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Sample GSM1705427 Query DataSets for GSM1705427
Status Public on Aug 07, 2015
Title 5%DMSO/0.1%Tween 20 in H20 - 1
Sample type RNA
 
Source name Emergent but non-fully-expanded 4th leaf_Dimethyl sulfoxide/Tween 20/H2O
Organism Zea mays
Characteristics cultivar: Golden Queen
tissue: Leaf
Treatment protocol For gene expression analysis, spot application of 10-OPEA was carried out by applying four 10µl droplets of either the control solution [ (H20/DMSO/0.1% Tween 20) (95:5:0.1; v/v/v)] or the same containing 2mM 10-OPEA onto the middle portion of partially emerged leaf 4 of 14-day old plants approximately 15 cm from the distal tip with 2 droplets on each side of the midrib 2 cm apart. At 90 min post treatment, control and 10-OPEA treated tissues were collected in liquid N2.
Growth protocol Zea mays (variety Golden Queen) seeds were germinated in MetroMix 200 (Sun Gro Horticulture Distribution, Inc.) supplemented with 14-14-14 Osmocote (Scotts Miracle-Gro) and grown in a greenhouse with a 12-h photoperiod, minimum of 300 μmol m−2 s−1 of photosynthetically active radiation supplied by supplemental lighting, 70% relative humidity, and temperature cycle of 24 °C/28 °C (night/day).
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using the Nucleospin RNA Plant kit (Macherey-Nagel bmbH Inc., Duren, Germany) according to the manufacturers protocol and First Strand cDNA was synthesized using the Superscript III First Strand cDNA synthesis kit (Invitrogen, Carlsbad, CA, USA) with random decamer primers.
Label biotin
Label protocol For each sample, 1 μg of total RNA was provided to the University of Florida Interdisciplinary Center Biotechnology Research (UF-ICBR) Gene Expression Core for cDNA synthesis, reverse transcription, and biotin labeling using the Affymetrix GeneChip 3′ IVT express kit and protocol (Affymetrix).
 
Hybridization protocol Biotin labeled samples were hybridized to Affymetrix maize GeneChips at UF-ICBR using a GeneChip Hybridization Oven 640 with standard hybridization protocol
Scan protocol Affymetrix maize GeneChips were scanned at UF ICBR with a GeneChip Scanner 3000 7G per standard procedure
Description Dimethyl sulfoxide/Tween 20/H2O
Data processing Data extraction was executed by the UF ICBR gene expression core and provided as CEL files. Data analysis was performed using ArrayStar 4 software (DNASTAR, Inc.). To minimize probe-specific affinity differences, all data were preprocessed using Robust MultiArray Analysis and quantile normalization. 
 
Submission date Jun 08, 2015
Last update date Aug 07, 2015
Contact name Alisa Huffaker
E-mail(s) ahuffaker@ucsd.edu
Phone 858-534-3988
Organization name UC San Diego
Department Cell & Developmental Biology
Street address 9500 Gilman Drive #0116
City La Jolla
State/province CA
ZIP/Postal code 92093-0116
Country USA
 
Platform ID GPL4032
Series (1)
GSE69659 Maize death acids, 9-lipoxygenase derived cyclopente(a)nones, display activity as cytotoxic phytoalexins and transcriptional mediators

Data table header descriptions
ID_REF
VALUE normalized signal

Data table
ID_REF VALUE
Zm.10676.1.S1_at 3.3453
Zm.847.1.S1_at 3.4698
Zm.8097.1.A1_at 2.7041
Zm.1871.1.A1_at 3.4763
Zm.12107.1.A1_at 3.9844
Zm.9297.1.A1_at 3.3288
Zm.17839.1.S1_at 7.6803
Zm.2227.1.A1_at 3.0211
Zm.19027.1.A1_at 3.9633
Zm.5744.1.A1_at 3.6897
Zm.8764.1.A1_at 3.6893
Zm.7900.1.A1_at 4.0246
Zm.3198.1.A1_a_at 9.4522
Zm.8415.1.A1_at 3.3055
Zm.9328.1.A1_s_at 2.6607
Zm.1579.1.S1_at 4.6871
Zm.2361.1.A1_at 4.3468
Zm.11758.1.A1_at 5.4270
Zm.6532.1.A1_a_at 7.0194
Zm.12139.1.A1_at 3.8490

Total number of rows: 17734

Table truncated, full table size 416 Kbytes.




Supplementary file Size Download File type/resource
GSM1705427_12001_Twn-DMSO_90mn-1_Maize_.CEL.gz 1.8 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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