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Platform GPL3443 Query DataSets for GPL3443
Status Public on Aug 30, 2006
Title VUMC MACF human 5K BAC v21
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 (see Ensembl), the Caltech 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 a SpotArray 72 robot (Perkin Elmer Life Sciences, Zaventum, Belgium) 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 - 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
Submission date Feb 10, 2006
Last update date Aug 30, 2006
Contact name Daoud Sie
E-mail(s) [email protected]
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 (96) GSM115131, GSM115132, GSM115133, GSM115134, GSM115135, GSM115136 
Series (4)
GSE5051 Cross-Platform Array Comparative Genomic Hybridization (array CGH) Meta-Analysis
GSE5138 Chromosomal abberations and transcriptional characteristics linked to the pathogenesis of diffuse large b-cell lymphomas
GSE8067 Multiple genes at the chromosome 20q amplicon contribute to colorectal adenoma to carcinoma progression

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
SANGER_PLATE_ID name of the 96-well plate from the Sanger 1 Mb BAC clone set
BIOSEQUENCE_TYPE Type of biosequence spotted on the array
REPORTER_USAGE Role of the reporter (experimental, control or empty)
Species
CHROMOSOME_NR Number of the chromosome to which the clone has been mapped
START Start position of the clone on the chromosome to which it has been mapped
END End 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 SANGER_PLATE_ID BIOSEQUENCE_TYPE REPORTER_USAGE Species CHROMOSOME_NR START END CLONE_ID SPOT_ID
1 1 1 1 1 RP11-196P2 BAC Experimental Homo sapiens 13 59214446 59374590 RP11-196P2
2 1 1 1 2 RP11-196P2 BAC Experimental Homo sapiens 13 59214446 59374590 RP11-196P2
3 1 1 1 3 RP11-196P2 BAC Experimental Homo sapiens 13 59214446 59374590 RP11-196P2
4 1 1 1 4 RP11-1150D24 BAC Experimental Homo sapiens 8 96053460 96235912 RP11-1150D24
5 1 1 1 5 RP11-1150D24 BAC Experimental Homo sapiens 8 96053460 96235912 RP11-1150D24
6 1 1 1 6 RP11-1150D24 BAC Experimental Homo sapiens 8 96053460 96235912 RP11-1150D24
7 1 1 1 7 RP11-210L5 BAC Experimental Homo sapiens 13 59837685 60013769 RP11-210L5
8 1 1 1 8 RP11-210L5 BAC Experimental Homo sapiens 13 59837685 60013769 RP11-210L5
9 1 1 1 9 RP11-210L5 BAC Experimental Homo sapiens 13 59837685 60013769 RP11-210L5
10 1 1 1 10 RP11-1078A14 BAC Experimental Homo sapiens 8 111102581 111308942 RP11-1078A14
11 1 1 1 11 RP11-1078A14 BAC Experimental Homo sapiens 8 111102581 111308942 RP11-1078A14
12 1 1 1 12 RP11-1078A14 BAC Experimental Homo sapiens 8 111102581 111308942 RP11-1078A14
13 1 1 1 13 RP11-138D23 BAC Experimental Homo sapiens 13 65278427 65443031 RP11-138D23
14 1 1 1 14 RP11-138D23 BAC Experimental Homo sapiens 13 65278427 65443031 RP11-138D23
15 1 1 1 15 RP11-138D23 BAC Experimental Homo sapiens 13 65278427 65443031 RP11-138D23
16 1 1 1 16 RP11-1085L2 BAC Experimental Homo sapiens 8 103299359 103498434 RP11-1085L2
17 1 1 1 17 RP11-1085L2 BAC Experimental Homo sapiens 8 103299359 103498434 RP11-1085L2
18 1 1 1 18 RP11-1085L2 BAC Experimental Homo sapiens 8 103299359 103498434 RP11-1085L2
19 1 1 1 19 RP11-100I7 BAC Experimental Homo sapiens 13 66393549 66558355 RP11-100I7
20 1 1 2 1 RP11-100I7 BAC Experimental Homo sapiens 13 66393549 66558355 RP11-100I7

Total number of rows: 17328

Table truncated, full table size 1486 Kbytes.






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