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Status
Public on Sep 02, 2010
Title
Maize Pioneer Hi-Bred 105K mRNA Microarray
Technology type
spotted oligonucleotide
Distribution
custom-commercial
Organism
Zea mays Manufacturer
Agilent
Manufacture protocol
Produced by:
Support
glass
Description
The Agilent “105K” microarray chip was designed for maize genomic and transcript sequences in an effort to cover most maize genes with at least one 60-mer oligonucleotide probe. A pool of about 1.4 million public and private ESTs was consulted, derived from diverse tissues and treatments. The majority of the sequences was derived from the B73 genotype, but there were other genotypes represented. A higher quality subset of 1.1 million ESTs was used to generate a transitory transcript assembly of about 66K transcript sequences of average length 1.0 kb. At least one 60-mer oligo was designed for nearly all of these transcripts, but at times more than one oligo was designed per transcript. In an effort to identify other genes, or perhaps parts of genes, not represented in the 66K transcript set, and to fill out the array, various BLAST analyses were conducted against the then (in fall 2006) available public B73 genomic sequences, namely B73 BACs in GenBank and the AZM5 GSS Assembly dataset produced by TIGR. The resulting array design is believed to encompass most maize genes at least once, but there are certainly genes missing, others represented more than once, and sequence errors or genotypic variation in the dataset, or oligos designed to straddling intron-exon junctions, or to chimeric junctions inherent in ESTs and their assemblies, that may deter some oligos from functioning against a B73-specific transcript sample. Subsequent efforts to estimate the number of unique genes in this microarray suggest about 45,000 genes. This “105K” format Agilent microarray consists of 103,685 oligos designed to maize genic sequences. The balance of the space on the “105K” microarray (105,073 total oligos) was reserved for technical and internal hybridization controls.
Contributor(s)
Hayes KR , Simmons CR , Hu B Submission date
Aug 18, 2010
Last update date
Apr 14, 2011
Contact name
Kevin Robert Hayes
E-mail(s)
kevin.hayes@pioneer.com Organization name
Pioneer Hi-Bred International
Street address
7200 NW 62nd Ave
City
Johnston
State/province
IA
ZIP/Postal code
50131-0184
Country
USA
Samples (370)
GSM589724 , GSM589725 , GSM589726 , GSM589727 , GSM589728 , GSM589729
GSM589730 ,
GSM589731 ,
GSM589732 ,
GSM589733 ,
GSM589734 ,
GSM589735 ,
GSM589736 ,
GSM589737 ,
GSM589738 ,
GSM589739 ,
GSM589740 ,
GSM589741 ,
GSM589742 ,
GSM589743 ,
GSM589744 ,
GSM589745 ,
GSM589746 ,
GSM589747 ,
GSM589748 ,
GSM589749 ,
GSM589750 ,
GSM589751 ,
GSM589752 ,
GSM589753 ,
GSM589754 ,
GSM589755 ,
GSM589756 ,
GSM589757 ,
GSM589758 ,
GSM589759 ,
GSM625400 ,
GSM625401 ,
GSM625402 ,
GSM625403 ,
GSM625404 ,
GSM625405 ,
GSM625406 ,
GSM625407 ,
GSM625408 ,
GSM625409 ,
GSM625410 ,
GSM625411 ,
GSM625412 ,
GSM625413 ,
GSM625414 ,
GSM625415 ,
GSM625416 ,
GSM625417 ,
GSM625418 ,
GSM625419 ,
GSM625420 ,
GSM625421 ,
GSM625422 ,
GSM625423 ,
GSM640035 ,
GSM640036 ,
GSM640037 ,
GSM640038 ,
GSM640039 ,
GSM640040 ,
GSM640041 ,
GSM640042 ,
GSM640043 ,
GSM640044 ,
GSM640045 ,
GSM640046 ,
GSM640047 ,
GSM640048 ,
GSM640049 ,
GSM640050 ,
GSM640051 ,
GSM640052 ,
GSM640053 ,
GSM640054 ,
GSM640055 ,
GSM640056 ,
GSM640057 ,
GSM640058 ,
GSM640059 ,
GSM640060 ,
GSM640061 ,
GSM640062 ,
GSM640063 ,
GSM640064 ,
GSM640065 ,
GSM640066 ,
GSM640067 ,
GSM640068 ,
GSM640069 ,
GSM640070 ,
GSM640071 ,
GSM640072 ,
GSM640073 ,
GSM640074 ,
GSM640075 ,
GSM640076 ,
GSM640077 ,
GSM640078 ,
GSM640079 ,
GSM640080 ,
GSM640081 ,
GSM640082 ,
GSM640083 ,
GSM640084 ,
GSM640085 ,
GSM640086 ,
GSM640087 ,
GSM640088 ,
GSM640089 ,
GSM640090 ,
GSM640091 ,
GSM640092 ,
GSM640093 ,
GSM640094 ,
GSM640095 ,
GSM640096 ,
GSM741394 ,
GSM741395 ,
GSM741396 ,
GSM741397 ,
GSM741398 ,
GSM741399 ,
GSM741400 ,
GSM741401 ,
GSM741402 ,
GSM741403 ,
GSM741404 ,
GSM741405 ,
GSM741406 ,
GSM741407 ,
GSM741408 ,
GSM741409 ,
GSM741410 ,
GSM741411 ,
GSM741412 ,
GSM741413 ,
GSM741414 ,
GSM741415 ,
GSM741416 ,
GSM741417 ,
GSM741418 ,
GSM741419 ,
GSM741420 ,
GSM741421 ,
GSM741422 ,
GSM741423 ,
GSM741424 ,
GSM741425 ,
GSM741426 ,
GSM741427 ,
GSM741428 ,
GSM741429 ,
GSM741430 ,
GSM741431 ,
GSM741432 ,
GSM741433 ,
GSM741434 ,
GSM741435 ,
GSM741436 ,
GSM741437 ,
GSM741438 ,
GSM741439 ,
GSM741440 ,
GSM741441 ,
GSM741442 ,
GSM741443 ,
GSM741444 ,
GSM741445 ,
GSM741446 ,
GSM741447 ,
GSM741448 ,
GSM741449 ,
GSM741450 ,
GSM741451 ,
GSM741452 ,
GSM741453 ,
GSM741454 ,
GSM741455 ,
GSM741456 ,
GSM741457 ,
GSM741458 ,
GSM741459 ,
GSM741460 ,
GSM741461 ,
GSM741462 ,
GSM741463 ,
GSM741464 ,
GSM741465 ,
GSM741466 ,
GSM741467 ,
GSM741468 ,
GSM741469 ,
GSM741470 ,
GSM741471 ,
GSM741472 ,
GSM741473 ,
GSM741474 ,
GSM741475 ,
GSM741476 ,
GSM741477 ,
GSM741478 ,
GSM741479 ,
GSM741480 ,
GSM741481 ,
GSM741482 ,
GSM741483 ,
GSM741484 ,
GSM741485 ,
GSM741486 ,
GSM741487 ,
GSM741488 ,
GSM741489 ,
GSM741490 ,
GSM741491 ,
GSM741492 ,
GSM741493 ,
GSM741494 ,
GSM741495 ,
GSM741496 ,
GSM741497 ,
GSM741498 ,
GSM741499 ,
GSM741500 ,
GSM741501 ,
GSM741502 ,
GSM741503 ,
GSM741504 ,
GSM741505 ,
GSM741506 ,
GSM741507 ,
GSM741508 ,
GSM741509 ,
GSM741510 ,
GSM741511 ,
GSM741512 ,
GSM741513 ,
GSM741514 ,
GSM741515 ,
GSM741516 ,
GSM741517 ,
GSM741518 ,
GSM741519 ,
GSM741520 ,
GSM741521 ,
GSM741522 ,
GSM741523 ,
GSM741524 ,
GSM741525 ,
GSM741526 ,
GSM741527 ,
GSM741528 ,
GSM741529 ,
GSM741530 ,
GSM741531 ,
GSM741532 ,
GSM741533 ,
GSM741534 ,
GSM741535 ,
GSM741536 ,
GSM741537 ,
GSM741538 ,
GSM741539 ,
GSM741540 ,
GSM741541 ,
GSM741542 ,
GSM741543 ,
GSM741544 ,
GSM741545 ,
GSM741546 ,
GSM741547 ,
GSM741548 ,
GSM741549 ,
GSM741550 ,
GSM741551 ,
GSM741552 ,
GSM741553 ,
GSM741554 ,
GSM741555 ,
GSM741556 ,
GSM741557 ,
GSM741558 ,
GSM741559 ,
GSM741560 ,
GSM741561 ,
GSM741562 ,
GSM741563 ,
GSM741564 ,
GSM741565 ,
GSM741566 ,
GSM741567 ,
GSM741568 ,
GSM741569 ,
GSM741570 ,
GSM741571 ,
GSM741572 ,
GSM741573 ,
GSM741574 ,
GSM741575 ,
GSM741576 ,
GSM741577 ,
GSM741578 ,
GSM741579 ,
GSM741580 ,
GSM741581 ,
GSM741582 ,
GSM741583 ,
GSM741584 ,
GSM741585 ,
GSM741586 ,
GSM741587 ,
GSM741588 ,
GSM741589 ,
GSM741590 ,
GSM741591 ,
GSM741592 ,
GSM741593 ,
GSM741594 ,
GSM741595 ,
GSM741596 ,
GSM741597 ,
GSM741598 ,
GSM741599 ,
GSM741600 ,
GSM741601 ,
GSM741602 ,
GSM741603 ,
GSM741604 ,
GSM741605 ,
GSM741606 ,
GSM741607 ,
GSM741608 ,
GSM741609 ,
GSM741610 ,
GSM741611 ,
GSM741612 ,
GSM741613 ,
GSM741614 ,
GSM741615 ,
GSM741616 ,
GSM741617 ,
GSM741618 ,
GSM741619 ,
GSM741620 ,
GSM741621 ,
GSM741622 ,
GSM741623 ,
GSM741624 ,
GSM741625 ,
GSM741626 ,
GSM741627 ,
GSM741628 ,
GSM741629 ,
GSM741630 ,
GSM741631 ,
GSM741632 ,
GSM741633 ,
GSM741634 ,
GSM741635 ,
GSM741636 ,
GSM741637 ,
GSM741638 ,
GSM741639 ,
GSM741640 ,
GSM741641 Series (6)
GSE23916 Diurnal Regulation of Gene Expression in Immature Ear Over a 72-Hour Period
GSE23917 Diurnal Regulation of Gene Expression in Leaves Over a 72-Hour Period
GSE23918 Diurnal Regulation of Gene Expression in Leaves and Immature Ears Over a 72-Hour Period
GSE25467 Maize coleoptilar node development: WT vs. rtcs
GSE26071 Examine gene expression in maize pulvini in gravitropsim
GSE29964 Genome-wide expression quantitative trait loci (eQTL) analysis in maize
Data table header descriptions ID Pioneer probe ID
COL Y Position on Agilent Microarray
ROW X Position on Agilent Microarray
NAME Agilent_Probe_ID
CONTROL_TYPE Control Spot ID
CLONE_ID SPOT_ID GENE_SYMBOL Agilent_Probe ID
TIGR_ID DFCI ZMGI 19 Accession
DESCRIPTION DFCI ZMGI 19 Annotation
SEQUENCE Probe Sequence
Data table ID COL ROW NAME CONTROL_TYPE CLONE_ID SPOT_ID GENE_SYMBOL TIGR_ID DESCRIPTION SEQUENCE A105072_GE_BrightCorner
1
1
GE_BrightCorner
pos
--control
A104873_GE_BrightCorner
1
2
GE_BrightCorner
pos
--control
A105071_GE_BrightCorner
1
3
GE_BrightCorner
pos
--control
A104872_DarkCorner
1
4
DarkCorner
pos
--control
A105070_DarkCorner
1
5
DarkCorner
pos
--control
A104871_DarkCorner
1
6
DarkCorner
pos
--control
A105069_DarkCorner
1
7
DarkCorner
pos
--control
A4225485
1
8
P1000302172
FALSE
TIGR: TC415566
P1000302172
TC415566
"TC415566 similar to UniRef100_A7PKP5 Cluster: Chromosome chr7 scaffold_20, whole genome shotgun sequence; n=1; Vitis vinifera|Rep: Chromosome chr7 scaffold_20, whole genome shotgun sequence - Vitis vinifera (Grape), partial (8%)"
AGTATTCCTTACAATCTCAGTTTGAACCCCATACTGAAAAATGCAGCTTGCTACCATACA
A4238718
1
9
P1000220196
FALSE
TIGR: CD959097
P1000220196
CD959097
CD959097
TTGCAGTAGTGATATTTATTTTCCTGATTATCAGTGGCATGAGTCTGTGCCTGTATGTTA
A4229324
1
10
P1000215839
FALSE
TIGR: DT652063
P1000215839
DT652063
"DT652063 homologue to UniRef100_Q7PC76 Cluster: Cellulose synthase-like A1; n=1; Oryza sativa Japonica Group|Rep: Cellulose synthase-like, partial (44%)"
AGATGCTCATGGAGATTGTGACGAACAAGAAAGTGACGATCTGGAAGAAGATCCACGTCA
A4205674
1
11
P1000231607
FALSE
TIGR: TC423742
P1000231607
TC423742
"TC423742 weakly similar to UniRef100_A7NUR2 Cluster: Chromosome chr18 scaffold_1, whole genome shotgun sequence; n=1; Vitis vinifera|Rep: Chromosome chr18 scaffold_1, whole genome shotgun sequence - Vitis vinifera (Grape), partial (22%)"
TGTGTGGCTTTCTAACTTGACCTACCTAGCTCCCATCCCCATGCATGTATAAACGAGATA
A4239386
1
12
P1000267936
FALSE
TIGR: TC425661
P1000267936
TC425661
TC425661
CTGGTCCATCATCATGATCATCATCTAGGTCTTCATCCTACATTTTGTTAAAGGAATATA
A4239612
1
13
P1000284154
FALSE
TIGR: TC375558
P1000284154
TC375558
"TC375558 UniRef100_Q9LKW7 Cluster: Calcium/proton exchanger CAX1-like protein; n=1; Zea mays|Rep: Calcium/proton exchanger CAX1-like protein - Zea mays (Maize), complete"
GTAAAGAGTGACTGTTCTATGCGTTTTTGCAGGATGGATCATCACATTATCTGAAGGGAC
A4205099
1
14
P1000271359
FALSE
TIGR: TC449438
P1000271359
TC449438
"TC449438 similar to UniRef100_A3WZK6 Cluster: Chromosome segregation and condensation protein ScpB; n=1; Nitrobacter sp. Nb-311A|Rep: Chromosome segregation and condensation protein ScpB - Nitrobacter sp. Nb-311A, partial (6%)"
CCGCTCGCCGCCACGTGGTCACCACACTTATGGTTCCCCTGCCTGTAAGACCAGGATAGA
A4240206
1
15
P1000267663
FALSE
TIGR: TC379341
P1000267663
TC379341
"TC379341 similar to UniRef100_Q75GC3 Cluster: Expressed protein, having alternative splicing products; n=1; Oryza sativa Japonica Group|Rep: Expressed protein, having alternative splicing products - Oryza sativa subsp. japonica (Rice), partial (55%)"
GGAGTGGCAGTTCAAAGACTGGCCCTTCAAGGACCATGTAGAGATCTTCAACAGAGGTGT
A4240428
1
16
P1000310066
FALSE
TIGR: CO450065
CO450065
CO450065
TTTATCTATTTTAGTTGGGGTGTTTGTCAGCTGACAAACGCTCTGTCCCTGCCCCTATTC
A4240648
1
17
P1000271306
FALSE
TIGR: TC453834
P1000271306
TC453834
"TC453834 homologue to UniRef100_Q2RAA8 Cluster: Expressed protein; n=2; Oryza sativa Japonica Group|Rep: Expressed protein - Oryza sativa subsp. japonica (Rice), partial (6%)"
AAACAACGCCAAGAGTGATTGTTAGGCAGTGTTTTGTTTGTATGATCTTAGTTTGTTTGT
A4198620
1
18
P1000282576
FALSE
TIGR: TC386138
P1000282576
TC386138
"TC386138 weakly similar to UniRef100_A7P3S1 Cluster: Chromosome chr1 scaffold_5, whole genome shotgun sequence; n=1; Vitis vinifera|Rep: Chromosome chr1 scaffold_5, whole genome shotgun sequence - Vitis vinifera (Grape), partial (45%)"
ATATGGGCCAGTTGTGCAGATTCTTGATCCTCCAAAGGACGGGTTTGATCTCACAATGAA
A4207046
1
19
P1000257033
FALSE
TIGR: TC386732
P1000257033
TC386732
"TC386732 similar to UniRef100_Q688X5 Cluster: WRKY transcription factor; n=1; Oryza sativa Japonica Group|Rep: WRKY transcription factor - Oryza sativa subsp. japonica (Rice), partial (31%)"
CTATTAGCTGATCGAATTCAGGGCAGCTGGACGTTGCTGCCGTTGCTGTGGACGACGAAG
A4241294
1
20
P1000217633
FALSE
TIGR: TC387611
P1000217633
TC387611
TC387611
ACTAGAAAATCATGTCTCTCATGTGGTCTTTTTGGCCCCCCTGAATTTTCATCCTGCGTC
105072 22904 Kbytes .Supplementary data files not provided
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