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Sample GSM2746047 Query DataSets for GSM2746047
Status Public on Aug 15, 2020
Title root tip region 2 after 48 h water-stress, biological rep2
Sample type RNA
 
Source name root tip region 2 after 48 h water-stress
Organism Glycine max
Characteristics cultivar: cv.Magellan
treatment group: water-stressed treatment
tissue: root tip
Treatment protocol Seedlings with primary roots approximately 15 mm in length were transplanted against the interior surface of Plexiglas cylinders (14.5 cm diameter) filled with a 1:1 (v/v) mixture of vermiculite (no. 2A, Therm-ORock East Inc., New Eagle, PA, USA) and Turface (Profile Products LLC, Buffalo Grove, IL, USA) at water potentials of -0.1 MPa (well-watered treatment, moistened to the drip point) or -1.6 MPa (water-stressed treatment). Totally around 300 roots for each sample with three biological replicates were collected and the root tips were sectioned into regions 1–2 (water stressed) and 1–3 (well-watered controls) after 5h and 48h respectively. The root samples were immediately frozen with liquid nitrogen and then stored at −80 °C.
Growth protocol Soybean (cv.Magellan) seeds were surface sterilized in 1% NaClO solution for 2 min, rinsed in deionized water for 30 min and germinated between sheets of germination paper moistened with a solution containing 5 mm CaCl2 and 5 mm Ca(NO3)2 for 36 h at 29 °C and near-saturation humidity in the dark.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from the root tissues using TRIZOL reagent (Invitrogen, Carlsbad, CA, USA). Genomic DNA was eliminated by digesting the RNA with Turbo DNA-free DNaseI (Ambion) according to the manufacturer’s instructions. After DNaseI treatment, RNA concentration was determined and checked the quality using an Agilent 2100 Bioanalyzer (Agilent Technologies, CA). Total RNA was used for Affymetrix Soybean Genome GeneChip analysis following the manufacturer's recommended protocols (Affymetrix, CA). The cDNA synthesis, cRNA amplification, and synthesis of sense strand cDNAs were carried out using the Ambion WT expression kit.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
 
Hybridization protocol Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Scan protocol The arrays were scanned with a GeneChip 7G Plus high-resolution scanner.
Description Gene expression data from soybean root tip water-stress
Data processing The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
 
Submission date Aug 16, 2017
Last update date Aug 15, 2020
Contact name Babu Valliyodan
E-mail(s) valliyodanb@missouri.edu
Phone 5738846313
Organization name University of Missouri
Department Plant Sciences
Lab Nguyen laboratory
Street address 1-31 Ag Building
City Columbia
State/province Missouri
ZIP/Postal code 65201
Country USA
 
Platform ID GPL4592
Series (1)
GSE102749 Gene expression of soybean root tips under water deficits

Data table header descriptions
ID_REF
VALUE MAS5.0 signal intensity

Data table
ID_REF VALUE
AFFX-BioB-3_at 484.9985482
AFFX-BioB-5_at 465.767856
AFFX-BioB-M_at 605.6936631
AFFX-BioC-3_at 453.4218994
AFFX-BioC-5_at 463.5425311
AFFX-BioDn-3_at 6827.482103
AFFX-BioDn-5_at 3665.580132
AFFX-CreX-3_at 21179.02296
AFFX-CreX-5_at 17450.3298
AFFX-DapX-3_at 9.578016552
AFFX-DapX-5_at 8.812683734
AFFX-DapX-M_at 7.416008082
AFFX-Gm_18SrRNA_at 17074.50173
AFFX-Gma-A00196-1_s_at 15.84750086
AFFX-Gma-AB076373-1_at 16.45644056
AFFX-Gma-AF292559-2_s_at 6.791093794
AFFX-Gma-AF292559-3_s_at 7.732958221
AFFX-Gma-AF292559-4_s_at 35.08870454
AFFX-Gma-AF292560-1_s_at 7.497959063
AFFX-Gma-AF298789-1_at 32.9107361

Total number of rows: 61170

Table truncated, full table size 1941 Kbytes.




Supplementary file Size Download File type/resource
GSM2746047_Root_48hWSR2-S2.CEL.gz 5.0 Mb (ftp)(http) CEL
Processed data included within Sample table

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