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 Arabidopsis oligonucleotide microarrays are printed on aminosilane-coated “Superamine” slides (Telechem) or “Powermatrix” slides (Full Moon Biosystems), using Telechem Type SMP3 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.
Re-hydration and UV cross linking can be done well in advance before microarray hybridization, and the slides can be stored at room temperature for several months. However we do not recommend storage of washed microarray slides. 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 oligo array on glass. The whole maize array set 1.9 version contains 56310 unique probes from maize and array A contains 29270 of them. The number of total spots including empty and controls is 32448.
Genetic factors that respond to N in maize leaf tissue
Data table header descriptions
ID
Spot identifier for each feature
BLOCK
The block number in which the oligo was spotted (48 total)
ROW
The row within each block that the oligo was spotted (26 total)
COLUMN
The column within each block that the oligo was spotted (26 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).
GB_ACC
GenBank Accession Number
TIGR_ID
An identifier used by TIGR to identify a particular oligo on the array (~58k 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).
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_TA_MATCH
The Plant Transcript Assembly build for Maize matching EST assemblies that match with 100% identity over 100% length of the oligo sequence.
MAIZE_B73_TA_MATCH
The Plant Transcript Assembly build for Maize B73 matching EST assemblies that match with 100% identity over 100% length of the oligo sequence.
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.
CHROMOSOME
The chromosome(s) found to contain this sequence.
SPOT_ID
Data table
ID
BLOCK
ROW
COLUMN
VENDOR_ID
NAME
GB_ACC
TIGR_ID
OLIGO_CATEGORY
PUTATIVE_ANNOTATION
OTHER_MAIZE_MATCH_100_100
MAIZE_TA_MATCH
MAIZE_B73_TA_MATCH
MAIZE_MATCH_95_100
MATCH_RICE_MODEL
EC
GO
CHROMOSOME
SPOT_ID
422946
1
1
1
MZ00040724
NP592869|AY155475.1|AAO17556.1
TM00040724
S
Opaque-2 regulatory protein. {Zea mays,} ^|^GB|CAA33550.1|22388|ZMOPA2 opaque-2 protein {Zea mays,}
NA
NA
NA
NA
NA
NA
NA
N/A
NP592869|AY155475.1|AAO17556.1
422947
1
1
2
MZ00040730
TC294144
TM00040730
GA
unknown protein {Oryza sativa (japonica cultivar-group),}
Less...
More...