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Platform GPL3055 Query DataSets for GPL3055
Status Public on Dec 19, 2005
Title VUMC MACF human 30K oligo v30
Technology type spotted oligonucleotide
Distribution non-commercial
Organism Homo sapiens
Manufacturer VUMC Microarray Core Facility
Manufacture protocol The Human Release 2.0 oligonucleotide library, containing 60-mer oligonucleotides representing 28830 unique genes as designed by Compugen (San Jose, CA, USA), was obtained from Sigma-Genosys (Zwijndrecht, The Netherlands). The oligonucleotides were dissolved at 10 uM concentration in 50 mM sodium phosphate buffer pH 8.5 and single spotted onto CodeLink™ slides (Amersham Biosciences), using an SA-72 microarrayer (Perkin Elmer) 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 once (no replicate spots)
 
Web link http://www.vumc.nl/microarrays
Contributor(s) van den IJssel P, Ylstra B
Citation(s) 16361265
Submission date Nov 08, 2005
Last update date Dec 20, 2005
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 (73) GSM82461, GSM82462, GSM82463, GSM198746, GSM198747, GSM198764 
Series (3)
GSE3264 Oligonucleotide-based arrayCGH
GSE8067 Multiple genes at the chromosome 20q amplicon contribute to colorectal adenoma to carcinoma progression
GSE13191 Genomic Profiles Associated with Early Micrometastasis in Lung Cancer: Relevance of 4q Deletion

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
SPOT_ID
UNIGENE UniGene accession number as supplied by Compugen
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 SPOT_ID UNIGENE 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_148960 298539 CGEN_HUMAN_LIB2_6010300136_0 Homo sapiens claudin 19 (CLDN19), mRNA. cell adhesion [0007155] 1 A12 oligo Experimental 1 42868227 42868286
2 1 1 1 2 NM_021965 406261 CGEN_HUMAN_LIB2_6010300184_0 Homo sapiens phosphoglucomutase 5 (PGM5), mRNA. cell adhesion [0007155] 1 A24 oligo Experimental 9 68343702 68343761
3 1 1 1 3 NM_000582 313 CGEN_HUMAN_LIB2_6010300138_0 Homo sapiens secreted phosphoprotein 1 (osteopontin, bone sialoprotein I, early T-lymphocyte activation 1) (SPP1), mRNA. cell adhesion [0007155] 1 E12 oligo Experimental 4 89261011 89261070
4 1 1 1 4 NM_033257 347285 CGEN_HUMAN_LIB2_6010300186_0 Homo sapiens DiGeorge syndrome critical region gene 6-like (DGCR6L), mRNA. cell adhesion [0007155] 1 E24 oligo Experimental 22 18682103 18682162
5 1 1 1 5 NM_002231 323949 CGEN_HUMAN_LIB2_6010300140_0 Homo sapiens kangai 1 (suppression of tumorigenicity 6, prostate; CD82 antigen (R2 leukocyte antigen, antigen detected by monoclonal and antibody IA4)) (KAI1), mRNA. cell adhesion [0007155] 1 I12 oligo Experimental 11 44583203 44583262
6 1 1 1 6 J05213 49215 CGEN_HUMAN_LIB2_6010300188_0 Homo sapiens sialoprotein precursor (IBSP) mRNA, complete cds. cell adhesion [0007155] 1 I24 oligo Experimental 4 89090128 89090187
7 1 1 1 7 AF195420 303006 CGEN_HUMAN_LIB2_6010300142_0 Homo sapiens ODZ3 (ODZ3) mRNA, partial cds. cell adhesion [0007155] 1 M12 oligo Experimental 4 183643171 183643230
8 1 1 1 8 NM_001307 278562 CGEN_HUMAN_LIB2_6010300190_0 Homo sapiens claudin 7 (CLDN7), mRNA. cell adhesion [0007155] 1 M24 oligo Experimental 17 7105877 7105936
9 1 1 1 9 NM_012211 256297 CGEN_HUMAN_LIB2_6010300520_0 Homo sapiens integrin, alpha 11 (ITGA11), mRNA. cell-matrix adhesion [0007160] 2 A12 oligo Experimental 15 66383214 66383273
10 1 1 1 10 NM_005874 22405 CGEN_HUMAN_LIB2_6010300568_0 Homo sapiens leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 2 (LILRB2), mRNA. cell-cell signaling [0007267] 2 A24 oligo Experimental 19 59470286 59470345
11 1 1 1 11 L36531 91296 CGEN_HUMAN_LIB2_6010300522_0 Homo sapiens integrin alpha 8 subunit mRNA, 3' end. cell-matrix adhesion [0007160] 2 E12 oligo Experimental 10 15689733 15689792
12 1 1 1 12 NM_001817 12 CGEN_HUMAN_LIB2_6010300570_0 Homo sapiens carcinoembryonic antigen-related cell adhesion molecule 4 (CEACAM4), mRNA. cell-cell signaling [0007267] 2 E24 oligo Experimental 19 46823994 46824053
13 1 1 1 13 BC036525 188790 CGEN_HUMAN_LIB2_6010300524_0 Homo sapiens, clone IMAGE:5265764, mRNA. cell-matrix adhesion [0007160] 2 I12 oligo Experimental 11 101339547 101339606
14 1 1 1 14 NM_003222 61796 CGEN_HUMAN_LIB2_6010300572_0 Homo sapiens transcription factor AP-2 gamma (activating enhancer binding protein 2 gamma) (TFAP2C), mRNA. cell-cell signaling [0007267] 2 I24 oligo Experimental 20 54647570 54647629
15 1 1 1 15 NM_006329 11494 CGEN_HUMAN_LIB2_6010300526_0 Homo sapiens fibulin 5 (FBLN5), mRNA. cell-matrix adhesion [0007160] 2 M12 oligo Experimental 14 91406191 91406250
16 1 1 1 16 NM_000029 3697 CGEN_HUMAN_LIB2_6010300574_0 Homo sapiens angiotensinogen (serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 8) (AGT), mRNA. cell-cell signaling [0007267] 2 M24 oligo Experimental 1 227153157 227153216
17 1 1 1 17 NM_002468 82116 CGEN_HUMAN_LIB2_6010300904_0 Homo sapiens myeloid differentiation primary response gene (88) (MYD88), mRNA. signal transduction [0007165] 3 A12 oligo Experimental 3 38159272 38159331
18 1 1 1 18 AB007957 67619 CGEN_HUMAN_LIB2_6010300952_0 Homo sapiens mRNA, chromosome 1 specific transcript KIAA0488. signal transduction [0007165] 3 A24 oligo Experimental 1 148484000 148484059
19 1 1 1 19 NM_002462 76391 CGEN_HUMAN_LIB2_6010300906_0 Homo sapiens myxovirus (influenza virus) resistance 1, interferon-inducible protein p78 (mouse) (MX1), mRNA. signal transduction [0007165] 3 E12 oligo Experimental 21 41752662 41752721
20 1 1 1 20 NM_004938 153924 CGEN_HUMAN_LIB2_6010300954_0 Homo sapiens death-associated protein kinase 1 (DAPK1), mRNA. signal transduction [0007165] 3 E24 oligo Experimental 9 87552665 87552724

Total number of rows: 30000

Table truncated, full table size 5580 Kbytes.




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