GEO help: Mouse over screen elements for information.
Status
Public on Jun 27, 2006
Title
MERH03-S1-0002 (Rhodococcus sp. RHA1 22K)
Technology type
spotted oligonucleotide
Distribution
custom-commercial
Organism
Rhodococcus jostii RHA1 Manufacturer
The Microarray Facility of the Prostate Centre at Vancouver General Hospital
Manufacture protocol
Oligonucleotides are consolidated into 384-well plates, lyophilized by speed-Vac, and resuspended in 3x SSC to a printing concentration of 30uM. Oligos are printed on aminosilane slides (Erie, Hudson, NH, USA) with a Biorobotics Microgrid II microarray printer (Genomic Solutions). Microspot 10K quill pins (Biorobotics) in a 48-pin tool were used to deposit <0.5 nL per spot onto the slide. The resulting microarrays have a 4 x12 subgrid layout with 392 spots per subgrid, each spot having approximate diameter and pitch of 90 µm and 190µm, respectively. A 280-bp GFP (green fluorescent protein) oligo was printed in subgrid corners to assist in placing on the grid. The slides were crosslinked in a UV Stratalinker 2400 (Stratagene) at 300mJ. Array quality was assessed by visual inspection and hybridization of representative slides from a print run by dye-labelled random 9-mer oligonucleotides. The quality control images were aquired via the ScanArray Express from Perkin Elmer at a 10 micron resolution and quantified with the Imagene 6.0 software suite.
Support
glass
Coating
aminosilane
Contributor(s)
Anderson SA , Lehman M , Dangerfield B Submission date
Jun 23, 2006
Last update date
May 25, 2012
Contact name
Shawn Anderson
E-mail(s)
shawn.anderson@vch.ca Phone
604-875-4111 (63436)
Fax
604-875-5654
Organization name
University of British Columbia
Department
Urological Sciences
Lab
Microarray Facility, Dr. Colleen Nelson
Street address
The Prostate Centre at Vancouver General Hospital, 2660 Oak Street
City
Vancouver
State/province
B.C.
ZIP/Postal code
V6H 3Z6
Country
Canada
Samples (45)
GSM119454 , GSM119455 , GSM119456 , GSM119457 , GSM119458 , GSM119460
GSM119461 ,
GSM119462 ,
GSM119463 ,
GSM154397 ,
GSM154398 ,
GSM154399 ,
GSM154400 ,
GSM154401 ,
GSM154402 ,
GSM154764 ,
GSM154765 ,
GSM154766 ,
GSM210354 ,
GSM210355 ,
GSM210356 ,
GSM262274 ,
GSM262283 ,
GSM262284 ,
GSM262285 ,
GSM262286 ,
GSM262287 ,
GSM262561 ,
GSM262562 ,
GSM262563 ,
GSM263126 ,
GSM263127 ,
GSM263128 ,
GSM263129 ,
GSM263130 ,
GSM263131 ,
GSM263135 ,
GSM263136 ,
GSM263137 ,
GSM263138 ,
GSM263139 ,
GSM263140 ,
GSM693915 ,
GSM693916 ,
GSM693917 Series (11)
GSE5268 Effects of biphenyl on Rhodococcus sp. RHA1
GSE5269 Effects of ethylbenzene on Rhodococcus sp. RHA1
GSE5270 Effects of benzoate on Rhodococcus sp. RHA1
GSE5280 Effect of biphenyl, ethylbenzene, and benzoate on Rhodococcus sp. RHA1
GSE6683 Effects of phthalate on Rhodococcus sp. RHA1
GSE6684 Effects of terephthalate on Rhodococcus sp. RHA1
GSE6685 Effect of phthalate and terephthalate on Rhodococcus sp. RHA1
GSE6709 Effects of cholesterol on Rhodococcus sp. RHA1
GSE8480 Rhodococcus sp. RHA1 grown on propane versus pyruvate
GSE10378 Desiccation and control transcriptomes of Rhodococcus jostii RHA1
GSE28048 Effects of cholic acid on Rhodococcus sp. RHA1
Data table header descriptions ID ORF SPOT_ID manufID Microarray facility generated ID
METAROW Field row
METACOLUMN Field column
ROW Subgrid row
COLUMN Subgrid column
GENENAME GENE_PRODUCT SEQUENCE Oligo probe sequence
RO_ALIGN first base of the alignment of the probe to the sequence
OLIGO_ID ELEMENT genetic element in the organism the probe is from
ORGANISM manufPLATE Microarray facility generated plate ID
COMMENT
Data table ID ORF SPOT_ID manufID METAROW METACOLUMN ROW COLUMN GENENAME GENE_PRODUCT SEQUENCE RO_ALIGN OLIGO_ID ELEMENT ORGANISM manufPLATE COMMENT 1
GFP Oligo
GFP Oligo
1
1
1
1
CAATTGGCGATGGCCCTGTCCTTTTACCAGACAACCATTACCTGTCCACACAATCTGCCCTTTCGAAAGA
XX0001-P1-0035-DE037-001-A12
GFP
2
RHA1_ro10437 RHA1_04109__07185
1
1
1
2
conserved hypothetical protein
CTCCGGCCAACTGCCGTTGCGAGACGGACAAATGCTCTCACCTGGAAAGGTGGGTGCCGAGATCAGCCTC
pRHL2_ro10437_147
9635
Plasmid2
Rhodococcus sp. RHA1
MERH03-P1-0027-DE034-001-M24
n/a
3
RHA1_ro10437 RHA1_04109__07185
1
1
1
3
conserved hypothetical protein
CTCCGGCCAACTGCCGTTGCGAGACGGACAAATGCTCTCACCTGGAAAGGTGGGTGCCGAGATCAGCCTC
pRHL2_ro10437_147
9635
Plasmid2
Rhodococcus sp. RHA1
MERH03-P1-0027-DE034-001-M24
n/a
4
No Oligo
No Oligo
1
1
1
4
MERH03-P1-0028-DE034-001-A12
3xSSC Buffer
5
No Oligo
No Oligo
1
1
1
5
MERH03-P1-0028-DE034-001-A12
3xSSC Buffer
6
No Oligo
No Oligo
1
1
1
6
MERH03-P1-0028-DE034-001-E12
3xSSC Buffer
7
No Oligo
No Oligo
1
1
1
7
MERH03-P1-0028-DE034-001-E12
3xSSC Buffer
8
No Oligo
No Oligo
1
1
1
8
MERH03-P1-0028-DE034-001-I12
3xSSC Buffer
9
No Oligo
No Oligo
1
1
1
9
MERH03-P1-0028-DE034-001-I12
3xSSC Buffer
10
No Oligo
No Oligo
1
1
1
10
MERH03-P1-0028-DE034-001-M12
3xSSC Buffer
11
No Oligo
No Oligo
1
1
1
11
MERH03-P1-0028-DE034-001-M12
3xSSC Buffer
12
No Oligo
No Oligo
1
1
1
12
MERH03-P1-0028-DE034-001-A24
3xSSC Buffer
13
No Oligo
No Oligo
1
1
1
13
MERH03-P1-0028-DE034-001-A24
3xSSC Buffer
14
No Oligo
No Oligo
1
1
1
14
MERH03-P1-0028-DE034-001-E24
3xSSC Buffer
15
No Oligo
No Oligo
1
1
1
15
MERH03-P1-0028-DE034-001-E24
3xSSC Buffer
16
No Oligo
No Oligo
1
1
1
16
MERH03-P1-0028-DE034-001-I24
3xSSC Buffer
17
No Oligo
No Oligo
1
1
1
17
MERH03-P1-0028-DE034-001-I24
3xSSC Buffer
18
No Oligo
No Oligo
1
1
1
18
MERH03-P1-0028-DE034-001-M24
3xSSC Buffer
19
No Oligo
No Oligo
1
1
1
19
MERH03-P1-0028-DE034-001-M24
3xSSC Buffer
20
GFP Oligo
GFP Oligo
1
1
1
20
CAATTGGCGATGGCCCTGTCCTTTTACCAGACAACCATTACCTGTCCACACAATCTGCCCTTTCGAAAGA
XX0001-P1-0035-DE037-001-A12
GFP
22080 4412 Kbytes .Supplementary data files not provided
Less...
More...