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Platform GPL10743 Query DataSets for GPL10743
Status Public on Aug 03, 2010
Title VUMC MACF human 5K BAC v37
Technology type spotted DNA/cDNA
Distribution non-commercial
Organism Homo sapiens
Manufacturer VUMC Microarray Core Facility
Manufacture protocol as described in: Carvalho et al (J. Clin. Path.,2004, vol. 57, 644-646). DNA from the 1 Mb resolution Sanger BAC clone set, the OncoBac set, and in house clones of interest, supplemented with clones from the Children’s Hospital Oakland Research Institute (CHORI), amounting to a total of 4678 clones with known chromosomal positions, was isolated according to the CHORI protocol. Amplification of the DNA was done by ligation mediated polymerase chain reaction (PCR) according to Snijders et al. (Nat. Genet.,2001, vol.29, 263-264) and PCR clones were purified using Montage PCR μ96 filter plates (Millipore BV, Amsterdam, the Netherlands). Clones were spotted in triplicate at a concentration of 1 μg/µl, in 150 mM sodium phosphate (pH 8.5), on CodeLink™ slides (Amersham BioSciences, Roosendaal, the Netherlands), 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 other
 
Description - clones were mapped to the UCSC July 2003 Freeze of the Human Golden Path (NCBI build 34)
- oncobacs were mapped using their overgo-primers and are available via www.ensembl.org
 
Web link http://www.vumc.nl/microarrays
Contributor(s) van den Ijssel P, Ylstra B
Citation(s) 16361265
Submission date Jul 29, 2010
Last update date Sep 30, 2010
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 (37) GSM574254, GSM574258, GSM647736, GSM647737, GSM647738, GSM647739 
Series (2)
GSE23418 Small bowel adenocarcinoma copy number profiles are more closely related to colorectal than to gastric cancers
GSE26389 Losses of chromosome 5q and 14q mark a subset of gastric cancers with good clinical outcome

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
INT_CLONE_NAME International name to identify BAC or PAC clone
CHROMOSOME Number of the chromosome to which the clone has been mapped
POSITION Position of the clone on the chromosome to which it has been mapped
CLONE_ID
SPOT_ID

Data table
ID ROW COL SUBGRIDROW SUBGRIDCOL INT_CLONE_NAME CHROMOSOME POSITION CLONE_ID SPOT_ID
1 1 1 1 1 RP11-196P2;Colon2; Colon7 13 59214446 RP11-196P2
2 1 1 1 2 RP11-196P2;Colon2; Colon7 13 59214446 RP11-196P2
3 1 1 1 3 RP11-196P2;Colon2; Colon7 13 59214446 RP11-196P2
4 1 1 1 4 RP11-1150D24;Colon2; 8q_CHORI_2 8 96053460 RP11-1150D24
5 1 1 1 5 RP11-1150D24;Colon2; 8q_CHORI_2 8 96053460 RP11-1150D24
6 1 1 1 6 RP11-1150D24;Colon2; 8q_CHORI_2 8 96053460 RP11-1150D24
7 1 1 1 7 RP11-210L5;Colon2; Colon7 13 59837685 RP11-210L5
8 1 1 1 8 RP11-210L5;Colon2; Colon7 13 59837685 RP11-210L5
9 1 1 1 9 RP11-210L5;Colon2; Colon7 13 59837685 RP11-210L5
10 1 1 1 10 RP11-1078A14;Colon2; 8q_CHORI_2 8 111102581 RP11-1078A14
11 1 1 1 11 RP11-1078A14;Colon2; 8q_CHORI_2 8 111102581 RP11-1078A14
12 1 1 1 12 RP11-1078A14;Colon2; 8q_CHORI_2 8 111102581 RP11-1078A14
13 1 1 1 13 RP11-138D23;Colon2; Colon7 13 65278427 RP11-138D23
14 1 1 1 14 RP11-138D23;Colon2; Colon7 13 65278427 RP11-138D23
15 1 1 1 15 RP11-138D23;Colon2; Colon7 13 65278427 RP11-138D23
16 1 1 1 16 RP11-1085L2;Colon2; 8q_CHORI_2 8 103299359 RP11-1085L2
17 1 1 1 17 RP11-1085L2;Colon2; 8q_CHORI_2 8 103299359 RP11-1085L2
18 1 1 1 18 RP11-1085L2;Colon2; 8q_CHORI_2 8 103299359 RP11-1085L2
19 1 1 1 19 RP11-100I7;Colon2; Colon7 13 66393549 RP11-100I7
20 1 1 2 1 RP11-100I7;Colon2; Colon7 13 66393549 RP11-100I7

Total number of rows: 17328

Table truncated, full table size 1047 Kbytes.




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