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Platform GPL2878 Query DataSets for GPL2878
Status Public on Sep 24, 2005
Title Agilent-013223 D. rerio (Zebrafish) Oligo Microarray G2518A Option 001 (Feature Number version)
Technology type in situ oligonucleotide
Distribution custom-commercial
Organism Danio rerio
Manufacturer Agilent Technologies
Manufacture protocol see manufacturer's web site at http://www.agilent.com/
Catalog number G2518A Option 001
 
Description
Agilent has developed a genome-wide zebrafish microarray to enable scientists to study gene expression profiling at the global level and enhance our understanding of zebrafish biology and gene functions related to mammalian models.

Arrays of this design have barcodes that begin with 16013223 or 2513223.

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 GPL7244.
 
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 (68) GSM256781, GSM256829, GSM256830, GSM256832, GSM256834, GSM256837 
Series (6)
GSE10157 Altered gene expression in zebrafish embryos exposed to tert-butylhydroquinone and 2,3,7,8-tetrachlorodibenzo-p-dioxin
GSE15410 AB* zebrafish embryos exposed to 1 ng/mL TCDD from 1d to 5d post-fertilization.
GSE21134 The gene profile of zebrafish guanine binding protein-like 2 (Gnl2) mutant embryos versus wild-type embryos at 22 hours post-fertilization
Relations
Alternative to GPL7244

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
GENE Entrez Gene ID
GENE_SYMBOL Gene Symbol
GENE_NAME Gene Name
UNIGENE_ID UnigeneID
ENSEMBL_ID EnsemblID
TIGR_ID TIGRID
ACCESSION_STRING Accession String
CHROMOSOMAL_LOCATION Chromosomal Location
CYTOBAND Cytoband
DESCRIPTION Description
GO_ID GoIDs

Data table
ID COL ROW NAME SPOT_ID CONTROL_TYPE REFSEQ GB_ACC GENE GENE_SYMBOL GENE_NAME UNIGENE_ID ENSEMBL_ID TIGR_ID ACCESSION_STRING CHROMOSOMAL_LOCATION CYTOBAND DESCRIPTION GO_ID
1 105 215 BrightCorner BrightCorner pos
2 105 214 NegativeControl NegativeControl neg
3 105 213 TC296459 A_15_P101275 FALSE TC296459 tc|TC296459 chr22:1008099-1008158 Dr|22p13 Z502_HUMAN (Q8TBZ5) Zinc finger protein 502, partial (24%) [TC296459]
4 105 212 A_15_P113455 A_15_P113455 FALSE
5 105 211 NM_001002396 A_15_P102857 FALSE NM_001002396 NM_001002396 436669 zgc:92710 zgc:92710 Dr.31697 ENSDART00000011455 TC294947 ref|NM_001002396|gb|BC076190|ens|ENSDART00000011455|tc|TC294947 chr4:6250631-6250572 Dr|4p16.1 Danio rerio zgc:92710 (zgc:92710), mRNA [NM_001002396] GO:0005198(structural molecule activity)|GO:0005923(tight junction)|GO:0016021(integral to membrane)
6 105 210 E1A_r60_n9 E1A_r60_n9 pos
7 105 209 Pro25G Pro25G pos
8 105 208 NM_205630 A_15_P101258 FALSE NM_205630 NM_205630 402926 zgc:77228 zgc:77228 Dr.29725 TC294605 ref|NM_205630|gb|BC065326|tc|TC294605 chrNA:258486086-258486027 Danio rerio zgc:77228 (zgc:77228), mRNA [NM_205630] GO:0005554(molecular_function unknown)|GO:0008372(cellular_component unknown)
9 105 207 AL728617 A_15_P115307 FALSE AL728617 Dr.25621 TC275013 gb|AL728617|tc|TC275013 chr7:42796360-42796301 Dr|7p14.1 AL728617 Danio rerio embryonic inner ear subtracted cDNA Danio rerio cDNA clone BN0AA100ZF06 5', mRNA sequence [AL728617]
10 105 206 NM_201163 A_15_P121022 FALSE NM_201163 NM_201163 394138 zgc:56605 zgc:56605 Dr.25168 TC293983 ref|NM_201163|gb|BC067140|tc|TC293983 chr19:19144520-19144461 Dr|19p13.11 Danio rerio zgc:56605 (zgc:56605), mRNA [NM_201163] GO:0004066(asparagine synthase (glutamine-hydrolyzing) activity)|GO:0006529(asparagine biosynthesis)|GO:0006541(glutamine metabolism)|GO:0008152(metabolism)|GO:0008372(cellular_component unknown)|GO:0008652(amino acid biosynthesis)|GO:0016874(ligase activity)
11 105 205 TC268141 A_15_P113402 FALSE TC268141 tc|TC268141 chr11:23727153-23727094 Dr|11p14.3 Q6NYT6 (Q6NYT6) LOC407660 protein (Fragment), complete [TC268141]
12 105 204 NM_213466 A_15_P121392 FALSE NM_213466 NM_213466 406775 zgc:63770 zgc:63770 Dr.9070 ENSDART00000020251 TC280492 ref|NM_213466|gb|BC055238|ens|ENSDART00000020251|tc|TC280492 chr23:1448292-1448351 Danio rerio zgc:63770 (zgc:63770), mRNA [NM_213466] GO:0000398(nuclear mRNA splicing, via spliceosome)|GO:0003723(RNA binding)|GO:0006397(mRNA processing)|GO:0008372(cellular_component unknown)
13 105 203 NM_212629 A_15_P115797 FALSE NM_212629 NM_212629 322815 zgc:55404 zgc:55404 Dr.503 ENSDART00000024595 TC269337 ref|NM_212629|gb|BC044390|ens|ENSDART00000024595|tc|TC269337 chr20:30878566-30878507 Dr|20q11.21 Danio rerio zgc:55404 (zgc:55404), mRNA [NM_212629] GO:0004842(ubiquitin-protein ligase activity)|GO:0006512(ubiquitin cycle)|GO:0008372(cellular_component unknown)
14 105 202 Pro25G Pro25G pos
15 105 201 AI396947 A_15_P111405 FALSE AI396947 336846 wu:fb07f02 wu:fb07f02 Dr.34083 gb|AI396947 chr19:9277634-9277575 Dr|19p13.2 fb07f02.x1 zebrafish fin day1 regeneration Danio rerio cDNA 3', mRNA sequence [AI396947]
16 105 200 BI673395 A_15_P106519 FALSE BI673395 Dr.14484 gb|BI673395 chr9:27525846-27525905 Dr|9p21.2 ft42e05.x1 Gong zebrafish ovary Danio rerio cDNA clone IMAGE:5153361 3' similar to contains element MER6 repetitive element ;, mRNA sequence [BI673395]
17 105 199 NM_199800 A_15_P110705 FALSE NM_199800 NM_199800 327401 zgc:66448 zgc:66448 Dr.477 ENSDART00000033211 TC294373 ref|NM_199800|gb|BC059207|ens|ENSDART00000033211|tc|TC294373 chr16:20038035-20037976 Dr|16p12.3 Danio rerio zgc:66448 (zgc:66448), mRNA [NM_199800] GO:0003676(nucleic acid binding)|GO:0003677(DNA binding)|GO:0005634(nucleus)|GO:0006355(regulation of transcription, DNA-dependent)|GO:0008270(zinc ion binding)
18 105 198 NM_001002153 A_15_P116069 FALSE NM_001002153 NM_001002153 415243 zgc:86674 zgc:86674 Dr.18217 TC281850 ref|NM_001002153|gb|BC071358|tc|TC281850 chr14:47021108-47021050 Dr|14q21.3 Danio rerio zgc:86674 (zgc:86674), mRNA [NM_001002153] GO:0005554(molecular_function unknown)|GO:0008372(cellular_component unknown)
19 105 197 NM_199922 A_15_P101155 FALSE NM_199922 NM_199922 334701 zgc:63796 zgc:63796 Dr.23198 ENSDART00000046095 TC271012 ref|NM_199922|gb|BC056830|ens|ENSDART00000046095|tc|TC271012 chr19:2529184-2529243 Dr|19p13.3 Danio rerio zgc:63796 (zgc:63796), mRNA [NM_199922] GO:0005554(molecular_function unknown)|GO:0008372(cellular_component unknown)
20 105 196 CA474044 A_15_P104802 FALSE CA474044 335353 wu:fj05c03 wu:fj05c03 Dr.34518 gb|CA474044 chr7:54891481-54891422 Dr|7p11.2 AGENCOURT_10696168 NCI_CGAP_ZKid1 Danio rerio cDNA clone IMAGE:6795043 5', mRNA sequence [CA474044]

Total number of rows: 22575

Table truncated, full table size 6646 Kbytes.




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Supplementary file Size Download File type/resource
GPL2878_old_annotations.txt.gz 2.0 Mb (ftp)(http) TXT

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