NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Platform GPL1992 Query DataSets for GPL1992
Status Public on Apr 28, 2005
Title Maize oligo array version 1.3 array A
Technology type spotted oligonucleotide
Distribution non-commercial
Organism Zea mays
 
Description Spotted oligo array on glass. The whole maize array set 1.3 version contains 56310 unique probes from maize and array A contains 29132 of them. The number of total spots including empty and controls is 32448.
 
Web link http://www.maizearray.org
Contributor(s) Buell CR
Submission date Apr 25, 2005
Last update date Jun 16, 2005
Contact name Li Zheng
E-mail(s) maizearray_only@tigr.org
Phone 301-795-7000
Organization name The Institute for Genomic Research
Department
Lab Robin Buell
Street address 9712 Medical Center Dr.
City Rockville
State/province MD
ZIP/Postal code 20850
Country USA
 
Samples (86) GSM88828, GSM88832, GSM88834, GSM88840, GSM88844, GSM88846 
Series (6)
GSE3890 Gene expression profiling of bundle sheath and mesophyll cell types of wild-type maize seedlings.
GSE9352 Gene expression in Maize root region 2 at low water potential
GSE9369 Gene expression in Maize root region 2 at low water potential-developmental control

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)
VENDER_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
SPOT_ID
TIGR_ID The unique oligo ID assigned by the TIGR databases to each oligo
OLIGO_CATEGORY A single or multiple letter code designating the database(s) source that this oligo was mapped to: G Gene Index, A AZM, R Maize Repeat Database, O Organelle, S Special
PUTATIVE_ANNOTATION The putative annotation for this oligo. The annotation is generated by searching the representative longest sequence against a non-redundant amino acid database. The annotation from the top nraa hit (above certain cutoff (P_value of E-10)) was used as the putative annotation of the oligo. NA means no match was present in the nraa database above the cutoff value.
TOP_NRAA_HIT Genbank accession number(s) for the clone.
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 numbers of the top 3 maize matches of the oligo sequence with greater than 95% identity over 100% of the oligo sequence, but less than 100% identity. 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. Note, we only provide the top 3 matches.
MATCH_RICE_MODEL The accessions numbers of the top 3 rice models that the maize oligo align with. The longest representative sequence (the sequence in Name field) was searched against the TIGR Rice Annotation Database (Release 2) and the top 3 rice models above cutoff (P_value E-25) were listed in this field. The rice model names are separated by ; for the entries with more than 1 match.
EC The putative EC assignment for the oligo. Multiple EC# were connected by |. The longest representative sequence (the sequence in Name field) was searched against the nraa database and go.pep database to get the EC assignment using cutoff E-25 (P_value).

Data table
ID BLOCK ROW COLUMN VENDER_ID NAME GB_ACC SPOT_ID TIGR_ID OLIGO_CATEGORY PUTATIVE_ANNOTATION TOP_NRAA_HIT OTHER_MAIZE_MATCH_100_100 MAIZE_MATCH_95_100 MATCH_RICE_MODEL EC
134883 1 1 1 MZ00040724 NP592869 NP592869 TM00040724 G Opaque-2, regulatory, protein., {Zea, mays;}, ^|^GB|CAA33550.1|22388|ZMOPA2, opaque-2, protein, {Zea, mays;} SP|P12959|OP2_MAIZE NA NA 9631.m05725;9635.m00796 NA
134884 1 1 2 MZ00040730 TC245883 TIGR:TC245883 TM00040730 GA unknown, protein, {Oryza, sativa, (japonica, cultivar-group);} GB|BAC84209.1|34394796|AP005259 AZM4_82419 NA 9635.m00975;9631.m05804 NA
134885 1 1 3 MZ00040748 NP668669 NP668669 TM00040748 G OSJNBa0041A02.18, {Oryza, sativa, (japonica, cultivar-group);} GB|CAE01825.2|32482851|OSJN00077 NA NA NA 2.1.1.100
134886 1 1 4 MZ00040754 NP668875 NP668875 TM00040754 G unknown, protein, {Oryza, sativa, (japonica, cultivar-group);} GB|BAC79881.1|33146883|AP004333 NA NA NA NA
134887 1 1 5 MZ00040772 TC241997 TIGR:TC241997 TM00040772 GA adenylyl, cyclase, associated, protein, {Gossypium, hirsutum;} GB|BAA36585.1|4126473|AB014884 AZM4_59579 NA 9631.m05008;9636.m03490 NA
134888 1 1 6 MZ00040778 NP671733 NP671733 TM00040778 GA Late, embryogenesis, abundant, protein,, group, 3, (LEA)., {Zea, mays;}, ^|^PIR|S41387|S41387, group, 3, Lea, protein, MGL3, -, maize, {Zea, mays;}, ^|^GB|AAA83402.1|452560|ZMU05226, group, 3, Lea, protein, MGL3, {Zea, mays;}, ^|^GB|CAA82632.1|2654379|ZMLEAMGL3, Group, 3, Lea, protein, MGL3, {Zea, mays;}, ^|^GB|BAA05550.1|454873|MZEG3LP, group, 3, Lea, protein, MGL3, {Zea, mays;} SP|Q42376|LEA3_MAIZE AZM4_15689 NA 9633.m04368;9629.m04930 NA
134889 1 1 7 MZ00040796 AZM4_81341 TIGR:AZM4_81341 TM00040796 A OSJNBb0014D23.10, {Oryza, sativa, (japonica, cultivar-group);} GB|CAE05276.3|38605805|OSJN00289 OGFCR10TM; AZM4_81340 9632.m03131;9630.m03029;9636.m00711 NA
134890 1 1 8 MZ00040802 TC229118 TIGR:TC229118 TM00040802 GAO Photosystem, II, reaction, center, L, protein, (PSII, 5, kDa, protein)., {Nicotiana, tabacum;}, ^|^SP|P60149|PSBL_SECCE, Photosystem, II, reaction, center, L, protein, (PSII, 5, kDa, protein)., {Secale, cereale;}, ^|^SP|P60148|PSBL_POPDE, Photosystem, II, reaction, center, L, protein, (PSII, 5, kDa, protein)., {Populus, deltoides;}, ^|^SP|P60147|PSBL_PEA, Photosystem, II, reaction, center, L, protein, (PSII, 5, kDa, protein)., {Pisum, sativum;}, ^|^SP|P60146|PSBL_NICTO, Photosystem, II, reaction, center, L, protein, (PSII, 5, kDa, protein)., {Nicotiana, tom SP|P60139|PSBL_TOBAC AZM4_38555;psbL NA NA NA
134891 1 1 9 MZ00013020 NP003871 NP003871 TM00013020 GA heat, shock, transcription, factor, (clone, hsfb), -, maize, {Zea, mays;}, ^|^GB|CAA58117.1|886742|ZMHSFB, heat, shock, factor, {Zea, mays;} PIR|S61448|S61448 AZM4_72245 NA 9629.m05320;9633.m04253;9631.m06312 NA
134892 1 1 10 MZ00013026 NP004194 NP004194 TM00013026 G disease, resistance, gene, analog, PIC18, {Zea, mays;} GB|AAC83566.1|3982628|AF056158 NA NA 9629.m02505;9629.m02501;9631.m06253 NA
134893 1 1 11 MZ00013044 NP004695 NP004695 TM00013044 G Nitrate, reductase, [NADH], 3, (EC, 1.7.1.1), (NR)., {Zea, mays;}, ^|^PIR|T02240|T02240, nitrate, reductase, [NAD(P)H], (EC, 1.7.1.2), -, maize, {Zea, mays;}, ^|^GB|AAA62316.1|676850|ZMU20450, nitrate, reductase, {Zea, mays;} SP|P49102|NIA3_MAIZE NA NA 9636.m03665;9636.m03667;9630.m05247 1.7.1.1|1.7.1.2|1.7.1.3|1.7.99.4|1.6.6.1|1.8.3.1|1.6.6.3|1.6.2.2
134894 1 1 12 MZ00013050 NP174416 NP174416 TM00013050 GA unknown, {Zea, mays;} GB|AAF31170.1|6906857|AF148498 AZM4_38212 NA 9634.m04756;9630.m00423;9632.m05018 NA
134895 1 1 13 MZ00013068 AZM4_69540 TIGR:AZM4_69540 TM00013068 A inwardly, rectifying, potassium, channel, {Zea, mays;} GB|CAD18901.1|18077659|ZMA421640 NA NA 9630.m01384;9629.m01080;9629.m05388 NA
134896 1 1 14 MZ00013074 NP432526 NP432526 TM00013074 G ornithine, carbamoyltransferase, {Zea, mays;} GB|AAL75995.1|18568263|AF466646 NA NA 9630.m04631;9629.m05491 2.1.3.3
134897 1 1 15 MZ00013092 NP538812 NP538812 TM00013092 GA NA PUHDM25TB NA NA NA
134898 1 1 16 MZ00013098 NP539422 NP539422 TM00013098 GA AP2, domain, transcription, factor, {Zea, mays;} GB|AAM95247.1|22415744|AY125490 AZM4_136983 NA 9631.m00720;9636.m04603 NA
134899 1 1 17 MZ00000480 AI622173 AI622173 TM00000480 G hypothetical, protein, A_IG002N01.1, -, Arabidopsis, thaliana, {Arabidopsis, thaliana;}, ^|^GB|AAB61014.1|2191127|IG002N01, A_IG002N01.1, {Arabidopsis, thaliana;} PIR|T01705|T01705 NA NA NA NA
134900 1 1 18 MZ00000486 TC229757 TIGR:TC229757 TM00000486 GA contains, ESTs, C28373(C60860),AU092907(C60860), similar, to, Arabidopsis, thaliana, chromosome, 4,, AT4g28590, unknown, protein, {Oryza, sativa, (japonica, cultivar-group);}, ^|^GB|BAB89578.1|20160633|AP003252, contains, ESTs, C28373(C60860),AU092907(C60860), similar, to, Arabidopsis, thaliana, chromosome, 4,, AT4g28590, unknown, protein, {Oryza, sativa, (japonica, cultivar-group);} GB|BAB68110.1|15624057|AP003734 AZM4_22068 NA 9629.m06036 NA
134901 1 1 19 MZ00000504 AI629905 AI629905 TM00000504 GA putative, glycosyltransferase, protein, {Oryza, sativa, (japonica, cultivar-group);} GB|AAS07065.1|41469091|AC120529 AZM4_101405 NA 9631.m02932;9632.m05282 NA
134902 1 1 20 MZ00000510 AI637048 AI637048 TM00000510 G NA NA NA NA NA

Total number of rows: 32448

Table truncated, full table size 6129 Kbytes.




Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp

Supplementary data files not provided
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap