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Platform GPL2871 Query DataSets for GPL2871
Status Public on Sep 24, 2005
Title Agilent-012600 Arabidopsis 3 Oligo Microarray (4142A (Feature Number version)
Technology type in situ oligonucleotide
Distribution custom-commercial
Organism Arabidopsis thaliana
Manufacturer Agilent Technologies
Manufacture protocol see manufacturer's web site at http://www.agilent.com/
Catalog number G4142A
 
Description
The content on this microarray is derived from the ATH1 v.5 database of The Institute for Genomic Research (TIGR) and from the Arabidopsis MPSS database at the University of Delaware. Nearly 40,000 features represents 28,500 genes from TIGR and more than 10,000 unannotated transcripts from University of Delaware. This microarray will be useful for scientists studying gene activity associated with various plant organ functions, stages of growth, and biotic and abiotic stresses.

Arrays of this design have barcodes that begin with 16012600 or 2512600.

Orientation:
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.

*** A different version of this platform with the Agilent Probe names in the ID column is assigned accession number GPL7270.
 
Submission date Sep 23, 2005
Last update date Dec 06, 2012
Organization Agilent Technologies
E-mail(s) cag_sales-na@agilent.com
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 (39) GSM132997, GSM133000, GSM133001, GSM133005, GSM133008, GSM133013 
Series (4)
GSE5718 The protective role of silicon in the Arabidopsis-powdery mildew pathosystem
GSE7359 Comparison of expression in Arabidopsis mutant tdt-1 and wild type
GSE9346 The function of CERK1 receptor-like kinase in the chitin elicitor signaling in Arabidopsis
Relations
Alternative to GPL7270

Data table header descriptions
ID Agilent feature number
COL Column
ROW Row
NAME Name
SPOT_ID Spot identifier
CONTROL_TYPE Control type
REFSEQ RefSeqAccession
GB_ACC GenBankAccession
UNIGENE_ID UnigeneID
TIGR_ID TIGRID
ACCESSION_STRING Accession String
CHROMOSOMAL_LOCATION Chromosomal Location
DESCRIPTION Description
GO_ID GoIDs

Data table
ID COL ROW NAME SPOT_ID CONTROL_TYPE REFSEQ GB_ACC UNIGENE_ID TIGR_ID ACCESSION_STRING CHROMOSOMAL_LOCATION DESCRIPTION GO_ID
1 103 430 BrightCorner BrightCorner pos
2 103 428 NegativeControl NegativeControl neg
3 103 426 CHR4:011162877-011162936 A_84_P727047 FALSE chr4:011162877-011162936
4 103 424 At5g08139.1 A_84_P249915 FALSE NM_180459 AK117658 At.5451 TC272676 tair|At5g08139.1|ref|NM_180459|tc|TC272676|gb|AK117658 chr5:2617737-2617796 zinc finger (C3HC4-type RING finger) family protein contains Pfam profile: PF00097 zinc finger, C3HC4 type (RING finger) [At5g08139.1] GO:0003677(DNA binding)|GO:0008270(zinc ion binding)|GO:0016567(protein ubiquitination)|GO:0000151(ubiquitin ligase complex)|GO:0003723(RNA binding)|GO:0004842(ubiquitin-protein ligase activity)|GO:0005515(protein binding)|GO:0006355(regulation of transcription, DNA-dependent)
5 103 422 At5g58700.1 A_84_P15025 FALSE NM_125257 AY093217 At.26665 TC274885 tair|At5g58700.1|ref|NM_125257|tc|TC274885|gb|AY093217 chr5:23730499-23730440 phosphoinositide-specific phospholipase C family protein contains Pfam profile: PF00388 phosphatidylinositol-specific phospholipase C [At5g58700.1] GO:0004629(phospholipase C activity)|GO:0005509(calcium ion binding)|GO:0007165(signal transduction)|GO:0007242(intracellular signaling cascade)|GO:0004435(phosphoinositide phospholipase C activity)|GO:0006629(lipid metabolism)|GO:0008372(cellular_component unknown)
6 103 420 At3g25840.1 A_84_P21220 FALSE NM_113486 AY092978 At.37317 NP301388 tair|At3g25840.1|ref|NM_113486|tc|NP301388|tc|TC264229 chr3:9454363-9454304 protein kinase family protein contains Pfam profile: PF00069 eukaryotic protein kinase domain [At3g25840.1] GO:0003723(RNA binding)|GO:0005634(nucleus)|GO:0004672(protein kinase activity)|GO:0006397(mRNA processing)|GO:0006468(protein amino acid phosphorylation)|GO:0004674(protein serine/threonine kinase activity)|GO:0009507(chloroplast)|GO:0005524(ATP binding)
7 103 418 Pro25G Pro25G pos
8 103 416 CHR2:007091049-007091108 A_84_P738279 FALSE chr2:007091049-007091108
9 103 414 At4g29360.2 A_84_P21426 FALSE NM_179225 AY072133 At.31933 TC263903 tair|At4g29360.2|tair|At4g29360.1|ref|NM_179225|ref|NM_119081 chr4:14451662-14451603 glycosyl hydrolase family 17 protein similar to elicitor inducible chitinase Nt-SubE76 GI:11071974 from [Nicotiana tabacum] [At4g29360.2] GO:0004553(hydrolase activity, hydrolyzing O-glycosyl compounds)|GO:0005975(carbohydrate metabolism)|GO:0012505(endomembrane system)
10 103 412 At5g22120.1 A_84_P128986 FALSE NM_147893 NM_147893 At.20150 TC262913 tair|At5g22120.1|ref|NM_147893|tc|TC262913 chr5:7334523-7334464 expressed protein [At5g22120.1] GO:0005554(molecular_function unknown)|GO:0008372(cellular_component unknown)
11 103 410 E1A_r60_a20 E1A_r60_a20 pos
12 103 408 CHR2:010582653-010582594 A_84_P701206 FALSE chr2:010582653-010582594
13 103 406 NA NA ignore
14 103 404 Pro25G Pro25G pos
15 103 402 At3g08670.1 A_84_P554500 FALSE NM_111701 NM_111701 At.40244 TC267436 tair|At3g08670.1|ref|NM_111701|tc|TC267436 chr3:2636260-2636319 expressed protein [At3g08670.1] GO:0005739(mitochondrion)|GO:0009664(cell wall organization and biogenesis (sensu Magnoliophyta))|GO:0005199(structural constituent of cell wall)|GO:0009928(cell surface (sensu Magnoliophyta))
16 103 400 At5g15270.1 A_84_P712997 FALSE NM_180709 NM_180709 At.31826 TC254821 tair|At5g15270.1|ref|NM_180709|tc|TC254821 chr5:4961753-4961812 KH domain-containing protein various predicted proteins, Arabidopsis thaliana and Oryza sativa [At5g15270.1] GO:0003676(nucleic acid binding)|GO:0008372(cellular_component unknown)
17 103 398 At4g14960.1 A_84_P143169 FALSE NM_117582 NM_117582 At.22368 TC260997 tair|At4g14960.1|tair|At4g14960.2|ref|NM_117582|ref|NM_179057 chr4:8548733-8548674 tubulin alpha-6 chain (TUA6) nearly identical to SP|P29511 Tubulin alpha-6 chain {Arabidopsis thaliana} [At4g14960.1] GO:0005874(microtubule)|GO:0007018(microtubule-based movement)|GO:0009073(aromatic amino acid family biosynthesis)|GO:0046785(microtubule polymerization)|GO:0005200(structural constituent of cytoskeleton)|GO:0045298(tubulin)
18 103 396 At2g43420.1 A_84_P89009 FALSE NM_129903 AY045841 At.12189 TC272600 tair|At2g43420.1|ref|NM_129903|tc|TC272600|tc|TC272945 chr2:18038446-18038387 3-beta hydroxysteroid dehydrogenase/isomerase family protein contains Pfam profile PF01073 3-beta hydroxysteroid dehydrogenase/isomerase domain; similar to NAD(P)-dependent steroid dehydrogenase from Homo sapiens [SP|Q15738], Mus musculus [SP|Q9R1J0]... GO:0005783(endoplasmic reticulum)|GO:0008460(dTDP-glucose 4,6-dehydratase activity)|GO:0006694(steroid biosynthesis)|GO:0008831(dTDP-4-dehydrorhamnose reductase activity)|GO:0009225(nucleotide-sugar metabolism)|GO:0003824(catalytic activity)|GO:0003854(3-beta-hydroxy-delta5-steroid dehydrogenase activity)|GO:0003978(UDP-glucose 4-epimerase activity)|GO:0006012(galactose metabolism)|GO:0045226(extracellular polysaccharide biosynthesis)
19 103 394 At3g28470.1 A_84_P16498 FALSE NM_113767 NM_113767 At.10904 TC256899 tair|At3g28470.1|ref|NM_113767|tc|TC256899 chr3:10675891-10675832 myb family transcription factor (MYB35) similar to Atmyb103 GB:AAD40692 from [Arabidopsis thaliana]; contains PFAM profile: myb DNA binding domain PF00249 [At3g28470.1] GO:0003677(DNA binding)|GO:0006355(regulation of transcription, DNA-dependent)|GO:0003700(transcription factor activity)|GO:0005634(nucleus)
20 103 392 NA NA ignore

Total number of rows: 44290

Table truncated, full table size 12498 Kbytes.






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