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Platform GPL2902 Query DataSets for GPL2902
Status Public on Dec 31, 2005
Title VUMC MACF human 19K oligo vSAE4
Technology type spotted oligonucleotide
Distribution non-commercial
Organism Homo sapiens
Manufacturer VUMC Microarray Core Facility
Manufacture protocol The Human Release 1.0 oligonucleotide library, containing 18861 60-mer oligonucleotides representing 17260 unique genes as designed by Compugen (San Jose, CA, USA) was obtained from Sigma-Genosys (Zwijndrecht, The Netherlands). The oligonucleotides were dissolved at 10 µM concentration in 150 mM sodium phosphate buffer pH 8.5 and single spotted onto CodeLink slides (Amersham Biosciences) using a SpotArray Enterprise non-contact microarray printer (Perkin Elmer). After printing slides were processed and blocked prior to use according to the manufacturer’s protocol.
Catalog number 300011 (Amersham, slides only)
Support glass
Coating hydrophilic polymer containing N-hydroxysuccinimide (NHS) ester reactive groups
 
Description - oligonucleotide sequences are available via www.ensemble.org after agreeing to Compugen's conditions
- oligonucleotides were mapped by Ensembl to the NCBI35 version of the human genome
 
Web link http://www.vumc.nl/microarrays
Contributor(s) van den IJssel P, Ylstra B
Submission date Sep 29, 2005
Last update date Jun 13, 2008
Contact name Daoud Sie
E-mail(s) d.sie@vumc.nl
Phone +31 20 4442428
Organization name Vrije Universiteit Medical Center
Department Pathology
Lab Microarray Core Facility
Street address De Boelelaan 1117
City Amsterdam
ZIP/Postal code 1081 HV
Country Netherlands
 
Samples (45) GSM81933, GSM81934, GSM81935, GSM81936, GSM81937, GSM81938 
Series (2)
GSE3598 Bleomycin exposed lymphoblastoid cells
GSE8288 Identification of markers associated with deregulated hTERT during HPV-medaited transformation

Data table header descriptions
ID
ROW Coordinate for row number of features
COL Coordinate for column number of features
GB_ACC GeneBank accession number as supplied by Compugen LINK_PRE:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=Nucleotide&term=
UNIGENE UniGene accession number as supplied by Compugen
SPOT_ID
COMPUGEN_SERIAL_NR Serial number of the oligonucleotide as supplied by Compugen
GENE_DESCRIPTION Description of the gene from which the oligo has been designed as supplied by Compugen
GENE_ONTOLOGY Ontology of the gene from which the oligo has been designed as assigned by Compugen
PLATE_NR Number of the 384-well plate in which the oligo was supplied
WELL_NR Well number within the 384-well plate in which the oligo was supplied
BIOSEQUENCE_TYPE Type of biosequence spotted on the array
REPORTER_USAGE Role of the reporter (control or experimental)
CHROMOSOME_NR Number of the chromosome to which the oligonucleotide has been mapped
START Start position of the oligonucleotide on the chromosome to which it has been mapped
END End position of the oligonucleotide on the chromosome to which it has been mapped

Data table
ID ROW COL GB_ACC UNIGENE SPOT_ID COMPUGEN_SERIAL_NR GENE_DESCRIPTION GENE_ONTOLOGY PLATE_NR WELL_NR BIOSEQUENCE_TYPE REPORTER_USAGE CHROMOSOME_NR START END
1 1 1 M33197 Hs.169476 CGEN_HUMCTRL_10001_1 glyceraldehyde-3-phosphate dehydrogenase (GAPDH) mRNA glycolysis [0006096] 2 A1 oligo Control positive
2 1 2 NM_000155 Hs.75641 CGEN_HUM_1000393_1 Homo sapiens galactose-1-phosphate uridylyltransferase (GALT) mRNA galactose metabolism [0006012] 2 A17 oligo Experimental
3 1 3 NM_015361 Hs.268053 CGEN_HUM_1000005_1 Homo sapiens KIAA0029 protein (KIAA0029), mRNA cell growth and/or maintenance [0008151] 1 A9 oligo Experimental 2 136230253 136230312
4 1 4 M33197 Hs.169476 CGEN_HUMCTRL_10001_1 glyceraldehyde-3-phosphate dehydrogenase (GAPDH) mRNA glycolysis [0006096] 3 A1 oligo Control positive
5 1 5 NM_002526 Hs.153952 CGEN_HUM_1000777_1 Homo sapiens 5' nucleotidase (CD73) (NT5), mRNA DNA metabolism [0006259] 3 A17 oligo Experimental 6 86237796 86237855
6 1 6 NM_003935 Hs.194685 CGEN_HUM_1001157_1 Homo sapiens topoisomerase (DNA) III beta (TOP3B) mRNA DNA modification [0006304] 4 A9 oligo Experimental 22 20649225 20649284
7 1 7 M33197 Hs.169476 CGEN_HUMCTRL_10001_1 glyceraldehyde-3-phosphate dehydrogenase (GAPDH) mRNA glycolysis [0006096] 5 A1 oligo Control positive
8 1 8 U13223 CGEN_HUM_1001545_1 Human forkhead protein FREAC-5 mRNA, partial cds transcription regulation [0006355] 5 A17 oligo Experimental
9 1 9 AB037901 Hs.149918 CGEN_HUM_1001925_1 Homo sapiens GASC-1 mRNA, complete cds transcription regulation [0006355] 6 A9 oligo Experimental
10 1 10 M33197 Hs.169476 CGEN_HUMCTRL_10001_1 glyceraldehyde-3-phosphate dehydrogenase (GAPDH) mRNA glycolysis [0006096] 7 A1 oligo Control positive
11 1 11 U97060 CGEN_HUM_1002313_1 Homo sapiens Slug mRNA, partial cds repression of transcription from Pol II promoter [0000122] 7 A17 oligo Experimental
12 1 12 NM_014497 Hs.169984 CGEN_HUM_1002693_1 Homo sapiens nuclear protein (NP220), mRNA mRNA splicing [0006371] 8 A9 oligo Experimental
13 1 13 M33197 Hs.169476 CGEN_HUMCTRL_10001_1 glyceraldehyde-3-phosphate dehydrogenase (GAPDH) mRNA glycolysis [0006096] 9 A1 oligo Control positive
14 1 14 NM_006585 Hs.15071 CGEN_HUM_1003081_1 Homo sapiens chaperonin containing TCP1, subunit 8 (theta) (CCT8), mRNA protein folding [0006457] 9 A17 oligo Experimental 21 29361129 29361188
15 1 15 NM_002831 Hs.63489 CGEN_HUM_1003461_1 Homo sapiens protein tyrosine phosphatase, non-receptor type 6 (PTPN6) mRNA protein dephosphorylation [0006470] 10 A9 oligo Experimental 12 6937118 6937177
16 1 16 M33197 Hs.169476 CGEN_HUMCTRL_10001_1 glyceraldehyde-3-phosphate dehydrogenase (GAPDH) mRNA glycolysis [0006096] 11 A1 oligo Control positive
17 1 17 AB037722 Hs.8707 CGEN_HUM_1003849_1 Homo sapiens mRNA for KIAA1301 protein, partial cds proteolysis and peptidolysis [0006508] 11 A17 oligo Experimental 2 196889642 196889701
18 1 18 NM_006813 Hs.75969 CGEN_HUM_1004229_1 Homo sapiens proline-rich protein with nuclear targeting signal (B4-2), mRNA proline metabolism [0006560] 12 A9 oligo Experimental 6 89851277 89851336
19 1 19 M33197 Hs.169476 CGEN_HUMCTRL_10001_1 glyceraldehyde-3-phosphate dehydrogenase (GAPDH) mRNA glycolysis [0006096] 13 A1 oligo Control positive
20 1 20 AL050371 Hs.8128 CGEN_HUM_1004617_1 Homo sapiens mRNA; cDNA DKFZp566G2246 (from clone DKFZp566G2246) phospholipid metabolism [0006644] 13 A17 oligo Experimental 22 30340081 30340140

Total number of rows: 19200

Table truncated, full table size 3481 Kbytes.






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