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Platform GPL3255 Query DataSets for GPL3255
Status Public on Jul 01, 2006
Title VUMC MACF human 19K oligo v33
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. 384-well plates 1-39 containing 14485 unique oligonucleotides were spotted in duplo onto CodeLink™ slides (Amersham Biosciences) using an OmniGrid® 100 microarrayer (Genomic Solutions, Ann Arbor, MI, USA) equipped with SMP3 pins (TeleChem International, Sunnyvale, CA, USA). 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.ensembl.org after agreeing to Compugen's conditions
- oligonucleotides were mapped by Ensembl to the NCBI35 version of the human genome
- all plates were printed twice (duplicate spots)
 
Web link http://www.vumc.nl/microarrays
Contributor(s) van den IJssel P, Ylstra B
Submission date Dec 15, 2005
Last update date Jul 01, 2006
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 (54) GSM88932, GSM92657, GSM92658, GSM92659, GSM92660, GSM92661 
Series (1)
GSE3892 Diffuse large B cell lymphomas

Data table header descriptions
ID
ROW Coordinate for row number of block of features
COL Coordinate for column number of block of features
SUBGRIDROW Coordinate for row number of feature within a block
SUBGRIDCOL Coordinate for column number of feature within a block
GB_ACC GeneBank accession number as supplied by Compugen
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 SUBGRIDROW SUBGRIDCOL 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 1 1 NM_016516 48499 CGEN_HUM_1000102_1 Homo sapiens tumor antigen SLP-8p (HCC8), mRNA cell growth and/or maintenance [0008151] 1 A12 oligo Experimental 2 64031066 64031125
2 1 1 1 2 M37190 62349 CGEN_HUM_1000108_1 Human ras inhibitor mRNA, 3' end cell growth and/or maintenance [0008151] 1 A24 oligo Experimental 20 19929915 19929974
3 1 1 1 3 AF263538 86232 CGEN_HUM_1000126_1 Homo sapiens growth differentiation factor 3 (GDF3) mRNA, complete cds cell growth and/or maintenance [0008151] 1 E12 oligo Experimental 12 7739549 7739608
4 1 1 1 4 NM_006812 76228 CGEN_HUM_1000132_1 Homo sapiens amplified in osteosarcoma (OS-9), mRNA cell growth and/or maintenance [0008151] 1 E24 oligo Experimental 12 56401473 56401532
5 1 1 1 5 NM_004962 2171 CGEN_HUM_1000150_1 Homo sapiens growth differentiation factor 10 (GDF10) mRNA cell growth and/or maintenance [0008151] 1 I12 oligo Experimental 10 48049483 48049542
6 1 1 1 6 AK024434 143878 CGEN_HUM_1000156_1 Homo sapiens mRNA for FLJ00024 protein, partial cds cell growth and/or maintenance [0008151] 1 I24 oligo Experimental 9 131165724 131165783
7 1 1 1 7 NM_012135 140944 CGEN_HUM_1000174_1 Homo sapiens DNA segment on chromosome X (unique) 2654 expressed sequence (D6S2654E), mRNA cell growth and/or maintenance [0008151] 1 M12 oligo Experimental 6 3796218 3796277
8 1 1 1 8 NM_016397 5184 CGEN_HUM_1000180_1 Homo sapiens hypothetical protein (HSPC130), mRNA cell growth and/or maintenance [0008151] 1 M24 oligo Experimental 20 57003445 57003504
9 1 1 1 9 NM_004109 744 CGEN_HUM_1000486_1 Homo sapiens ferredoxin 1 (FDX1) mRNA energy pathways [0006091] 2 A12 oligo Experimental 11 109839000 109839059
10 1 1 1 10 NM_005011 180069 CGEN_HUM_1000492_1 Homo sapiens nuclear respiratory factor 1 (NRF1) mRNA energy pathways [0006091] 2 A24 oligo Experimental 7 128990345 128990404
11 1 1 1 11 NM_003198 155202 CGEN_HUM_1000510_1 Homo sapiens transcription elongation factor B (SIII), polypeptide 3 (110kD, elongin A) (TCEB3), mRNA energy pathways [0006091] 2 E12 oligo Experimental 1 23823412 23823471
12 1 1 1 12 NM_005174 155433 CGEN_HUM_1000516_1 Homo sapiens ATP synthase, H+ transporting, mitochondrial F1 complex, gamma polypeptide 1 (ATP5C1), nuclear gene encoding mitochondrial protein, mRNA energy pathways [0006091] 2 E24 oligo Experimental 10 7889684 7889743
13 1 1 1 13 NM_015954 24332 CGEN_HUM_1000534_1 Homo sapiens CGI-26 protein (LOC51071), mRNA main pathways of carbohydrate metabolism [0006092] 2 I12 oligo Experimental 12 16080518 16080577
14 1 1 1 14 NM_000365 83848 CGEN_HUM_1000540_1 Homo sapiens triosephosphate isomerase 1 (TPI1) mRNA gluconeogenesis [0006094] 2 I24 oligo Experimental 12 6846683 6846742
15 1 1 1 15 NM_016435 CGEN_HUM_1000558_1 Homo sapiens gastric-associated differentially-expressed protein YA61P (LOC51229), mRNA glycolysis [0006096] 2 M12 oligo Experimental
16 1 1 1 16 NM_002947 1608 CGEN_HUM_1000564_1 Homo sapiens replication protein A3 (14kD) (RPA3) mRNA glycolysis [0006096] 2 M24 oligo Experimental 7 7453283 7453342
17 1 1 1 17 NM_016516 48499 CGEN_HUM_1000102_1 Homo sapiens tumor antigen SLP-8p (HCC8), mRNA cell growth and/or maintenance [0008151] 1 A12 oligo Experimental 2 64031066 64031125
18 1 1 1 18 M37190 62349 CGEN_HUM_1000108_1 Human ras inhibitor mRNA, 3' end cell growth and/or maintenance [0008151] 1 A24 oligo Experimental 20 19929915 19929974
19 1 1 1 19 AF263538 86232 CGEN_HUM_1000126_1 Homo sapiens growth differentiation factor 3 (GDF3) mRNA, complete cds cell growth and/or maintenance [0008151] 1 E12 oligo Experimental 12 7739549 7739608
20 1 1 1 20 NM_006812 76228 CGEN_HUM_1000132_1 Homo sapiens amplified in osteosarcoma (OS-9), mRNA cell growth and/or maintenance [0008151] 1 E24 oligo Experimental 12 56401473 56401532

Total number of rows: 30000

Table truncated, full table size 5478 Kbytes.






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