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Platform GPL11357 Query DataSets for GPL11357
Status Public on Dec 27, 2010
Title Agilent-028081 Human Genome CGH + SNP Microarray (Feature Number version)
Technology type in situ oligonucleotide
Distribution custom-commercial
Organism Homo sapiens
Manufacturer Agilent Technologies
Manufacture protocol See manufacturer's web site at http://www.agilent.com/
 
Description 028081_D_20100413

Agilent human genome CGH + SNP 420K microarray design, April 2010

Arrays of this design have barcodes that begin with 16028081 or 2528081.

Orientation:
Features are numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software.

The ID column represents the Agilent Feature Extraction feature number.

Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface).

To match data scanned on an Axon scanner, use the RefNumber column contained in the Agilent-provided GAL file as the ID_REF column in sample submissions.
 
Submission date Dec 23, 2010
Last update date Jun 19, 2018
Organization Agilent Technologies
E-mail(s) [email protected]
Phone 877-424-4536
URL http://www.agilent.com
Department
Street address
City Palo Alto
State/province CA
ZIP/Postal code 94304
Country USA
 
Samples (6) GSM3954346, GSM3954347, GSM3954348, GSM3954349, GSM4095016, GSM4095059
Series (3)
GSE134498 DNA copy number alteration analysis of radioresistant and radiosensitive prostate cancer cell lines
GSE134500 DNA copy number alteration analysis and gene expression profiles comparing radioresistant to radiosensitive prostate cancer cell lines
GSE137959 Copy-Number abberation profiles of glioma patient tissue samples and corresponding xenografted tumor samples as well as cell lines derived there-of
Relations
Alternative to GPL11363

Data table header descriptions
ID Agilent feature number
COL Column
ROW Row
SPOT_ID Spot identifier
CONTROL_TYPE Control type
GB_ACC GenBank or RefSeq Accession
GENE_SYMBOL Gene Symbol
GENE_NAME Gene Name
ACCESSION_STRING Accession String
CHROMOSOMAL_LOCATION Chromosomal Location
CYTOBAND Cytoband
DESCRIPTION Description
SNP_ID_LIST dbSNP identifier
RANGE_GB RefSeq accession.version of chromosome (NCBI Build 37, UCSC hg19)
RANGE_START Start coordinate of oligonucleotide relative to RANGE_GB
RANGE_END End coordinate of oligonucleotide relative to RANGE_GB

Data table
ID COL ROW SPOT_ID CONTROL_TYPE GB_ACC GENE_SYMBOL GENE_NAME ACCESSION_STRING CHROMOSOMAL_LOCATION CYTOBAND DESCRIPTION SNP_ID_LIST RANGE_GB RANGE_START RANGE_END
1 528 796 HsCGHBrightCorner pos
2 528 794 DarkCorner pos
3 528 792 DarkCorner pos
4 528 790 A_20_P00152442 snp dbsnp|rs10111905 chr8:98394822-98394822 q22.1 NA rs10111905 NC_000008.10 98394822 98394822
5 528 788 A_16_P30142363 FALSE NM_006279 ST3GAL3 ST3 beta-galactoside alpha-2,3-sialyltransferase 3 ref|NM_006279|ref|NM_174963|ref|NM_174964|ref|NM_174965|ref|NM_174966|ref|NM_174967|ref|NM_174968|ref|NM_174969|ref|NM_174970|ref|NM_174971 chr1:44365341-44365390 hs|p34.1 Homo sapiens ST3 beta-galactoside alpha-2,3-sialyltransferase 3 (ST3GAL3), transcript variant 10, mRNA. NC_000001.10 44365341 44365390
6 528 786 A_14_P113678 FALSE NM_004884 IGDCC3 immunoglobulin superfamily, DCC subclass, member 3 ref|NM_004884 chr15:65638662-65638721 hs|q22.31 Homo sapiens immunoglobulin superfamily, DCC subclass, member 3 (IGDCC3), mRNA. NC_000015.9 65638662 65638721
7 528 784 A_16_P01975040 FALSE chr8:97649870-97649929 hs|q22.1 NC_000008.10 97649870 97649929
8 528 782 A_20_P00106340 snp dbsnp|rs853744 chr1:214083953-214083953 q32.3 NA rs853744 NC_000001.10 214083953 214083953
9 528 780 A_16_P40402871 FALSE chr15:53173200-53173259 hs|q21.3 NC_000015.9 53173200 53173259
10 528 778 A_20_P00264666 snp dbsnp|rs10882123 chr10:94642494-94642494 q23.33 NA rs10882123 NC_000010.10 94642494 94642494
11 528 776 A_20_P00110889 snp dbsnp|rs13398413 chr2:77980691-77980691 p12 NA rs13398413 NC_000002.11 77980691 77980691
12 528 774 A_18_P25393309 FALSE NM_001159767 BZW2 basic leucine zipper and W2 domains 2 ref|NM_001159767|ref|NM_014038|ref|NR_027624 chr7:16722416-16722475 hs|p21.1 Homo sapiens basic leucine zipper and W2 domains 2 (BZW2), transcript variant 1, mRNA. NC_000007.13 16722416 16722475
13 528 772 A_20_P00175738 snp dbsnp|rs12861722 chr13:59335084-59335084 q21.1 NA rs12861722 NC_000013.10 59335084 59335084
14 528 770 A_16_P01933371 FALSE NM_001080416 MYBL1 v-myb myeloblastosis viral oncogene homolog (avian)-like 1 ref|NM_001080416|ref|NM_001144755 chr8:67513935-67513994 hs|q13.1 Homo sapiens v-myb myeloblastosis viral oncogene homolog (avian)-like 1 (MYBL1), transcript variant 1, mRNA. NC_000008.10 67513935 67513994
15 528 768 A_16_P39979791 FALSE chr13:63688859-63688918 hs|q21.31 NC_000013.10 63688859 63688918
16 528 766 A_16_P01459466 FALSE NM_015050 FTSJD2 FtsJ methyltransferase domain containing 2 ref|NM_015050 chr6:37446951-37447007 hs|p21.2 Homo sapiens FtsJ methyltransferase domain containing 2 (FTSJD2), mRNA. NC_000006.11 37446951 37447007
17 528 764 A_16_P21578664 FALSE NM_001163278 ODZ1 odz, odd Oz/ten-m homolog 1(Drosophila) ref|NM_001163278|ref|NM_001163279|ref|NM_014253 chrX:123514426-123514485 hs|q25 Homo sapiens odz, odd Oz/ten-m homolog 1(Drosophila) (ODZ1), transcript variant 1, mRNA. NC_000023.10 123514426 123514485
18 528 762 A_20_P00110859 snp dbsnp|rs6737296 chr2:77212204-77212204 p12 NA rs6737296 NC_000002.11 77212204 77212204
19 528 760 A_18_P10406278 FALSE NM_001357 DHX9 DEAH (Asp-Glu-Ala-His) box polypeptide 9 ref|NM_001357 chr1:182836136-182836195 hs|q25.3 Homo sapiens DEAH (Asp-Glu-Ala-His) box polypeptide 9 (DHX9), mRNA. NC_000001.10 182836136 182836195
20 528 758 A_16_P00294641 FALSE NM_022743 SMYD3 SET and MYND domain containing 3 ref|NM_022743|ref|NM_001167740 chr1:246498643-246498702 hs|q44 Homo sapiens SET and MYND domain containing 3 (SMYD3), transcript variant 2, mRNA. NC_000001.10 246498643 246498702

Total number of rows: 420288

Table truncated, full table size 78570 Kbytes.




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