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Platform GPL9334

Query DataSets for GPL9334

Status

Public on Jan 21, 2010

Title

Aspen 7K Array version 2.1

Technology type

spotted DNA/cDNA

Distribution

non-commercial

Organism

Manufacturer

Michigan Tech and University of Georgia

Manufacture protocol

1. Array design: The second generation aspen 7K array contains replicate subarrays of 6,705 elements in a 4×4 grid with a spot diameter of ~150 μm and a spacing of 200 μm. These elements represent ~5,400 unique JGI Populus gene models, and include various positive and negative controls (Lucidea Universal ScoreCard, Amersham) to monitor target labeling and hybridization efficiency, as well as many known function genes derived from our previous and ongoing research. 2. Print area: The replicate subarrays occupy an approximately 18×37 mm area on the non-barcode side. Spots were printed with Corning Pronto! spotting solution at the Genomics Technology Support Facility of Michigan State University. 3. Spot layout: Each grid contains 12 spike controls on the top left corner. These include calibration controls (from high to low concentrations), ratio controls (different ratio combinations between Cy3 and Cy5 targets), and negative controls. Each grid contains 21×21 spots, except for the last row which has variable number of empty spots. 4. Spikes: To take advantage of the spike controls, appropriate spike mRNA samples need to be included during target labeling (see Amersham manual). However, the use of spike mRNA in hybridization is optional, and will not affect the array analysis (e.g., using global per chip normalization etc). 5. Clone information: ESTs were obatined from Populus tremuloides (Ranjan et al. 2004) or Populus fremontii x angustifolia. Sequence information can be obtained by searching the GenBank or our ESTdb (http://aspenDB.uga.edu) using the MTU clone IDs. As is the case for other large-scale projects, there are likely errors in the annotation. 6. This platform contains a non-redundant clone list from the full array (GPL6992). Duplicate spots (EST clones in the subarrays or spike controls) are represented only once. Ranjan P, Kao Y-Y, Jiang H, Joshi CP, Harding SA, Tsai C-J (2004) Suppression subtractive hybridization-mediated transcriptome analysis from multiple tissues of aspen (Populus tremuloides) trees altered in phenylpropanoid metabolism. Planta 219: 694-704.

Submission date

Oct 01, 2009

Last update date

Jan 21, 2010

Contact name

Chung-Jui Tsai

E-mail(s)

Organization name

University of Georgia

Department

School of Forestry and Natural Resources

Street address

120 Green Street

City

Athens

State/province

GA

ZIP/Postal code

30606

Country

USA

Samples (6)

GSM458168, GSM458169, GSM458170, GSM458171, GSM458172, GSM458173

Series (1)

Gene expression response of Populus tremuloides cell suspension cultures to salicyl alcohol feeding

Data table header descriptions
ID
Clone ID	In-house clone ID
Description	Gene description
JGI_gene_model	JGI Populus gene model name
Genome_location	JGI Populus gene model position in genome
GB_ACC	GenBank accession number
SPOT_ID

Data table
ID	Clone ID	Description	JGI_gene_model	Genome_location	GB_ACC	SPOT_ID
1	4CL1	4-coumarate-CoA ligase (4CL1, full-length cDNA)	grail3.0100002702	LG_I:1432116-1435302	AF041049
2	4CL2	4-coumarate-CoA ligase (4CL2, full-length CDS)	grail3.0099003002	LG_XIX:4083532-4087345	AF041050
3	4CL3	4-coumarate-CoA ligase (4CL3, full-length CDS)	estExt_fgenesh4_pg.C_1210004	scaffold_121:49867-56929		4-coumarate-CoA ligase 4CL3, full-length CDS
4	4CL3-3UTR	4-coumarate-CoA ligase (4CL3, 3'-CDS 640bp)	estExt_fgenesh4_pg.C_1210004	scaffold_121:49867-56929		4-coumarate-CoA ligase 4CL3, 3'-CDS 640bp
5	4CL4	4-coumarate-CoA ligase (4CL4, full-length CDS)	gw1.XVIII.2818.1	LG_XVIII:9666118-9671112		4-coumarate-CoA ligase 4CL4, full-length CDS
6	4CL5	4-coumarate-CoA ligase (4CL5, full-length CDS)	fgenesh4_pg.C_LG_III001773	LG_III:17994254-17998436		4-coumarate-CoA ligase 4CL5, full-length CDS
7	ADC	Arginine decarboxylase (ADC, partial)	NA	NA		Arginine decarboxylase ADC, partial
8	ANS1	Anthocyanidin synthase (ANS1, 3'-UTR)	grail3.0018022801	LG_III:11400392-11401847		Anthocyanidin synthase ANS1, 3'-UTR
9	ANS2	Anthocyanidin synthase (ANS2, 3'-UTR)	eugene3.00010988	LG_I:8507517-8509264		Anthocyanidin synthase ANS2, 3'-UTR
10	AOS1(psu)	(sequence not confirmed)Allene oxide synthase (AOS1, 3'-UTR)	gw1.IV.4073.1			sequence not confirmed Allene oxide synthase AOS1, 3'-UTR
11	APX1(psu)	(sequence not confirmed)ascorbate peroxidase	estExt_fgenesh4_pm.C_LG_IV0530			sequence not confirmed ascorbate peroxidase
12	ARF1a	ADP-ribosylation factor (ARF1, full-length cDNA)	estExt_fgenesh4_pm.C_LG_VIII0406	LG_VIII:6218729-6220961	AY229879
13	ARF1b	ADP-ribosylation factor (ARF1, full-length cDNA)	estExt_fgenesh4_pm.C_LG_VIII0406	LG_VIII:6218729-6220961	AY229879
14	ARF2	ADP-ribosylation factor (ARF2, full-length cDNA)	estExt_Genewise1_v1.C_LG_X0744	LG_X:14366437-14368678	AY229880
15	BAN1	Anthocyanidin reductase (ANR/BAN1, 3'-UTR)	estExt_fgenesh4_pm.C_LG_IV0055	LG_IV:1671017-1673302		Anthocyanidin reductase ANR/BAN1, 3'-UTR
16	BAN2	Anthocyanidin reductase (ANR/BAN2, 3'-UTR)	estExt_fgenesh4_pm.C_LG_XI0107	LG_XI:3895226-3897581		Anthocyanidin reductase ANR/BAN2, 3'-UTR
17	Blank	NA	NA	NA		--unknown
18	Buffer	NA	NA	NA		--unknown
19	c1	--spike control	NA	NA		--spike control
20	c10	--spike control	NA	NA		--spike control

Total number of rows: 6573

Table truncated, full table size 675 Kbytes.

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Supplementary data files not provided

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