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Sample GSM1468799 Query DataSets for GSM1468799
Status Public on Aug 09, 2014
Title SALK_033618C_3h_NaCl_rep1
Sample type RNA
 
Source name SALK_033618C, 3h, NaCl, replicate 1
Organism Arabidopsis thaliana
Characteristics treatment: NaCl
genotype: SALK_033618C
tissue: whole plant
age: Four-week-old seedlings
Treatment protocol Four-week-old seedlings of T3 homozygous lines of the AtbHLH112-overexpression plants, mutant (SALK_033618C) plants and wild type of Columbia Arabidopsis thaliana with or without 150 mM NaCl treatment for 3 hours. The whole seedlings including root and shoot were harvested and pooled for each treatment before freezing in liquid nitrogen and storage at -80ºC for RNA isolation.
Growth protocol AtbHLH112-overexpression plants, mutant (SALK_033618C) plants and wild type of Columbia Arabidopsis thaliana seedlings grown in freshwater-irrigated pots filled with the artificial soil (Vermiculite: perlite: soil = 3:1:1, v/v) in a relative humidity of 55% under long-day conditions (16-h light/8-h dark)at 22°C (±2°C).
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using TRIZOL Reagent (Cat#15596-018,Life technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).
Label Cy3
Label protocol Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).
 
Hybridization protocol Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.
Scan protocol Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit. Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).
Description Gene expression after 3h in NaCl-treatmented Arabidopsis seedlings of SALK_033618C
Data processing The scanned images were analyzed with R-software (The R Project for Statistical Computing, http:// www. r-project.org/) of SAS system statistics to obtain background subtracted and spatially detrended Processed Signal intensities.
 
Submission date Aug 08, 2014
Last update date Aug 09, 2014
Contact name Yujia Liu
E-mail(s) lyjizbd@126.com
Phone 0086-0451-84892020
Organization name Harbin University of Commerce
Street address 1 Xuehai Street
City Harbin
State/province Heilongjiang
ZIP/Postal code 150028
Country China
 
Platform ID GPL12621
Series (1)
GSE60260 Arabidopsis AtbHLH112 protein positively regulates tolerance to abiotic stress and binds to the E-box and a novel motif GCG-box

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
A_84_P800302 5.3740635
A_84_P20838 4.712332
A_84_P763788 9.051754
A_84_P840007 8.24904
A_84_P13493 2.228742
A_84_P863067 14.383702
A_84_P76784 11.918624
A_84_P856120 12.304746
A_84_P844437 7.33134
A_84_P825165 12.785901
A_84_P792466 2.2583244
A_84_P768557 2.2619693
A_84_P851423 9.865077
A_84_P808310 14.037925
A_84_P501920 8.09758
A_84_P759826 6.76211
A_84_P13114 12.334132
A_84_P766049 2.2835116
A_84_P14691 9.09473
A_84_P216048 15.310966

Total number of rows: 43661

Table truncated, full table size 949 Kbytes.




Supplementary file Size Download File type/resource
GSM1468799_GE1_107_0013.txt.gz 8.9 Mb (ftp)(http) TXT
Processed data included within Sample table

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