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Status
Public on Sep 16, 2008
Title
EcoArray Fathead minnow 44K v1.0
Technology type
in situ oligonucleotide
Distribution
custom-commercial
Organism
Pimephales promelas Manufacturer
EcoArray, Agilent
Manufacture protocol
EcoArray selected Agilent Technologies as the manufacturer of our microarrays for environmental toxicology. Agilent uses SurePrint inkjet deposition of in situ synthesized 60-mer oligonucleotides and superior quality 1” x 3” (24.2 mm x 76.2 mm) treated glass slides for overall excellent performance of their microarrays. This process minimizes variability across each production lot (batch to batch) and provides the highest consistency in slide-to-slide comparisons. These glass slide microarrays are designed for either a one- or two-color (cyanine-3 and cyanine-5) labeling reaction, the most reliable and sensitive methods for detecting differentially expressed genes. Agilent’s Feature Extraction software, when used with a high-resolution (5μm) scanner, provides QA metrics for each individual microarray, ensuring quality results. Each slide contains four individual 44K arrays.
Catalog number
Contact EcoArray for purchase
Support
glass
Coating
unknown
Description
Our fathead minnow(FHM) microarray was constructed by first compiling all known gene sequences for fathead minnows: 250,000 ESTs published by the JGI plus our own proprietary sequences obtained from suppression subtractive hybridizations and normalized library construction. We then assembled these genes to discern ~47,000 non-overlapping unique sequences (contigs and singlets). Homology searches (Blast) were performed on these sequences in order to provide annotation (gene name) and ontology (gene function) information where present. A total of 21,495 contigs were assembled. Probes were designed using Agilent’s web-based E-Array program.
Web link
http://www.ecoarray.com Contributor(s)
Carter BJ , Larkin PM , Denslow ND Submission date
Sep 10, 2008
Last update date
Sep 16, 2008
Contact name
Barbara Joan Carter
E-mail(s)
bcarter@appliedfoodtechnologies.com Organization name
Applied Food Technologies
Department
R&D
Lab
146
Street address
12085 Research Drive
City
Alachua
State/province
FL
ZIP/Postal code
32615
Country
USA
Samples (163)
GSM353863 , GSM353867 , GSM353868 , GSM353869 , GSM353870 , GSM353873
GSM353876 ,
GSM353877 ,
GSM353880 ,
GSM353945 ,
GSM353946 ,
GSM353947 ,
GSM353948 ,
GSM353949 ,
GSM353954 ,
GSM353955 ,
GSM356556 ,
GSM356557 ,
GSM356558 ,
GSM356559 ,
GSM356560 ,
GSM356561 ,
GSM356562 ,
GSM356563 ,
GSM356601 ,
GSM356602 ,
GSM356603 ,
GSM356604 ,
GSM356605 ,
GSM356606 ,
GSM356621 ,
GSM356622 ,
GSM356623 ,
GSM356628 ,
GSM356629 ,
GSM356630 ,
GSM377753 ,
GSM377766 ,
GSM377773 ,
GSM377774 ,
GSM377788 ,
GSM377789 ,
GSM377790 ,
GSM377791 ,
GSM377793 ,
GSM377794 ,
GSM377795 ,
GSM377796 ,
GSM399553 ,
GSM399554 ,
GSM399557 ,
GSM399558 ,
GSM399559 ,
GSM399615 ,
GSM399616 ,
GSM399617 ,
GSM399618 ,
GSM399619 ,
GSM399620 ,
GSM399621 ,
GSM399622 ,
GSM399623 ,
GSM399624 ,
GSM399625 ,
GSM417500 ,
GSM417501 ,
GSM417502 ,
GSM417503 ,
GSM417504 ,
GSM417541 ,
GSM417542 ,
GSM417543 ,
GSM417544 ,
GSM417545 ,
GSM417546 ,
GSM417548 ,
GSM417549 ,
GSM417550 ,
GSM417552 ,
GSM417553 ,
GSM417554 ,
GSM417555 ,
GSM417556 ,
GSM417557 ,
GSM417705 ,
GSM417706 ,
GSM417707 ,
GSM417708 ,
GSM417709 ,
GSM417710 ,
GSM417711 ,
GSM417712 ,
GSM417713 ,
GSM417717 ,
GSM417718 ,
GSM417720 ,
GSM417723 ,
GSM417726 ,
GSM417727 ,
GSM417728 ,
GSM417752 ,
GSM417753 ,
GSM417754 ,
GSM417755 ,
GSM575362 ,
GSM575363 ,
GSM575518 ,
GSM575520 ,
GSM575521 ,
GSM575523 ,
GSM575524 ,
GSM575526 ,
GSM575527 ,
GSM575529 ,
GSM575530 ,
GSM575532 ,
GSM575533 ,
GSM575534 ,
GSM575536 ,
GSM575539 ,
GSM636878 ,
GSM636879 ,
GSM636880 ,
GSM636881 ,
GSM636882 ,
GSM636883 ,
GSM636884 ,
GSM636885 ,
GSM636886 ,
GSM636887 ,
GSM636888 ,
GSM636889 ,
GSM636890 ,
GSM636891 ,
GSM636892 ,
GSM636893 ,
GSM636894 ,
GSM636895 ,
GSM636896 ,
GSM636897 ,
GSM636898 ,
GSM636899 ,
GSM636900 ,
GSM636901 ,
GSM1066099 ,
GSM1066100 ,
GSM1066101 ,
GSM1066102 ,
GSM1066103 ,
GSM1066104 ,
GSM1066105 ,
GSM2460204 ,
GSM2460205 ,
GSM2460206 ,
GSM2460207 ,
GSM2460208 ,
GSM2460209 ,
GSM2460210 ,
GSM2460211 ,
GSM2460212 ,
GSM2460213 ,
GSM2460214 ,
GSM2460215 Series (10)
GSE14100 Effects of trenbolone, flutamide and a mix of both in fathead minnow ovaries
GSE14235 Gene expression signatures for 17α-ethinylestradiol and ZM 189,154, singly and combined, in fathead minnow testis
GSE15115 Small fish comp tox FHM haloperidol 96 h ovary
GSE15216 Effects of haloperidol on zebrafish and fathead minnow gene expression
GSE15924 Fathead minnow ovaries exposed in vivo or in vitro to fadrozole
GSE16645 Site-specific impacts on gene expression and behavior in fathead minnows exposed to streams adjacent to STPs
GSE23490 Linkage of behavioral and genomic impacts of a wastewater effluent on the fathead minnow
GSE25928 Gene expression profiling of fathead minnows (Pimephales promelas) following an acute exposure to pulp and paper mill effluents
GSE43601 Transcriptional signature of progesterone-induced germinal vesicle breakdown in the fathead minnow ovary (Pimephales promelas)
GSE93663 Fathead minnow liver samples: control, EE2 and EE2/zm
Data table header descriptions ID ProbeID EcoArray probe ID number or Agilent description of feature
TargetID Unique identifier for EcoArray FASTA sequence in EcoArray's database
GI GB_ACC SPOT_ID Row Row number assigned by Agilent
Col Column number assigned by Agilent
SEQUENCE Nucleotide sequence of 60-mer probe
NR_Hit_Acc# Top hit in the Non-redundant database (NCBI)
NR_E-Value E-value for top hit in the Non-redundant database (NCBI)
NR_Hit_Def Definition provided for the top hit in the Non-redundant database (NCBI)
NT_Hit_Acc# Top hit in the Nucelotide database (NCBI)
NT_E-Value E-value for top hit in the Nucleotide database (NCBI)
NTHit_Def Definition provided for the top hit in the Nucleotide database (NCBI)
Gene_Title Gene definition - lower e-value for NR or NT top hit
GO:_Bio Biological process gene ontology categories
GO:_Cell Cellular component gene ontology categories
GO:_Molec Molecular function gene ontology categories
Hum_Homol_Acc Accession number for matching human homology gene
Hum_Homol_Gene Definition for human homology gene
Zebrafish Matching homolog in zebrafish (Danio rerio) database
Data table ID ProbeID TargetID GI GB_ACC SPOT_ID Row Col SEQUENCE NR_Hit_Acc# NR_E-Value NR_Hit_Def NT_Hit_Acc# NT_E-Value NTHit_Def Gene_Title GO:_Bio GO:_Cell GO:_Molec Hum_Homol_Acc Hum_Homol_Gene Zebrafish 1
GE_BrightCorner
GE_BrightCorner
GE_BrightCorner
1
1
2
DarkCorner
DarkCorner
DarkCorner
1
2
3
DarkCorner
DarkCorner
DarkCorner
1
3
4
DarkCorner
DarkCorner
DarkCorner
1
4
5
DarkCorner
DarkCorner
DarkCorner
1
5
6
DarkCorner
DarkCorner
DarkCorner
1
6
7
DarkCorner
DarkCorner
DarkCorner
1
7
8
DarkCorner
DarkCorner
DarkCorner
1
8
9
DarkCorner
DarkCorner
DarkCorner
1
9
10
DarkCorner
DarkCorner
DarkCorner
1
10
11
DarkCorner
DarkCorner
DarkCorner
1
11
12
EA_Pp_55545
FHM_JGI_only_filt.7826.C1___1rc_nr0nt1
FHM_JGI_only_filt.7826.C1___1rc_nr0nt1
1
12
GATATTTCTGCAAACTTGTAAATAGAGTTAAATAAATGTTAGGGGTGAGATCTCTCTCCC
NP_700880
1.3033
erythrocyte membrane protein 1 (PfEMP1) [Plasmodium falciparum 3D7] >gi|23495941|gb|AAN35604.1| erythrocyte membrane protein 1 (PfEMP1) [Plasmodium falciparum 3D7]
AY427671
1.40E-45
Danio rerio RGS12TS-S mRNA, complete cds, alternatively spliced
Regulator Of G-protein Signalling 12 /
GO:0009968; negative regulation of signal transduction GO:0007165; signal transduction
(no info)
GO:0005096; GTPase activator activity GO:0004871; signal transducer activity GO:0005057; receptor signaling protein activity GO:0005515; protein binding
378970
13
EA_Pp_65622
FHM_JGI_only_filt.3463.C2___1_nr0nt_minus
FHM_JGI_only_filt.3463.C2___1_nr0nt_minus
1
13
ACATAAAGCTCATGTTCACGCATCTTCTTCTCTTAAAAATTGTGCCAATATCCACAGACA
No Hit
BX530035
1.89E-09
Zebrafish DNA sequence from clone CH211-257I19 in linkage group 21, complete sequence
14
EA_Pp_64839
gi_73500372_gb_DT230237.1_DT230237___1_nr0nt_minus
73500372 DT230237.1 1
14
ATCCACTGTAAGACCAAATATTCGCTGAAAATGACAAAAAAGAGGAAATTAAACGACAGC
EAA77871
0.315287
hypothetical protein FG07677.1 [Gibberella zeae PH-1] >gi|46126599|ref|XP_387853.1| hypothetical protein FG07677.1 [Gibberella zeae PH-1]
BX005355
2.01E-06
Zebrafish DNA sequence from clone CH211-222M2, complete sequence
15
EA_Pp_66948
FHM_JGI_only_filt.12123.C1___1_nrnt
FHM_JGI_only_filt.12123.C1___1_nrnt
1
15
AGCCCATTAGGGTTCCCCAGGGAAATAAGTTTTGAATTTGACTGAATGTGATGAATACCT
AAH52142
0
Similar to forssman glycolipid synthetase [Danio rerio] >gi|41056179|ref|NP_956623.1| similar to forssman glycolipid synthetase [Danio rerio]
BC052142
0
Danio rerio zgc:56701, mRNA (cDNA clone MGC:56701 IMAGE:6034178), complete cds
Zgc:56701 /
GO:0005975; carbohydrate metabolism
GO:0016020; membrane
GO:0016758; transferase activity, transferring hexosyl groups
NP_065202
28
393300
16
EA_Pp_71427
gi_73658209_gb_DT317493.1_DT317493___0
73658209 DT317493.1 1
16
ATTTTTCCCAACCAAACCCGGAGGGGGGGAAATTTTGGGGGGAACCGGGAAGGGACCCCG
No Hit
AC004009
0.809532
Homo sapiens PAC clone RP5-1103I5 from 7, complete sequence
17
EA_Pp_50853
FHM_JGI_only_filt.4111.C1___1_nrnt
FHM_JGI_only_filt.4111.C1___1_nrnt
1
17
CAATCTCCTTGGGTTTAAGACGTCTATTGTGAAGACTTTTGGTTTGTAAATATATGGATG
NP_001025315
0
hypothetical protein LOC560495 [Danio rerio] >gi|55251309|emb|CAH68904.1| novel protein similar to human and mouse E2F transcription factor family [Danio rerio]
BX255963
0
Zebrafish DNA sequence from clone CH211-195D17 in linkage group 20, complete sequence
E2F Transcription Factor 6 /
GO:0000074; regulation of progression through cell cycle GO:0006350; transcription GO:0000083; G1/S-specific transcription in mitotic cell cycle GO:0006355; regulation of transcription, DNA-dependent GO:0007049; cell cycle
GO:0005662; DNA replication factor A complex GO:0005667; transcription factor complex GO:0005634; nucleus
GO:0003700; transcription factor activity GO:0003677; DNA binding
NP_937987
1876
560495
18
EA_Pp_57995
gi_73454987_gb_DT194936.1_DT194936___1rc_nr0nt
73454987 DT194936.1 1
18
CACATGGTCTTTATACGTAGTCGTTCAAAAGTTTAGGGTTTATGGGTTTTTTCACCGAGG
XP_827252
7.8956
hypothetical protein Tb09_211_1080 [Trypanosoma brucei] >gi|70831417|gb|EAN76922.1| hypothetical protein, unlikely [Trypanosoma brucei]
BX465859
5.37E-10
Zebrafish DNA sequence from clone DKEYP-67G10 in linkage group 4, complete sequence
19
EA_Pp_63064
gi_72442616_gb_DT098631.1_DT098631___1_nrnt
72442616 DT098631.1 1
19
TGGCATCACTATTGACAGAGAGAATCCTCAATGGTATTATTACTTCCTTTGTGGAGTGAG
NP_001007433
0
hypothetical protein LOC492791 [Danio rerio] >gi|55250009|gb|AAH85413.1| Zgc:101686 [Danio rerio]
BX005048
1.80E-40
Zebrafish DNA sequence from clone CH211-167M1, complete sequence
Galactokinase 2 /
GO:0006012; galactose metabolism GO:0008152; metabolism GO:0046835; carbohydrate phosphorylation GO:0016310; phosphorylation
GO:0005737; cytoplasm
GO:0016301; kinase activity GO:0004335; galactokinase activity GO:0005524; ATP binding GO:0016773; phosphotransferase activity, alcohol group as acceptor GO:0016740; transferase activity GO:0000166; nucleotide binding
NP_002035
2585
492791
20
EA_Pp_66889
gi_73559092_gb_DT257143.1_DT257143___1rc_nrnt
73559092 DT257143.1 1
20
ATGCATTTCTTCGGAGAGCAGTAGAGACATTGCTTAGCACCTGCTTTGAAGCCATAGTGA
XP_696215
0
PREDICTED: similar to Galanin receptor type 1 (GAL1-R) (GALR1) [Danio rerio]
BX572622
0
Zebrafish DNA sequence from clone CH211-150O20 in linkage group 19, complete sequence
Galanin Receptor 1 /
GO:0006811; ion transport GO:0007218; neuropeptide signaling pathway GO:0007194; negative regulation of adenylate cyclase activity GO:0007186; G-protein coupled receptor protein signaling pathway GO:0007268; synaptic transmission GO:0007165; signal transduction GO:0007586; digestion
GO:0016021; integral to membrane GO:0005886; plasma membrane GO:0016020; membrane
GO:0001584; rhodopsin-like receptor activity GO:0004930; G-protein coupled receptor activity GO:0004966; galanin receptor activity GO:0004871; signal transducer activity GO:0004872; receptor activity
NP_001471
2587
567820
44407 22297 Kbytes .Supplementary data files not provided
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