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Sample GSM3031725

Query DataSets for GSM3031725

Status

Public on May 22, 2019

Title

WT_MYB5aOE_replicate 3

Sample type

RNA

Source name

Wild Type Shiraz; leaves; control of the VvMYB5a overepression_Replicate 3

Organism

Vitis vinifera

Characteristics

cultivar: Shiraz
genotype/valiation: wild type
vintage: 2010
tissue: leaves

Growth protocol

Grapevine plants (Vitis vinifera cv. Shiraz, BVRC12 clone) were grown in Coombe Vineyard (University of Adelaide, Urrbrae, South Australia). For the genetic transformation embryogenic calli were collected from anthers during the 2009 season. For the microarray analysis performed on grapevine, three biological replicates of fully expanded leaves were collected from control and transgenic plants before the onset of the altered phenotype.

Extracted molecule

total RNA

Extraction protocol

Total RNA was isolated from ~100 mg of the ground grapevine leaves tissue using the Spectrum™ Plant Total RNA kit (Sigma-Aldrich).

Label

Cy3

Label protocol

cDNA synthesis and labeling reactions were performed according to the NimbleGen Arrays User’s Guide (V 3.2).

Hybridization protocol

Hybridization and washing procedures were performed according to the NimbleGen Arrays User’s Guide (V 3.2).

Scan protocol

Each microarray was scanned using a ScanArray 4000XL (Perkin-Elmer) at 532 nm (Cy-3 absorption peak) and GenePix Pro7 software (Molecular Devices) according to the manufacturer’s instructions.

Data processing

Images were analyzed using NimbleScan v2.5 software (Roche), background correction and standard RMA normalization were selected.

Submission date

Mar 06, 2018

Last update date

May 22, 2019

Contact name

Alessandra Amato

E-mail(s)

alessandra.amato@univr.it

Organization name

University of Verona

Street address

strada le grazie 15

City

ZIP/Postal code

37134

Country

Italy

Platform ID

GPL17894

Series (1)

GSE111468

The MYB5-driven MBW complex recruits a WRKY factor to enhance the expression of targets involved in vacuolar hyper-acidification and trafficking in grapevine

Data table header descriptions
ID_REF
VALUE	Nimblescan v2.5 software calculated RMA-normalized signal intensities.

Data table
ID_REF	VALUE
CHR10_GSVIVT00006725001_T01	377.7032
CHR10_GSVIVT00007268001_T01	382.8544
CHR10_GSVIVT00021093001_T01	278.1525
CHR10_GSVIVT00021115001_T01	85.748
CHR10_GSVIVT00021131001_T01	228.1179
CHR10_GSVIVT00021157001_T01	160.1179
CHR10_GSVIVT00021158001_T01	228.0692
CHR10_GSVIVT00021206001_T01	109.1933
CHR10_GSVIVT00021217001_T01	1089.8492
CHR10_GSVIVT00021273001_T01	2575.1609
CHR10_GSVIVT00021290001_T01	50.4716
CHR10_GSVIVT00021333001_T01	37.9337
CHR10_GSVIVT00021341001_T01	45.1967
CHR10_GSVIVT00021361001_T01	43.3369
CHR10_GSVIVT00021408001_T01	154.2747
CHR10_GSVIVT00021438001_T01	14332.1947
CHR10_GSVIVT00021476001_T01	140.9696
CHR10_GSVIVT00021483001_T01	122.5294
CHR10_GSVIVT00021487001_T01	465.996
CHR10_GSVIVT00021498001_T01	730.9825

Total number of rows: 29549

Table truncated, full table size 864 Kbytes.

Supplementary file	Size	Download	File type/resource
GSM3031725_WTAO08_3.pair.gz	2.2 Mb	(ftp)(http)	PAIR
Processed data included within Sample table