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Platform GPL11184 Query DataSets for GPL11184
Status Public on Jan 26, 2011
Title Loblolly pine 26K cDNA array v2.0, PtGen2
Technology type spotted DNA/cDNA
Distribution non-commercial
Organism Pinus taeda
Manufacturer Dr. Jeff Dean Laboratory, Warnell School of Forestry and Natural Resources, University of Georgia
Manufacture protocol Plasmid DNAs that had been propagated in the EST sequencing pipeline were re-arrayed and consolidated into new plates to using a BioMek 2000 liquid handling robot (Beckman Coulter, Fullerton, CA). Samples were then diluted five-fold in millipure dH20 (mp dH20) and 5mL was transferred to a 96-well plate (ABgene AB-0900, Thermo Fisher Scientific Inc. Waltham, MA) for PCR amplification. PCR reactions were performed in a 100mL volume containing 10 mM Tris (pH 8.8), 3.5 mM MgCl2, 25 mM KCl, 0.25 mM (ea.) dNTP, 0.4 mM pSLFOR2 primer {5’-AAAACGACGGCCAGTGCCAAG-3’}, 0.4mM pSLREV2 primer {5’-GCTTCCGGCTGCTATGTTGTGTGG-3’}, and 1 mL of homemade Taq polymerase. PCR reactions were incubated at 95oC for 3 min., followed by 30 amplification cycles (95oC for 30 sec., 58oC for 1 min., 72oC for 2.5 min.) and then incubated at 72oC for 7 min. Each reaction product was verified by agarose gel electrophoresis prior to samples being vacuum desiccated in a Savant Speed Vac Plus Model SC210A (Thermo Fisher Scientific Inc., Waltham, MA). Samples were resuspended in 30mL spotting buffer (150mM PO₄ 1.5M Betaine, 0.001% SDS) with a Robbins Scientific HydraTM96 liquid handling robot and 15mL was transferred to 384 well Corning Costar spotting plates 07-200-747(Corning Inc., Corning, NY). Printing was done at the Vanderbilt Microarray Shared Resource (VMSR) facility. cDNAs were spotted onto Corning UltrGAPS slides (Corning Inc., Corning, NY) and printed with a BioRobotics Microgrid II (Genomic Solutions, Ann Arbor, MI) with a 48 pin print head
Submission date Nov 09, 2010
Last update date Aug 09, 2012
Contact name Adam W. Barb
Organization name University of Georgia
Department Biochemistry and Molecular Biology
Lab B302A
Street address 180 E. Green Street
City Athens
State/province GA
ZIP/Postal code 30602
Country USA
Samples (174) GSM619307, GSM619308, GSM619309, GSM619310, GSM619311, GSM619312 
Series (2)
GSE25216 Microarray analysis and scale-free gene networks identify candidate regulators in drought-stressed roots of loblolly pine (P. taeda L.).
GSE32551 Stage-specific transcriptional changes during zygotic embryogenesis in maritime pine (Pinus pinaster Ait.)
Alternative to GPL15915

Data table header descriptions
ID Gene_ID: Unique probe ID corresponding to physical address on the array (metarow, metacolumn, row, column)
UniScript_ID 3' assembled contig IDs. Contig sequences used to design primers for multi-EST contigs. Sequences available at
CLONE_ID cDNA Clone ID. Sequences used to design primers for singleton ESTs. Sequences available at Genbank
ACCESSION_NCBInr NCBI non-redundant database BlastX accession
DESCRIPTION_NCBInr NCBI non-redundant database BlastX description
E_VALUE_NCBInr NCBI non-redundant database BlastX expect-value
ACCESSION_SWISSPROT SwissProt database BlastX accession
DESCRIPTION_SWISSPROT SwissProt database BlastX description
E_VALUE_SWISSPROT SwissProt database BlastX expect-value

Data table
ID UniScript_ID CLONE_ID ACCESSION_NCBInr DESCRIPTION_NCBInr E_VALUE_NCBInr ACCESSION_SWISSPROT DESCRIPTION_SWISSPROT E_VALUE_SWISSPROT SPOT_ID 0_18541 STRS1_54_D04_A034 gb|ACS12983.1| "2,4-dienoyl-CoA reductase [Jatropha curcas]" 2.00E-29 Q9X248|FABG_THEMA 3-oxoacyl-[acyl-carrier-protein] reductase - Thermotoga maritima 9.00E-09 0_18544 STRS1_54_E08_A034 Q9LVT1|DRL39_ARATH Putative disease resistance protein At5g47280 - Arabidopsis thaliana (Mouse-ear cress) 8.00E-04 0_18547 STRS1_55_B03_A034 emb|CAK29867.1| monooxygenase [Picea abies] emb|CAK29877.1| monooxygenase [Picea abies] emb|CAK29880.1| monooxygenase [Picea abies] emb|CAK29886.1| monooxygenase [Picea abies] emb|CAK29888.1| monooxygenase [Picea abies] emb|CAK29889.1| monooxygenase [Picea abies] emb|CAK29892.1| monooxygenase [Picea abies] emb|CAK29895.1| monooxygenase [Picea abies] emb|CAK29896.1| monooxygenase [Picea abies] emb|CAK29897.1| monooxygenase [Picea abies] emb|CAK29898.1| monooxygenase [Picea abies] emb|CAK29905.1| monooxygenase [Picea abies] 4.00E-49 Q96375|ABA2_CAPAN "Zeaxanthin epoxidase, chloroplast precursor - Capsicum annuum (Bell pepper)" 1.00E-05 0_18551 STRS1_55_C01_A034 gb|AAW69346.1| 60S ribosomal protein L10-A-like protein [Magnaporthe grisea] 2.00E-94 Q09127|RL10A_SCHPO 60S ribosomal protein L10-A - Schizosaccharomyces pombe (Fission yeast) 8.00E-75 0_18735 STRS1_65_E11_A034 gb|AAX92686.1| DNA-(adenosine-N6-)-methyltransferase [Picea abies] 2.00E-48 Q9Y5N5|N6MT1_HUMAN N(6)-adenine-specific DNA methyltransferase 1 - Homo sapiens (Human) 2.00E-09 0_18739 STRS1_65_G08_A034 gb|EEF44130.1| "Phosphatase DCR2, putative [Ricinus communis]" 5.00E-39 Q05924|DCR2_YEAST Phosphatase DCR2 - Saccharomyces cerevisiae (Baker's yeast) 1.00E-07 0_18742 STRS1_66_C02_A034 A4Z0B8|PURA_BRASO Adenylosuccinate synthetase - Bradyrhizobium sp. (strain ORS278) 3 0_18746 STRS1_66_E08_A034 Q8H0U8|RH42_ARATH DEAD-box ATP-dependent RNA helicase 42 - Arabidopsis thaliana (Mouse-ear cress) 1.6 Buffer Blank Buffer Blank Buffer Blank Buffer Blank Buffer Blank Buffer Blank Buffer Blank Buffer Blank 2_9986 NDL1_17_G10_A029 gb|AAC32136.1| YGL010w-like protein [Picea mariana] 9.00E-67 P25338|YGB0_YEAST Uncharacterized endoplasmic reticulum membrane protein YGL010W - Saccharomyces cerevisiae (Baker's yeast) 1.00E-10 2_9746 NDL1_18_B10_A029 ref|NP_191507.1| pfkB-type carbohydrate kinase family protein [Arabidopsis thaliana] sp|Q9M1B9.1|SCRK4_ARATH RecName: Full=Probable fructokinase-4 emb|CAB75445.1| fructokinase-like protein [Arabidopsis thaliana] gb|ABI49475.1| At3g59480 [Arabidopsis thaliana] 2.00E-68 Q9M1B9|SCRK4_ARATH Probable fructokinase-4 - Arabidopsis thaliana (Mouse-ear cress) 1.00E-69 0_2222 NDL1_18_D04_A029 ref|XP_002306498.1| GRAS family transcription factor [Populus trichocarpa] gb|EEE93494.1| GRAS family transcription factor [Populus trichocarpa] 4.00E-61 Q69VG1|CIGR1_ORYSJ Chitin-inducible gibberellin-responsive protein 1 - Oryza sativa subsp. japonica (Rice) 4.00E-22 2_7852 NDL1_18_D08_A029 O95388|WISP1_HUMAN WNT1-inducible-signaling pathway protein 1 precursor - Homo sapiens (Human) 7.8

Total number of rows: 26496

Table truncated, full table size 5290 Kbytes.

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

Supplementary file Size Download File type/resource 224.7 Kb (ftp)(http) GAL
GPL11184_PtGen2.master.annotation.txt.gz 5.3 Mb (ftp)(http) TXT

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