REHYDRATION AND PRINTING OF THE OLIGONUCLEOTIDE MICROARRAYS 1.Add 15 uL of 3XSSC to each well of the 300 pM oligonucleotide set to make a 20 μM oligonucleotide solution. 2.Transfer onto an orbital shaker for 1 h at RT at 100 rpm. The oligonucleotides are now ready for printing. 3.The maize oligonucleotide microarrays are printed on aminosilane-coated “Superamine” slides (Telechem) using Telechem Type 946 SMP2.0 printing pins. 4.Printing conditions: Single array element printed per oligonucleotide, 48 pins in the print head, 31% relative humidity, redipping after every 50 slides. The print head Z- velocity is set to a maximum of 10 mm/sec. 5.Bake slides for 2h at 80oC. Store dry and in darkness at RT. The microarrays are sent out to recipient scientists at this point. Prior to hybridization, these next steps should be followed: IMMOBILIZATION OF THE OLIGONUCLEOTIDE ARRAY ELEMENTS 1.Rehydrate the microarray slide over 50oC water for 5-10 seconds; snap-dry on a 65oC heating block for 5 seconds. Repeat this step 4-6 times, examining the slides under a dissection microscope (or using red reflectance imaging) to verify complete re-hydration of all the spots. If re-hydration is not complete, repeat the process several more times. 2.Crosslink the oligonucleotides to the slide surface by exposing the DNA-side of the microarray to UV irradiation. We employ a Stratalinker set at an energy level of 180 mJ. 3.Wash the slides in 1% SDS dissolved in sterile ddH2O for 5 min at RT. 4.Rinse the slides by plunging 10 times into sterile ddH2O. 5.Rinse in 100% ETOH for 30 seconds to 5 min, with gentle shaking. 6.Spin dry the slides in a centrifuge at 1000 rpm for 2 min. 7.Store the slides in a light-proof box under cool dry conditions.
Support
glass
Coating
aminosilane
Description
Spotted 70-mer oligo array on glass. The maize array set 46K version contains ~46,000 unique probes from maize
The block number in which the oligo was spotted (48 total)
ROW
The row within each block that the oligo was spotted (31 total)
COLUMN
The column within each block that the oligo was spotted (31 total)
VENDOR_ID
The unique oligo ID assigned by Operon
NAME
The accession of the longest representative sequence that matches the oligo with 100% identity over 100% of the oligo sequence. The sequence can be an Assembled Zea Mays (AZM) genomic sequence (eg. ZM4_13684), a GenBank entry (eg. BG319830), a TIGR Maize Gene Index entry (TC233604) or a Maize Repeat entry (e.g. ZRSgTERTOOT22542).
SPOT_ID
GB_ACC
GenBank Accession
TIGR_ID
An identifier used by TIGR to identify a particular oligo on the array (~46k oligos).
OLIGO_CATEGORY
Single or multiple letter code designating the source database(s) the oligo was designed from: G Gene Index, A AZM, R Maize Repeat Database, O Organelle, S Special ('pet' genes, root), T Transgenes
PUTATIVE_ANNOTATION
The annotation associated with this oligo obtained by BLASTing its sequence against one of several databases (TIGR Plant Transcript Assemblies, TIGR Plant Transcript Assemblies (Maize B73), TIGR Maize Database, GenBank, TIGR Gene Index, TIGR Rice Model, Enzyme Nomenclature, TIGR Maize Repeat).
TOP_NRAA_HIT
Top match of the oligo to the non redundant amino acid database.
OTHER_MAIZE_MATCH_100_100
The accession number of other maize matches of the oligo sequence with 100% identity over 100% of the oligo sequence. The sequence could be derived from the TIGR maize gene index, AZM, Maize Repeat database or other GenBank maize sequences. The accession numbers are separated by; for the entries with more than 1 match.
MAIZE_MATCH_95_100
The accession entry of other matching gene sequences that match with 95-100% identity over 100% length of the oligo sequence.
MATCH_RICE_MODEL
The feature name of the rice gene model assigned to this oligo, if available.
EC
The Enzyme Nomenclature number for the gene associated with this oligo, if available.
GO
The Gene Ontology identifier(s) assigned to this oligo, if available.
GO_SLIM
A reduced set of Gene Ontology Identifiers assigned to the oligo, if available.
CHROMOSOME
The chromosome(s) found to contain this sequence.
Data table
ID
BLOCK
ROW
COLUMN
VENDOR_ID
NAME
SPOT_ID
GB_ACC
TIGR_ID
OLIGO_CATEGORY
PUTATIVE_ANNOTATION
TOP_NRAA_HIT
OTHER_MAIZE_MATCH_100_100
MAIZE_MATCH_95_100
MATCH_RICE_MODEL
EC
GO
GO_SLIM
CHROMOSOME
10101
1
1
1
MZ00023554
TC248295
TIGR:TC248295
TM00023554
GA
Heat shock protein 82. {Oryza sativa;} ^|^PIR|S25541|S25541 heat shock protein 82 - rice (strain Taichung Native One) {Oryza sativa;} ^|^GB|BAD08897.1|42407751|AP003892 heat shock protein 82 {Oryza sativa (j-TRUNCATED-
unknown protein {Oryza sativa (japonica cultivar-group);}
GB|BAD09975.1|42408739|AP004708
NA
NA
LOC_Os08g40580;LOC_Os05g32590;LOC_Os07g46340
NA
NA
NA
1
10118
1
1
18
MZ00027846
TC249600
TIGR:TC249600
TM00027846
GA
ESTD24835(R2634) corresponds to a region of the predicted gene. Similar to Arabidopsis thaliana chromosome II BAC T06D20 genomic sequence, complete sequence.(U90439) {Oryza sativa (japonica cultivar-group);}-TRUNCATED-
GB|BAA81870.1|5295969|AB026295
AZM4_80417
NA
LOC_Os06g06780;LOC_Os01g12820
NA
NA
NA
N/A
10119
1
1
19
MZ00027864
TC251878
TIGR:TC251878
TM00027864
G
bHLH protein family-like {Oryza sativa (japonica cultivar-group);} ^|^GB|BAD34354.1|50726634|AP006169 bHLH protein family-like {Oryza sativa (japonica cultivar-group);} ^|^GB|BAD33962.1|50726350|AP005759 bHL-TRUNCATED-
GB|BAD46373.1|52077332|AP005759
NA
maize|TC251879;AZM4_27024;AZM4_101499
LOC_Os09g29930;LOC_Os08g38210;LOC_Os02g49480
NA
NA
NA
N/A
10120
1
1
20
MZ00027870
TC263128
TIGR:TC263128
TM00027870
G
hypothetical protein {Oryza sativa (japonica cultivar-group);} ^|^GB|BAB89166.1|20146385|AP003563 hypothetical protein {Oryza sativa (japonica cultivar-group);}
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