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Platform GPL3877 Query DataSets for GPL3877
Status Public on Jun 16, 2006
Title PRHU05-S1-0006 (PC Human Operon v2 21k)
Technology type spotted oligonucleotide
Distribution custom-commercial
Organism Homo sapiens
Manufacturer Microarray Facility - the Prostate Centre at Vancouver General Hospital
Manufacture protocol This array consists of 21,329 70mer probes representing 21,329 genes ( Operon Version 2.1 of the Human Genome Oligo Set). 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) Dangerfield B, Brahmbhatt S, Lehman M, Anderson S
Submission date Jun 14, 2006
Last update date Jan 18, 2013
Contact name Shawn Anderson
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 (238) GSM115459, GSM115460, GSM115461, GSM115462, GSM115463, GSM115464 
Series (10)
GSE5123 Expression profiling defines a recurrence signature in lung squamous cell carcinoma
GSE5828 Gene expression profiling classifies lung squamous cell carcinomas with N1 positive lymph nodes
GSE5843 Expression profiling defines a recurrence signature in lung adenocarcinoma

Data table header descriptions
Meta Row Field row
Meta Column Field column
Row Subgrid row
Column Subgrid column
Description Oligo probe description
Gene Symbol Official gene symbol
GB_LIST Refseq accession
Description Refseq Refseq description
GB_LIST Genbank accession

Data table
ID Meta Row Meta Column Row Column Description Gene Symbol GB_LIST Description Refseq GB_LIST CLONE ID SPOT_ID 1 1 1 1 GFP Oligo Marker -- CONTROL U17997 1 1 1 2 AK057513 H200020668 1 1 1 3 Q96M64 AK057355 H200020692 1 1 1 4 beta(1,6)-N-acetylglucosaminyltransferase V isoform 1; N-acetylglucosaminyltransferase IX; beta(1,6)-N-acetylglucosaminyltransferase V [Homo sapiens]. [Source:RefSeq;Acc:NM_144677] MGAT5B NM_198955,NM_144677 mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase, isoenzyme B AB114297 H200020626 1 1 1 5 AK057638 H200020650 1 1 1 6 AK057458 H200020674 1 1 1 7 AK057320 H200020698 1 1 1 8 vav-1 interacting Kruppel-like protein isoform b [Homo sapiens]. [Source:RefSeq;Acc:NM_024061] NP_076966 NM_138494 zinc finger protein 655 BC011816,AK128057 H200021000 1 1 1 9 Transforming protein p21 (K-Ras 2) (Ki-Ras) (c-K-ras). [Source:Uniprot/SWISSPROT;Acc:P01116] KRAS2 NM_033360,NM_004985 v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog BC010502 H200021024 1 1 1 10 AK056070 H200021048 1 1 1 11 AK056250 H200021072 1 1 1 12 AK054757 H200021006 1 1 1 13 M-phase phosphoprotein 9 (Fragment). [Source:Uniprot/SWISSPROT;Acc:Q99550] MPHOSPH9 NM_022782 M-phase phosphoprotein 9 AK096541 H200021030 1 1 1 14 AK128256,AK057161 H200021054 1 1 1 15 pseudoautosomal GTP-binding protein-like protein; pseudoautosomal GTP-binding protein-like [Homo sapiens]. [Source:RefSeq;Acc:NM_012227] GTPBP6 NM_012227 GTP binding protein 6 (putative) Y14391,AK097872 H200021078 1 1 1 16 3xSSC -- 3xSSC 1 1 1 17 3xSSC -- 3xSSC 1 1 1 18 3xSSC -- 3xSSC 1 1 1 19 3xSSC -- 3xSSC 1 1 1 20 3xSSC -- 3xSSC

Total number of rows: 23232

Table truncated, full table size 3224 Kbytes.

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Supplementary data files not provided

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