ratio 1 (100 : 300)
n/a
n/a
n/a
n/a
1
12
I
Ratio 1 (100 : 300)
8
1
8
1
Ratio02
Ratio 2 (300 : 100)
n/a
n/a
n/a
n/a
1
12
m
Ratio 2 (300 : 100)
9
1
9
1
Ratio02
Ratio 2 (300 : 100)
n/a
n/a
n/a
n/a
1
12
m
Ratio 2 (300 : 100)
10
1
10
1
Ratio02
Ratio 2 (300 : 100)
n/a
n/a
n/a
n/a
1
12
m
Ratio 2 (300 : 100)
11
1
11
1
Ratio02
Ratio 2 (300 : 100)
n/a
n/a
n/a
n/a
1
12
m
Ratio 2 (300 : 100)
12
1
12
1
Ratio03
Ratio 3 (1000 : 3000)
n/a
n/a
n/a
n/a
1
24
a
Ratio 3 (1000 : 3000)
13
1
13
1
Ratio03
Ratio 3 (1000 : 3000)
n/a
n/a
n/a
n/a
1
24
a
Ratio 3 (1000 : 3000)
14
1
14
1
Ratio03
Ratio 3 (1000 : 3000)
n/a
n/a
n/a
n/a
1
24
a
Ratio 3 (1000 : 3000)
15
1
15
1
Ratio03
Ratio 3 (1000 : 3000)
n/a
n/a
n/a
n/a
1
24
a
Ratio 3 (1000 : 3000)
16
1
16
1
3x SSC
3x SSC
n/a
n/a
n/a
n/a
1
12
e
3x SSC
17
1
17
1
3x SSC
3x SSC
n/a
n/a
n/a
n/a
1
12
e
3x SSC
18
1
18
1
Cntrl:dnaK
Landing Light
b0014
Z0014
ECs0014
E100000014
1
12
a
b0014
19
1
1
2
b0100
orf, hypothetical protein
b0100
Z0110
ECs0104
E100000100
2
12
a
b0100
20
1
2
2
b0100
orf, hypothetical protein
b0100
Z0110
ECs0104
E100000100
2
12
a
b0100
14400 1349 Kbytes .Supplementary data files not provided
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