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Status
Public on Dec 19, 2005
Title
VUMC MACF human 6K BAC v45
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 5284 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
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)
Web link
http://www.vumc.nl/microarrays Contributor(s)
van den IJssel P , Ylstra B Citation(s)
16361265 Submission date
Sep 13, 2005
Last update date
Jun 13, 2008
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 (160)
GSM75208 , GSM140130 , GSM140131 , GSM140132 , GSM140133 , GSM140134
GSM140135 ,
GSM140136 ,
GSM140137 ,
GSM140138 ,
GSM140139 ,
GSM140140 ,
GSM140141 ,
GSM140142 ,
GSM140143 ,
GSM140144 ,
GSM140145 ,
GSM140146 ,
GSM140147 ,
GSM140148 ,
GSM140149 ,
GSM140150 ,
GSM140151 ,
GSM140152 ,
GSM140153 ,
GSM140154 ,
GSM140155 ,
GSM140156 ,
GSM140157 ,
GSM140158 ,
GSM140159 ,
GSM140160 ,
GSM140161 ,
GSM140162 ,
GSM140163 ,
GSM140164 ,
GSM140165 ,
GSM197641 ,
GSM197677 ,
GSM197692 ,
GSM197693 ,
GSM197700 ,
GSM197701 ,
GSM197708 ,
GSM197710 ,
GSM197711 ,
GSM197712 ,
GSM197713 ,
GSM197714 ,
GSM197715 ,
GSM197746 ,
GSM197748 ,
GSM197750 ,
GSM197752 ,
GSM197753 ,
GSM197754 ,
GSM197755 ,
GSM197757 ,
GSM197758 ,
GSM197759 ,
GSM197760 ,
GSM197774 ,
GSM197775 ,
GSM197776 ,
GSM291359 ,
GSM291361 ,
GSM291362 ,
GSM291363 ,
GSM291364 ,
GSM291365 ,
GSM291366 ,
GSM291367 ,
GSM291368 ,
GSM291369 ,
GSM291370 ,
GSM291371 ,
GSM291372 ,
GSM291373 ,
GSM291374 ,
GSM291375 ,
GSM291376 ,
GSM291377 ,
GSM291378 ,
GSM291379 ,
GSM291380 ,
GSM291381 ,
GSM291382 ,
GSM291383 ,
GSM291384 ,
GSM291385 ,
GSM291386 ,
GSM291387 ,
GSM291388 ,
GSM291389 ,
GSM291390 ,
GSM291391 ,
GSM291392 ,
GSM291393 ,
GSM291394 ,
GSM291395 ,
GSM291396 ,
GSM291397 ,
GSM291398 ,
GSM291399 ,
GSM291400 ,
GSM291401 ,
GSM291402 ,
GSM291403 ,
GSM291404 ,
GSM291405 ,
GSM301419 ,
GSM301422 ,
GSM301425 ,
GSM301426 ,
GSM301427 ,
GSM301429 ,
GSM301430 ,
GSM301434 ,
GSM301442 ,
GSM301443 ,
GSM301444 ,
GSM301445 ,
GSM301449 ,
GSM301451 ,
GSM301452 ,
GSM301454 ,
GSM324795 ,
GSM324798 ,
GSM324801 ,
GSM324805 ,
GSM324806 ,
GSM324810 ,
GSM324812 ,
GSM324813 ,
GSM324814 ,
GSM324815 ,
GSM324816 ,
GSM324817 ,
GSM324818 ,
GSM324871 ,
GSM324872 ,
GSM324873 ,
GSM324874 ,
GSM574264 ,
GSM574266 ,
GSM574267 ,
GSM574268 ,
GSM574270 ,
GSM574271 ,
GSM574272 ,
GSM574273 ,
GSM574274 ,
GSM574276 ,
GSM574277 ,
GSM574278 ,
GSM574279 ,
GSM574280 ,
GSM574281 ,
GSM574285 ,
GSM574286 Series (8)
GSE3264 Oligonucleotide-based arrayCGH
GSE6042 DNA copy numbers of malignant glioma in culture
GSE8067 Multiple genes at the chromosome 20q amplicon contribute to colorectal adenoma to carcinoma progression
GSE11573 Chromosomal signatures of a subset of high-grade premalignant cervical lesions closely resemble invasive carcinomas
GSE11929 Identification of a subgroup of head and neck cancers lacking numerical chromosomal aberrations
GSE12020 Head and neck squamous cell carcinomas
GSE12951 Chromosomal aberrations in benign and malignant salivary gland myoepitheliomas
GSE23418 Small bowel adenocarcinoma copy number profiles are more closely related to colorectal than to gastric cancers
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
CLONE_ID SPOT_ID SANGER_PLATE_ID name of the 96-well plate from the Sanger 1 Mb BAC clone set
WELL_NR Well number within the 96-well plate of 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)
ORGANISM organism source of the feature
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
Data table ID ROW COL SUBGRIDROW SUBGRIDCOL INT_CLONE_NAME CLONE_ID SPOT_ID SANGER_PLATE_ID WELL_NR BIOSEQUENCE_TYPE REPORTER_USAGE ORGANISM CHROMOSOME_NR START END 1
1
1
1
1
CTD-2009c6
CTD-2009c6
BAC
Experimental
Homo sapiens
6
64226360
64421050
2
1
1
1
2
CTD-2009c6
CTD-2009c6
BAC
Experimental
Homo sapiens
6
64226360
64421050
3
1
1
1
3
CTD-2009c6
CTD-2009c6
BAC
Experimental
Homo sapiens
6
64226360
64421050
4
1
1
1
4
Empty
Empty
5
1
1
1
5
Empty
Empty
6
1
1
1
6
Empty
Empty
7
1
1
1
7
RP11-43b4
RP11-43b4
BAC
Experimental
Homo sapiens
6
20117735
20184590
8
1
1
1
8
RP11-43b4
RP11-43b4
BAC
Experimental
Homo sapiens
6
20117735
20184590
9
1
1
1
9
RP11-43b4
RP11-43b4
BAC
Experimental
Homo sapiens
6
20117735
20184590
10
1
1
1
10
Empty
Empty
11
1
1
1
11
Empty
Empty
12
1
1
1
12
Empty
Empty
13
1
1
1
13
CTD-2018p8
CTD-2018p8
BAC
Experimental
Homo sapiens
6
20601183
20601453
14
1
1
1
14
CTD-2018p8
CTD-2018p8
BAC
Experimental
Homo sapiens
6
20601183
20601453
15
1
1
1
15
CTD-2018p8
CTD-2018p8
BAC
Experimental
Homo sapiens
6
20601183
20601453
16
1
1
1
16
Empty
Empty
17
1
1
1
17
Empty
Empty
18
1
1
1
18
Empty
Empty
19
1
1
1
19
RP11-159c8
RP11-159c8
BAC
Experimental
Homo sapiens
6
20442776
20622576
20
1
1
1
20
RP11-159c8
RP11-159c8
BAC
Experimental
Homo sapiens
6
20442776
20622576
19200 1747 Kbytes .Supplementary data files not provided
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