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Platform GPL22267 Query DataSets for GPL22267
Status Public on Aug 18, 2016
Title Maize ologonucleotide array 2k version
Technology type spotted oligonucleotide
Distribution non-commercial
Organism Zea mays
Manufacturer University of Hamburg
Manufacture protocol PRINTING OF THE OLIGONUCLEOTIDE MICROARRAYS
The oligonucleotides were synthesized by Ocimum Biosolutions (Ijsselstein, Netherlands) and printed on poly-L-lysine coated glass slides with a Microgrid II printer (BioRobotics, Boston, USA).
1. Add 15 µL of 3x SSC to each well of the 300 µM 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 poly-L-lysine coated glass slides (Menzel, Thermo Fisher Scientific) using microspot 2500 pins.
4. Printing conditions:
Microarray printer (Microgrid II printer, BioRobotics, Boston, USA). 55% relative humidity. We used microspot 2500 pins and spotted all oligos and controls (used negative controls: H300010599, H300013976, H300014151, H300016837; positive controls: Control_oligo-7, Control_oligo-12, MZ00023408, MZ00023618, MZ00023663 in two replicates.
IMMOBILIZATION OF THE OLIGONUCLEOTIDE ARRAY ELEMENTS
1. Rehydrate the microarray slide over 56 °C water for 2-3 seconds; snap-dry on a 65 °C heating block for 5 seconds. Repeat this step 3 times, examining the slides under a dissection microscope to verify complete re-hydration of all the spots. 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 60 mJ. After crosslinking slides were once again dried on a 100 °C heating block.
2. Blocking of the slides was performed according to Diehl et al. (Nucleic Acids Research 2001, 29(7): e38). Therefore slides were incubated for 1 h in blocking solution (1 g succinic anhydride, 200 ml 1,2-Dichlorethane, 2.5 ml 1-Methylimidazole), then dipped twice in 1,2-Dichlorethane. At the end slides were placed for 2 min in boiling water and then briefly transferred to 98 % ethanol.
3. Air dry slides under a clean bench.
4. Store the slides in a light-proof box in a vacuum.
 
 
Submission date Aug 02, 2016
Last update date Aug 18, 2016
Contact name Stefan Scholten
E-mail(s) stefan.scholten@uni-hamburg.de
Phone 0049 40 42816329
Organization name University of Hamburg
Department Biocenter Klein Flottbek
Lab Developmental Biology and Biotechnology
Street address Ohnhorststrasse 18
City Hamburg
State/province Hamburg
ZIP/Postal code 22609
Country Germany
 
Samples (410) GSM2263726, GSM2263727, GSM2263728, GSM2263729, GSM2263730, GSM2263731 
Series (6)
GSE85283 Gene expression profiles of 13 European maize (Zea mays L.) inbred lines: factorial 1999LP1
GSE85284 Gene expression profiles of 29 European maize inbred lines and 26 of their hybrids: factorial 2010LP1
GSE85285 Gene expression profiles of 29 European maize inbred lines, factorial 2012LP1

Data table header descriptions
ID
Column The column in which the oligo was spotted (48 total)
Row The row in which the oligo was spotted (48 total)
Status Status of the probe (gene, negative or positive control, or buffer)
OLIGO_ID The oligo ID assigned by Operon and received from maize oligonucleotide array platform GPL6438
OLIGO_SEQUENCE Sequence of the spotted oligo
ANNOTATION Annotation type: E - Exon of gene, I - Intron, N - No gene body found, R - Repeat, S - Overlapping splicing site, AE - antisense strand of exon, AI - antisense strand of intron, AR - antisense strand of repeat. Annotation described in Seifert, F., Thiemann, A., Pospisil, H., & Scholten, S. (2012). Re-annotation of the maize oligonucleotide array. Maydica, 57(1), 49-55.
GENE Gene the oligonucleotide maps to
ORF ORF Name
SPOT_ID
TRANSCRIPT Transcripts of the gene covered by the oligonucleotide (multiple separated by |)
CHROMOSOME Chromosomes with gene (multiple separated by |)
TRANSCRIPT.GENE_COPIES_OLIGO Number of transcripts of this gene or gene copies covered by this oligonucleotide
OLIGOS_PER_GENE Number of distinct oligos mapping to this gene
GENES_PER_OLIGO Number of distinct genes covered by this oligonucleotide
DESCRIPTION Putative description of the gene function based on the BlastX analysis
TOP_HIT_DESCRIPTION BlastX top hit
TOP_HIT_ACCESSION Accession of the BlastX top hit
TOP_HIT_EVALUE Evalue of the BlastX analysis
TOP_HIT_SIMILARITY Similarity of this gene to the BlastX top hit
GO_TERMS Gene Ontology terms for this gene
ANNOTATION.1 Alternative annotation (see above)
GENE.1 Alternative gene (see above)
TRANSCRIPT.1 Alternative transcript (see above)
CHROMOSOME.1 Alternative chromosome (see above)
TRANSCRIPT.GENE_COPIES_OLIGO.1 Alternative transcript.gene_copies_oligo (see above)
OLIGOS_PER_GENE.1 Alternative oligos_per_gene (see above)
GENES_PER_OLIGO.1 Alternative genes_per_oligo (see above)
DESCRIPTION.1 Alternative description (see above)
TOP_HIT_DESCRIPTION.1 Alternative top_hit_description (see above)
TOP_HIT_ACCESSION.1 Alternative top_hit_accession (see above)
TOP_HIT_EVALUE.1 Alternative top_hit_evalue (see above)
TOP_HIT_SIMILARITY.1 Alternative top_hit_similarity (see above)
GO_TERMS.1 Alternative go_terms (see above)

Data table
ID Column Row Status OLIGO_ID OLIGO_SEQUENCE ANNOTATION GENE ORF SPOT_ID TRANSCRIPT CHROMOSOME TRANSCRIPT.GENE_COPIES_OLIGO OLIGOS_PER_GENE GENES_PER_OLIGO DESCRIPTION TOP_HIT_DESCRIPTION TOP_HIT_ACCESSION TOP_HIT_EVALUE TOP_HIT_SIMILARITY GO_TERMS ANNOTATION.1 GENE.1 TRANSCRIPT.1 CHROMOSOME.1 TRANSCRIPT.GENE_COPIES_OLIGO.1 OLIGOS_PER_GENE.1 GENES_PER_OLIGO.1 DESCRIPTION.1 TOP_HIT_DESCRIPTION.1 TOP_HIT_ACCESSION.1 TOP_HIT_EVALUE.1 TOP_HIT_SIMILARITY.1 GO_TERMS.1
A0001 1 1 Gene MZ00057059 CCTATGATAGAGATCACATTTGAGTTCATGTGAACATATGTTGTGGCTAGCTAGCATTGCAGGCTGCACG I GRMZM5G851490 GRMZM5G851490 T01 10 1 3 1 probable wrky transcription factor 42-like gi|242089433|ref|XP_002440549.1|hypothetical protein SORBIDRAFT_09g002970 [Sorghum bicolor] >gi|241945834|gb|EES18979.1| hypothetical protein SORBIDRAFT_09g002970 [Sorghum bicolor] XP_002440549 2.22E-42 67 0043967|0010485|0005829|0042393|0006348|0000123 NA NA NA NA NA NA NA NA NA NA NA NA NA
A0002 1 2 Gene MZ00055772 CCATATGTATTGCTGGCACCATGGGAATACACCCTTGCTGCATGTTGAACAGGTTTAAGGGGCATCTGTC I GRMZM2G056038 GRMZM2G056038 T01|T02 6 2 4 3 sterile alpha motif domain-containing protein gi|226502152|ref|NP_001142909.1|uncharacterized protein LOC100275340 [Zea mays] >gi|223974455|gb|ACN31415.1| unknown [Zea mays] NP_001142909 2.79E-87 100 0005737|0005739 E GRMZM2G056038 T03|T04 6 2 4 3 sterile alpha motif domain-containing protein gi|226502152|ref|NP_001142909.1|uncharacterized protein LOC100275340 [Zea mays] >gi|223974455|gb|ACN31415.1| unknown [Zea mays] NP_001142909 2.79E-87 100 0005737|0005739
A0003 1 3 Gene MZ00048077 AGCTGATGAACGAGCCGCGTTGCCAGTCCGACGTGTCGGGCCACGCCATC E GRMZM2G055585 GRMZM2G055585 T01|T02 3 2 1 1 mannan endo- -beta-mannosidase 7 gi|226496153|ref|NP_001145882.1|uncharacterized protein LOC100279398 precursor [Zea mays] >gi|224029303|gb|ACN33727.1| unknown [Zea mays] NP_001145882 0 99 0005737|0016740 NA NA NA NA NA NA NA NA NA NA NA NA NA
A0004 1 4 Gene MZ00043990 GATGGATGTCTGCACTGCACTCTACAATGCTAGTCTATCTACTTACTAAATAGTAGTATAATGGTCGTGA N MZ00043990 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
A0005 1 5 Gene MZ00043252 CCGCCGTGGTGTCGCTTTGGTTTTGAAATTTAGATTCCGTTGTCCTAAAATTTATCACTACGGTCTCCGG E GRMZM2G050514 GRMZM2G050514 T01|T02 1 2 1 1 glutamine synthetase gi|162462528|ref|NP_001105538.1|glutamine synthetase root isozyme 1 [Zea mays] >gi|699623|dbj|BAA03433.1| glutamine synthetase [Zea mays] >gi|194701040|gb|ACF84604.1| unknown [Zea mays] NP_001105538 0 100 0005730|0005886|0009987|0005622|0005829|0000166 NA NA NA NA NA NA NA NA NA NA NA NA NA
A0006 1 6 negative H300014151 CTGTTTACAAGTGCCAGTCCATGGGACTGTTACCTACACATGCATCGGATTGGTTAGCCTTCATTGAGCC NA NA control NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
A0007 1 7 Gene MZ00041720 CTTGTTCTACAGGGTGCAAAGCCATGGCCCATGGCCACTCGTTGACCATGTCACGTTTTTTTCGTTTGGT E GRMZM2G142097 GRMZM2G142097 T01|T02 1 2 2 1 50s ribosomal protein l18 gi|195659183|gb|ACG49059.1|50S ribosomal protein L18 [Zea mays] ACG49059 2.30E-40 100 0000166|0005622|0016787|0003677|0005488|0006810|0005215 NA NA NA NA NA NA NA NA NA NA NA NA NA
A0008 1 8 Gene MZ00041184 TCCCTCGAGATCTGGAGGAGATTGACAAGGAGATTGAGGACAAGAAGACAGAGCTGGAGCCCAAGGTCGT N MZ00041184 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
A0009 1 9 Gene MZ00039808 CTATCCACATGGGTTGCCCAACATGCTGACCTATGACTAAGGGTCTGTTTGGTTGGGCTGTGGCTGTGAA N MZ00039808 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
A0010 1 10 Gene MZ00038633 TATGTGTGTCTGGGGTCTGGACTCGGATTACTCAGCGTTCCGATCCTGAAGGAGAAGATCAAGGAGTACA N MZ00038633 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
A0011 1 11 Gene MZ00037195 GGGCTATAAAAGGAGCCCCTAGGCGCATGGAGGAGATACACAAGCAACCTTTGAGCATTCTTGATCATCC AI AC187260.3_FG002 FGT002 FGT002 6 NA NA NA NA NA AI AC208434.3_FG003 FGT003 1 NA NA NA NA NA
A0012 1 12 Gene MZ00036425 CAAGCTAACTGGGCGATAAGTGGTTCATGCAATGATGCAAGGCGATGATGCTCCGGGAAGCAAGAGCGCC N MZ00036425 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
A0013 1 13 Gene MZ00035006 GCCTTCACTTGTTTTGCTAGTGCTTGCAGCGGACATTTTCAAGGGGAAATATATAGATGCGTCTTTTTTT N MZ00035006 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
A0014 1 14 Gene MZ00032114 CGCATTTCTTAATCGCCTTCGACTCGTTATCTTCCGCTTCTGTATATGGGAATAGCTATAGGATAGTAAG E GRMZM2G171408 GRMZM2G171408 T01|T02|T03 7 3 3 1 armadillo beta-catenin-like repeat-containing protein gi|212721540|ref|NP_001132885.1|uncharacterized protein LOC100194379 [Zea mays] >gi|195614718|gb|ACG29189.1| spotted leaf protein 11 [Zea mays] >gi|224031127|gb|ACN34639.1| unknown [Zea mays] NP_001132885 0 100 0005739|0009536 NA NA NA NA NA NA NA NA NA NA NA NA NA
A0015 1 15 Gene MZ00030845 CATTAGCGGATCGGACCTAGCGTGGAACCTCTTGTGTAATAAAATAATAAGTGTCATCACATTCCTCGCC E GRMZM2G070825 GRMZM2G070825 T01|T02 1 2 1 1 gdsl-like lipase acylhydrolase family expressed gi|212274355|ref|NP_001130647.1|uncharacterized protein LOC100191748 precursor [Zea mays] >gi|194689734|gb|ACF78951.1| unknown [Zea mays] >gi|194703012|gb|ACF85590.1| unknown [Zea mays] >gi|223947331|gb|ACN27749.1| unknown [Zea mays] NP_001130647 0 100 9536 NA NA NA NA NA NA NA NA NA NA NA NA NA
A0016 1 16 Gene MZ00029597 CCGGAGGCACTGAGGCAGTGACTGATGAATGGAGACTTGTCGTCGGTTCCGTACGTGTGTGTCTGTCGGA E GRMZM2G032594 GRMZM2G032594 T01 8 1 1 1 plasma membrane associated protein gi|226494151|ref|NP_001149332.1|LOC100282955 [Zea mays] >gi|195626458|gb|ACG35059.1| plasma membrane associated protein [Zea mays] >gi|195646108|gb|ACG42522.1| plasma membrane associated protein [Zea mays] NP_001149332 1.11E-79 100 0006139|0006350|0003723|0005515|0016740|0005634 NA NA NA NA NA NA NA NA NA NA NA NA NA
A0017 1 17 Gene MZ00028401 AGGGATGCGGGATGCGTACGGTTGCAAGCCATTGGGGCGATGCTGGAGCAAATAAAGTGATGCAGTAAAA N MZ00028401 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
A0018 1 18 Gene MZ00027338 TGCATGGAGGGCGAACGAACTCAATAAAAGAATCAGCCGGGGGTTTGATTGTCCGTCTATGTATATCATG N MZ00027338 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
A0019 1 19 Gene MZ00026352 GCTAATAATACTCGTAGCCCAAGAACAAGAACCAGGATATGGGCCTTAATAATCACCTTGAACTGCCAAA E GRMZM2G031904 GRMZM2G031904 T01 2 1 1 1 hypothetical protein [Zea mays] gi|195619930|gb|ACG31795.1|hypothetical protein [Zea mays] ACG31795 9.23E-33 100 0003676|0000166|0009536 NA NA NA NA NA NA NA NA NA NA NA NA NA
A0020 1 20 Gene MZ00025380 GCCTAGCACGTACCTGCAATGCAATGGCTGCTATCTATCTATCGCTCGCTTCGCTATCTACCAGTGCAGT E GRMZM2G445602 GRMZM2G445602 T01 1 1 2 1 fiddlehead-like protein gi|223943375|gb|ACN25771.1|unknown [Zea mays] ACN25771 0 100 0009862|0042742|0006355|0009409|0043565|0046983|0003700|0005634 AE GRMZM2G445613 T01|T02 1 NA NA NA NA NA

Total number of rows: 2304

Table truncated, full table size 817 Kbytes.




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Supplementary file Size Download File type/resource
GPL22267_complete_annotation.txt.gz 325.1 Kb (ftp)(http) TXT

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