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Platform GPL2884 Query DataSets for GPL2884
Status Public on Sep 24, 2005
Title Agilent-013490 Mouse Genome CGH Microarray 44A G4414A (Feature Number version)
Technology type in situ oligonucleotide
Distribution commercial
Organism Mus musculus
Manufacturer Agilent Technologies
Manufacture protocol see manufacturer's web site at
Catalog number G4414A
Designed and validated for genome-wide profiling of DNA copy number changes, Agilents Mouse Genome CGH Microarray 44A is the only commercial product for high-resolution, genome-wide analyses of chromosomal abnormalities in cancer and other genetics diseases in this critical model organism. The microarray provides comprehensive genome-wide coverage with an emphasis on the most commonly studied genomic regions and cancer-related genes. It consists of over 43,000 60-mer oligonucleotide probes, empirically validated in multiple model systems, that span coding and noncoding sequences with an average spatial resolution of 35kb. Coupled with Agilents optimized assay protocols, this microarray allows researchers to identify and locate genetic alterations in this critical model organism with the highest resolution and precision.

Arrays of this design have barcodes that begin with 16013490 or 2513490.

Features are numbered 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 Sep 23, 2005
Last update date Feb 06, 2013
Organization Agilent Technologies
Phone 877-424-4536
Street address
City Palo Alto
State/province CA
ZIP/Postal code 94304
Country USA
Samples (58) GSM107792, GSM107793, GSM177424, GSM177437, GSM183793, GSM183794 
Series (7)
GSE4767 Genomic aberrations in MMTV-cdc25a;MMTV-neu murine cell line
GSE7384 The effect of paternal haploinsufficiency for Dnmt3L
GSE7600 Atm-/-,mTerc-/-,p53-/- triple knock-out lymphoma vs normal mouse DNA (GPL2884)
Alternative to GPL16598 (Probe Name version)

Data table header descriptions
ID Agilent feature number
COL Column
SPOT_ID Spot identifier
CONTROL_TYPE Control type
GB_ACC GenBankAccession
GB_RANGE NCBI Build 35.1 Accession.Version[start..end]

Data table
1 103 430 MmCGHBrightCorner pos
2 103 428 DarkCorner pos
3 103 426 A_53_P147517 FALSE NM_009019 Rag1 recombination activating gene 1 ref|NM_009019 chr2:101489244-101489303 mm|qE2 Mus musculus recombination activating gene 1 (Rag1), mRNA. NC_000068.4[101489244..101489303]
4 103 424 A_53_P144795 FALSE AK129281 gb|AK129281 chr18:035184324-035184380 mm|qB1 Mus musculus mRNA for mKIAA1082 protein. NC_000084.3[035184324..035184380]
5 103 422 A_53_P101724 FALSE AK018536 gb|AK018536 chrX:134424262-134424321 mm|qF1 Mus musculus adult male colon cDNA, RIKEN full-length enriched library, clone:9030605E16 product:unclassifiable, full insert sequence. NC_000086.4[134424262..134424321]
6 103 420 A_53_P157163 FALSE NM_011582 Thbs4 thrombospondin 4 ref|NM_011582 chr13:089839655-089839714 mm|qC3 Mus musculus thrombospondin 4 (Thbs4), mRNA. NC_000079.3[089839655..089839714]
7 103 418 A_53_P147390 FALSE NM_011403 Slc4a1 solute carrier family 4 (anion exchanger), member 1 ref|NM_011403 chr11:102459069-102459127 mm|qE1 Mus musculus solute carrier family 4 (anion exchanger), member 1 (Slc4a1), mRNA. NC_000077.3[102459069..102459127]
8 103 416 A_53_P115558 FALSE NM_008952 Pipox pipecolic acid oxidase ref|NM_008952 chr11:077962235-077962293 mm|qB5 Mus musculus pipecolic acid oxidase (Pipox), mRNA. NC_000077.3[077962235..077962293]
9 103 414 A_53_P113076 FALSE chr15:075322480-075322539 mm|qD3 NC_000081.3[075322480..075322539]
10 103 412 A_53_P117892 FALSE chr4:080649290-080649349 mm|qC3 NC_000070.3[080649290..080649349]
11 103 410 A_53_P123271 FALSE BC085285 gb|BC085285|gb|AK016817 chr1:125734874-125734933 mm|qE3 Mus musculus G protein-coupled receptor 39, mRNA (cDNA clone MGC:102647 IMAGE:30745457), complete cds. NC_000067.3[125734874..125734933]
12 103 408 A_53_P114550 FALSE NM_008010 Fgfr3 fibroblast growth factor receptor 3 ref|NM_008010 chr5:032788631-032788690 mm|qB1 Mus musculus fibroblast growth factor receptor 3 (Fgfr3), mRNA. NC_000071.3[032788631..032788690]
13 103 406 A_53_P110833 FALSE AK033056 gb|AK033056 chr5:142985416-142985475 mm|qG2 Mus musculus adult male eyeball cDNA, RIKEN full-length enriched library, clone:7530423P13 product:unclassifiable, full insert sequence. NC_000071.3[142985416..142985475]
14 103 404 A_53_P102817 FALSE NM_172754 AI449175 expressed sequence AI449175 ref|NM_172754 chr8:068066053-068066112 mm|qB3.3 Mus musculus expressed sequence AI449175 (AI449175), mRNA. NC_000074.3[068066053..068066112]
15 103 402 A_53_P142017 FALSE NM_177155 Klri2 killer cell lectin-like receptor family I member 2 ref|NM_177155 chr6:129764385-129764444 mm|qF3 Mus musculus killer cell lectin-like receptor family I member 2 (Klri2), mRNA. NC_000072.3[129764385..129764444]
16 103 400 A_53_P146842 FALSE AK219371 gb|AK219371 chr11:032241092-032241150 mm|qA4 Mus musculus cDNA, clone:Y2G0148E07, strand:minus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000038753, based on BLAT search. NC_000077.3[032241092..032241150]
17 103 398 A_53_P150877 FALSE NM_008739 Nsd1 nuclear receptor-binding SET-domain protein 1 ref|NM_008739 chr13:054327830-054327889 mm|qB1 Mus musculus nuclear receptor-binding SET-domain protein 1 (Nsd1), mRNA. NC_000079.3[054327830..054327889]
18 103 396 A_53_P177930 FALSE BC023499 gb|BC023499 chr12:033767145-033767204 mm|qA3 Mus musculus RIKEN cDNA E030025L21 gene, mRNA (cDNA clone MGC:32220 IMAGE:5008294), complete cds. NC_000078.3[033767145..033767204]
19 103 394 A_53_P125451 FALSE AK145463 gb|AK145463|gb|AK136190|gb|AK144069|gb|BC013442|gb|BC024735|gb|BC022170|gb|AJ223958|gb|AF033031 chr2:126328960-126329019 mm|qF1 Mus musculus 1 cell embryo 1 cell cDNA, RIKEN full-length enriched library, clone:I0C0049A20 product:unclassifiable, full insert sequence. NC_000068.4[126328960..126329019]
20 103 392 A_53_P105216 FALSE NM_011589 Timeless timeless homolog (Drosophila) ref|NM_011589 chr10:127751447-127751503 mm|qD3 Mus musculus timeless homolog (Drosophila) (Timeless), mRNA. NC_000076.3[127751447..127751503]

Total number of rows: 44290

Table truncated, full table size 9320 Kbytes.

Download family Format
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MINiML formatted family file(s) MINiMLHelp

Supplementary data files not provided

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