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Platform GPL15489

Query DataSets for GPL15489

Status

Public on Feb 12, 2013

Title

Combimatrix 90k TomatArray 1.0

Technology type

in situ oligonucleotide

Distribution

custom-commercial

Organism

Solanum lycopersicum

Manufacturer

University of Verona - Scientific and Technological Department - Plant Functional Genomics Centre

Manufacture protocol

Probes are directly synthesized on a 90k Combimatrix array by an in situ oligo synthesis system developed by Combimatrix Corporation (Mukilteo, USA) using the Combimatrix CustomArray synthesizer. Standard synthesis protocol provided by Combimatrix was used.

Description

20200 specific oligos (35-40mer) were designed on Tomato Gene Index Version 11 (LeGI v.11, June21, 2006) tentative consensus (TC) sequences by using the program design OligoArray 2.1 (Rouillard et al. 2003). As negative controls nine bacterial oligonucleotides sequences provided by Combimatrix were utilized. The 90K TomatArrayTM 1.0 was designed with four replicates of each probe randomly distributed across the array to allow measurement of the variability within the array. All the procedures provided were performed as indicated by Combimatrix protocols available at Combimatrix website (www.combimatrix.com)

Submission date

Apr 25, 2012

Last update date

Dec 21, 2012

Contact name

Antonio Di Matteo

E-mail(s)

adimatte@unina.it

Phone

00390812539208

Fax

00390812539486

Organization name

University of Naples Federico II

Department

DiSSPAPA

Lab

Structural and functional genomics

Street address

Via Universita' 100 - Parco Gussone - Edificio 75

City

Portici (NA)

ZIP/Postal code

80055

Country

Italy

Samples (22)

More...

GSM921787, GSM921788, GSM921789, GSM921790, GSM921791, GSM921792

Series (1)

Comparative gene expression analysis in fruits of a tomato introgression line performing higher level of total phenolics

Data table header descriptions
ID
SPOT_ID	TIGR identifier of the Tentative Consensus (TC) used for designing the specific oligonucleotide probe
GB ID	GeneBank Accession Number
Annotation	TC Annotation as retrieved from the NCBI’s non-redundant NR database
SEQUENCE	Sequence of the oligonucleotide probe

Data table
ID	SPOT_ID	GB ID	Annotation	SEQUENCE
1	TC169966	\|BE435573\|BG734675	1-aminocyclopropane-1-carboxylate oxidase	gtgtgtgattgttgtgtggtattttaaagggttctaaagc
2	TC169967	\|AW035744\|BP907805\|BI206463	nitrate reductase	ggaggaactattggtgttctaaattggatggtgatgatga
3	TC169964	NP651452\|AF447452\|AAO72744.1NP405745\|AF311943\|AAL26804.1	galactinol synthase	tgtgaacagatgttggaacagcactctatggaaattat
4	TC169965	\|AW648330\|AW648469\|BP875801	pto-like serine threonine kinase	tgccctatatctttcagagatgatgagttctgatgatga
5	TC169962	\|BI924039\|BG626095\|BG126690	ascorbate peroxidase	tctacagtgcagcaaaattgcgattttcttaatcctttc
6	TC169963	\|CK714807\|AI779132	cytochrome f	tggccgaaatgaatttctagattcgcagatttatcga
7	TC169961	\|BM956661	peroxidase	actgattgtaagagggttaattagttgattaggaggggtt
8	TC169968	\|AW038055NP211472\|S37645\|AAC60539.2NP000811\|M83211\|AAA34134.1NP000526\|M67474\|AAA34135.1NP602334\|X55884\|CAA39370.1	acid phosphatase	ccaaaagtgttgatttgggagatgatggaagagatgtgtg
9	TC169969	\|BI423085	cytochrome c heme attachment protein	tggatatgctattttggggtcaatctattaggaatagggt
10	TC190207	\|AW944890\|AI780836\|CN384693	---NA---	actgcctgttaatactgtcaagtctcattctgaagatca
11	TC190206	\|BP908505\|BP906680\|BP908043	---NA---	aggacatagaaggccttcttgagtattatggtttctcat
12	TC190205	\|BE462110\|BP908028	protein	ctaggatgttggaggtctcaagggaggaggctgag
13	TC190204	\|BP877174\|BP908448	protein	ttatgggaacgacgaattttgaatgtgaccaccca
14	TC190203	\|BP878251	heat shock protein 101	catacatcttctttcgtgacaggtgaggaagcaattta
15	TC190202	\|BG626529\|AW039286\|BP882588	far-red impaired responsive family protein far1 family protein	atgtcggatagcttgtttagccttttcccctttctttcca
16	TC181188	\|BF098088\|BM413555\|AJ784586	protein	gggaagatgaaaggcaatagagaggtggaatcaag
17	TC181189	\|BE459543	reticulon family protein	tcttcaaggtagttattgttctgtggcttctatctgtcat
18	TC181186	\|DN168864\|AW222231	at5g63860 mgi19_6	ctcagatatcaggtggttggagacataccatggcactta
19	TC181187	\|BE460556\|AW931211\|AW038122	sac3 ganp familyexpressed	tgaaggaatgggatgtagcatctttctgcaaagac
20	TC181184	\|BP886458\|BI922652	rna pseudouridylate synthase domain containing 2	tacaatgctcgagaagggaggagcacagttgaggt

Total number of rows: 20201

Table truncated, full table size 1995 Kbytes.

Download family	Format
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Supplementary data files not provided

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