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Platform GPL18659 Query DataSets for GPL18659
Status Public on May 01, 2015
Title Agilent-030142 ARO_Ophir_Egrandis_expression_18k
Technology type in situ oligonucleotide
Distribution custom-commercial
Organism Eucalyptus grandis
Manufacturer Agilent
Manufacture protocol http://www.genomics.agilent.com/literature.jsp?pgId=AG-PG-6&contentType=User+Manual&languageSelectionDD=English&page=1
 
Description Custum made Agilent expression array of 18K probes, designed based on eucalyptus version 1 array of 44K probes. A detailed description is described in a previous study (Abu-Abied M et al. Plant journal). Briefly, 71,208 contigs published in Novaes et al., 2008 study was run against public databases databases [e.g. NR (http://www.ncbi. nlm.nih.gov/), Arabidopsis (http://www.arabidopsis.org), proteins of other plants at TAIR (http://www.arabidopsis.org), PlantGDB (http://www.plantgdb.org) and UniRef (http://www.ebi.ac.uk) at EBI] to define the orientation. Orientation of contigs that had no hit was defined by either existence of poly-A or by discovering the ORF. Probes from each contig was designed by Tm optimizing using OLIGOWIZ (Wernersson and Nielsen, 2005). In version a subset of 18K probes were taken with a first priority for the probes that were found statistically significant in Abu-Abied M et al. Plant journal.
 
Submission date May 07, 2014
Last update date May 01, 2015
Contact name Ron Ophir
E-mail(s) ron@volcani.agri.gov.il
Organization name Agricultural Research Organization - the Volcani Center
Department Fruit Tree Sciences
Street address Hamacabim St.
City Rishon Le-Zion
ZIP/Postal code 75359
Country Israel
 
Samples (64) GSM1381342, GSM1381343, GSM1381344, GSM1381345, GSM1381346, GSM1381347 
Series (1)
GSE57375 Profiling gene expression during root induction in juvenile and mature cuttings of Eucalyptus grandis revealed developmental and auxin dependent regulation of the microtubule system

Data table header descriptions
ID The name of the probe
SEQUENCE The probe sequence
contig The contig, from which the probe was designed
query_length length of the query, used to search for orthologs of the Eucalyptus contig
A_thaliana_hit_name The best hit found in blast of the contig against TAIR
B2go_hit_name The best hit found in blast of the contig against GeneBank
PLANT_hit_name The best hit found in blast of the contig against PlantDB
Uniref50_hit_name The best hit found in blast of the contig against UniRef50
A_thaliana_HSP_querycover The percentage of the query, covered by the best hit found in blast of the contig against TAIR
B2go_HSP_querycover The percentage of the query, covered by the best hit found in blast of the contig against GeneBank
PLANT_HSP_querycover The percentage of the query, covered by the best hit found in blast of the contig against PlantDB
Uniref50_HSP_querycover The percentage of the query, covered by the best hit found in blast of the contig against UniRef50
A_thaliana_hit_significance The e-value of the high-scoring segment pairs of the query and the hit found in blast of the contig against TAIR
B2go_hit_significance The e-value of the high-scoring segment pairs of the query and the hit found in blast of the contig against GeneBank
PLANT_hit_significance The e-value of the high-scoring segment pairs of the query and the hit found in blast of the contig against PlantDB
Uniref50_hit_significance The e-value of the high-scoring segment pairs of the query and the hit found in blast of the contig against UniRef50
A_thaliana_hit_description The gene description of the best hit found in blast of the contig against TAIR
B2go_hit_description The gene description of the best hit found in blast of the contig against GeneBank
PLANT_hit_description The gene description of the best hit found in blast of the contig against PlantDB
SPOT_ID

Data table
ID SEQUENCE contig query_length A_thaliana_hit_name B2go_hit_name PLANT_hit_name Uniref50_hit_name A_thaliana_HSP_querycover B2go_HSP_querycover PLANT_HSP_querycover Uniref50_HSP_querycover A_thaliana_hit_significance B2go_hit_significance PLANT_hit_significance Uniref50_hit_significance A_thaliana_hit_description B2go_hit_description PLANT_hit_description SPOT_ID
EG_2424 CTTTCCCCGACTCTGAGCCATGGCCTGGCGCTGCGGATCGCTGTCTCGTCCCTGAT contig17497_length=257_numReads=2 0 0 0 0 0 0 0 0 0 EG_2424
EG_10621 TGGTTTCTCGGCTGCTGCAAGCGTTCGAGTATCTAATGAACTAGGAAGAGGGAGCTC KIRST.3964.C1_nseq=11 578 AT1G33090.1 gi|147823202|emb|CAN77557.1| gi|147823202|emb|CAN77557.1| UniRef50_B4FAL0 89.2733564 88.23529412 88.23529412 89.79238754 5E-54 5E-63 2E-63 8E-57 | Symbols: | MATE efflux family protein | chr1:11993438-11996522 FORWARD hypothetical protein [Vitis vinifera] hypothetical protein [Vitis vinifera] EG_10621
EG_3919 ATGAAGGAGGAGGGGATGGAGGTGAAGTACTTCTGGGCGAACACGCTGTTCCACAT contig34181_length=99_numReads=3 74 AT2G47590.1 gi|157350091|emb|CAO40029.1| gi|157350091|emb|CAO40029.1| UniRef50_A7Q0E4 97.2972973 97.2972973 97.2972973 97.2972973 0.000007 0.0009 0.00006 0.0002 | Symbols: PHR2 | PHR2 (PHOTOLYASE/BLUE-LIGHT RECEPTOR 2) | chr2:19528958-19530802 FORWARD unnamed protein product [Vitis vinifera] unnamed protein product [Vitis vinifera] EG_3919
EG_15181 CGAAGGCGCAAAGCACAAGTCTATGACAGTTGAGATGGCAGATGTTATGGCAAACT contig33007_length=94_numReads=2 94 AT4G14790.1 gi|157336518|emb|CAO71203.1| gi|157336518|emb|CAO71203.1| UniRef50_Q9SMX1 92.55319149 92.55319149 92.55319149 92.55319149 0.00004 0.00002 0.000002 0.002 "| Symbols: EDA15, ATSUV3 | ATSUV3 (embryo sac development arrest 15) | chr4:8496346-8499824 REVERSE" unnamed protein product [Vitis vinifera] unnamed protein product [Vitis vinifera] EG_15181
EG_11857 AACAAAATTCTACATCACAAGACTGGACACTGGCCGCAAAGTTGACGATCCAGAGC KIRST.7384.C1_nseq=23 0 0 0 0 0 0 0 0 0 EG_11857
EG_1753 GGACTATTCAGCTTCAACCGATTTGGTCAGCTTGGACTGGAAGAAGATGAAGATTCCTCC contig12873_length=264_numReads=3 264 AT5G24120.1 gi|157360176|emb|CAO69365.1| gi|157360176|emb|CAO69365.1| UniRef50_Q9ZNX9 98.86363636 98.86363636 98.86363636 98.86363636 1E-26 9E-28 1E-28 6E-25 "| Symbols: SIG5, SIGE | SIGE (RNA polymerase sigma subunit E); DNA binding / DNA-directed RNA polymerase/ sigma factor/ transcription factor | chr5:8157797-8159749 REVERSE" unnamed protein product [Vitis vinifera] unnamed protein product [Vitis vinifera] EG_1753
EG_5129 AGAAAGACTGGTCATGGTCCACTGGGAGGGAAGGTCGTAAGACTGAGGATGCTGAT KIRST.12278.C1_nseq=7 0 0 0 0 0 0 0 0 0 EG_5129
EG_5227 CTGGAGAACCAGATACCATTTTTCGTTGTCCAGAGGCTGTTCGAAATGGCGCTTAG KIRST.12609.C1_nseq=3 275 AT4G31980.1 gi|15236618|ref|NP_194926.1| gi|157339660|emb|CAO44201.1| UniRef50_A7P5Q2 98.18181818 98.18181818 94.90909091 94.90909091 7E-20 1E-17 7E-15 3E-14 "| Symbols: | similar to unknown protein [Arabidopsis thaliana] (TAIR:AT5G11290.1); similar to unnamed protein product [Vitis vinifera] (GB:CAO46056.1); similar to hypothetical protein [Vitis vinifera] (GB:CAN68458.1); contains InterPro domain Protein of unknown function DUF862, eukaryotic (InterPro:IPR008580); contains InterPro domain Protein of unknown function DUF247, plant (InterPro:IPR004158) | chr4:15464911-15469210 FORWARD" unknown protein [Arabidopsis thaliana] gi|2827637|emb|CAA16591.1| putative protein [Arabidopsis thaliana] gi|7270102|emb|CAB79916.1| putative protein [Arabidopsis thaliana] unnamed protein product [Vitis vinifera] EG_5227
EG_10275 CCCGTATGACAATCCCTCTGCATCTTATTTTTCTCGTCGCGTTAACCCTAGCATTGATCC KIRST.36905.C1_nseq=8 0 0 0 0 0 0 0 0 0 EG_10275
EG_12630 TGCAACAAGTGAGATTGATCGCATAGCTCGAGTTGCTTTTGAGACTGCTCGAAAGA KIRST.6819.C1_nseq=2 224 AT1G80560.1 gi|193290700|gb|ACF17658.1| gi|157349546|emb|CAO24764.1| UniRef50_Q9FMT1 96.42857143 96.42857143 96.42857143 96.42857143 6E-32 2E-30 5E-31 5E-29 "| Symbols: | 3-isopropylmalate dehydrogenase, chloroplast, putative | chr1:30292725-30295018 FORWARD" putative 3-isopropylmalate dehydrogenase large subunit [Capsicum annuum] unnamed protein product [Vitis vinifera] EG_12630
EG_8420 GCGCCAAATTGCGAAGAGTACTGAGTAGTTCTGCGAGGATTGGCTCTACATGGACAGATA KIRST.25678.C1_nseq=2 255 AT3G26220.1 gi|157863708|gb|ABV90875.1| gi|157863708|gb|ABV90875.1| UniRef50_A8IDV8 34.11764706 91.76470588 91.76470588 91.76470588 0.97 0.0000002 0.00000002 0.00000006 "| Symbols: CYP71B3 | CYP71B3 (cytochrome P450, family 71, subfamily B, polypeptide 3); oxygen binding | chr3:9597445-9599065 REVERSE" "inositol-1,4,5-triphosphate-5-phosphatase [Solanum lycopersicum]" "inositol-1,4,5-triphosphate-5-phosphatase [Solanum lycopersicum]" EG_8420
EG_9074 GAAAGAGAACAGGGTTGACGATGCTTTGAGTATGTTCAACAGAATGGTGGATGCTGGA KIRST.28870.C1_nseq=4 267 AT1G10270.1 gi|46095227|gb|AAS80150.1| gi|46095227|gb|AAS80150.1| UniRef50_Q6E438 83.52059925 98.87640449 75.28089888 98.87640449 2E-22 1E-26 9E-28 4E-27 | Symbols: GRP23 | GRP23 (GLUTAMINE-RICH PROTEIN23); binding | chr1:3363537-3366278 FORWARD ACT11D09.4 [Cucumis melo] ACT11D09.4 [Cucumis melo] EG_9074
EG_451 ATAACAGTCGAGGAAGCTCTGAACCATCCATACCTCTCGAGCCTCCATGAGATCAACG contig03586_length=274_numReads=8 273 AT1G07880.2 gi|25992532|gb|AAN77146.1| gi|25992532|gb|AAN77146.1| UniRef50_A2TDK2 98.9010989 98.9010989 98.9010989 98.9010989 2E-39 1E-38 1E-39 9E-26 | Symbols: ATMPK13 | ATMPK13 (ARABIDOPSIS THALIANA MAP KINASE 13); MAP kinase/ kinase | chr1:2434190-2435709 REVERSE mitogen-activated protein kinase [Gossypium barbadense] mitogen-activated protein kinase [Gossypium barbadense] EG_451
EG_220 AGGACATACTAAACATTCCGACGCCCAAAACTTTGCTCAAGCGGCTCTATCACGTG contig01839_KIRST.cl.5488.singlet 1230 AT1G31490.1 gi|157357271|emb|CAO63773.1| gi|157357271|emb|CAO63773.1| UniRef50_A7QKQ3 85.85365854 85.85365854 85.85365854 85.85365854 1E-125 1E-139 1E-140 1E-139 | Symbols: | transferase family protein | chr1:11271725-11273059 REVERSE unnamed protein product [Vitis vinifera] unnamed protein product [Vitis vinifera] EG_220
EG_81 TGATGTCCAAACGGATCTGACGATTAACTCATAATGCTCCTGGTGCAATTGCAATACTGC "Match1: contig00726_KIRST.cl.9479.singlet, Match2: KIRST.9479.C2_nseq=3" 0 0 0 0 0 0 0 0 0 EG_81
EG_13155 GTTGCATTAGTGGAATACGAAGGCGAGCAGCATGGTTTTCGCAAGGCTGAAAGTAT contig23127_length=103_numReads=7 102 AT5G36210.1 gi|195658571|gb|ACG48753.1| gi|115467076|ref|NP_001057137.1| UniRef50_A2YAN7 97.05882353 97.05882353 97.05882353 97.05882353 3E-11 0.000000002 3E-10 0.000000001 | Symbols: | serine-type peptidase | chr5:14265432-14270502 REVERSE acyl-peptide hydrolase-like [Zea mays] Os06g0215300 [Oryza sativa (japonica cultivar-group)] EG_13155
EG_7872 AAATTAGTTGACCAAGCCCGGATCGGGAAGTGGTGAATAGACAGGGCATTGATTTGT KIRST.22810.C1_nseq=2 0 0 0 0 0 0 0 0 0 EG_7872
EG_1722 TATAGTCCGTGATCTGGCATTGGAAGTGCAAGTAATCGTGTGGACATTTTCTCTGTGGCT contig12653_KIRST.cl.7327.singlet 0 0 0 0 0 0 0 0 0 EG_1722
EG_7726 GTATCTACGCGCTGTCGTCGCAGAACGACGTTGGGCTGCTCATGGTGCAGAACTAC KIRST.2203.C15_nseq=2 251 AT1G22900.1 gi|118483793|gb|ABK93789.1| gi|147779455|emb|CAN61168.1| UniRef50_Q45W75 99.20318725 99.20318725 99.20318725 98.00796813 8E-27 1E-30 6E-30 1E-28 | Symbols: | similar to disease resistance-responsive family protein [Arabidopsis thaliana] (TAIR:AT5G42500.1); similar to unnamed protein product [Vitis vinifera] (GB:CAO23438.1); similar to hypothetical protein [Vitis vinifera] (GB:CAN61168.1); contains InterPro domain Plant disease resistance response protein (InterPro:IPR004265) | chr1:8103899-8104480 REVERSE unknown [Populus trichocarpa] hypothetical protein [Vitis vinifera] EG_7726
EG_12353 AAAGTTACTGCTCTGATTCAACAAGCCGAGCTGCTCAGTTCCCTTGCGGTGAAAGT KIRST.967.C1_nseq=4 220 AT1G14350.2 gi|157355066|emb|CAO48427.1| gi|157355066|emb|CAO48427.1| UniRef50_Q5MG98 90 95.45454545 95.45454545 94.09090909 7E-20 2E-20 1E-21 7E-18 "| Symbols: AtMYB124, MYB124, FLP | FLP (FOUR LIPS) | chr1:4908422-4910642 FORWARD" unnamed protein product [Vitis vinifera] unnamed protein product [Vitis vinifera] EG_12353

Total number of rows: 15208

Table truncated, full table size 5669 Kbytes.




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