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Sample GSM566870 Query DataSets for GSM566870
Status Public on Dec 01, 2011
Title Control KNO3 roots - 8hours - repeat 1
Sample type RNA
 
Source name Control KNO3 roots - 8hours - repeat 1
Organism Arabidopsis thaliana
Characteristics tissue: roots
ecotype: Columbia
treatment: 5mM KNO3 on both sides for 8 hours
Treatment protocol We selected the 12-14 days old plants with balanced roots on both sides and they were transferred on 12x12cm segmented agar plates containing either 5mM KNO3 or 5mM KCl on both sides for the controls or 5mM KNO3 on one side and 5mM KCl on the other side for the split. These plates contained 60 ml of solid basal MS medium supplemented with 0.3mM sucrose. The KNO3 or KCl compartments were obtained by spreading concentrated KNO3 and KCl solution on the solid medium 24 hr before the experiments to allow diffusion of the solutions
Growth protocol Plants are grown on a custom-made basal Murashige and Skoog solid medium (no nitrogen, no sucrose), supplemented with 0.5 mM NH4-succinate, 0.1mM KNO3 and 3mM sucrose. After 8-10 days, the primary root was cut below the first two lateral roots and roots still grown on these plates for 4 more days. Then, each plant with two main roots was transferred on individual 10x10 cm plates containing the same 40 ml solid medium supplemented with 0.5mM NH4+-succinate as the nitrogen source. The solid medium was divided in two compartments by a trench to allow the physical separation of the two roots.
Extracted molecule total RNA
Extraction protocol RNA extractions were carried out on roots collected at 2 hours, 8 hours and 2 days after the beginning of the split-root treatment with TRIzol (Invitrogen)
Label biotin
Label protocol Samples were enzymatically fragmented and biotinylated using the IVT - labeling kit (Affymetrix)
 
Hybridization protocol Samples were hybridized using Affymetrix hybridization kit materials. Heat cocktails at 99° for 5 minutes, then 42° for 10 minutes centrifuge at max speed for 1 minute. Transfer 200μl of hyb solution to each array. Hybridize 16 hours at 45° at 60rpm. Fluidics washing is EukGE-WS2v4_450.
Scan protocol Affymetrix Gene ChIP Scanner 3000 7G
Data processing Data were processed using MAS5.0v
 
Submission date Jul 15, 2010
Last update date Aug 15, 2018
Contact name Sandrine Ruffel
E-mail(s) sandrine0ruffel@gmail.com
Phone 2129954918
URL http://coruzzilab.bio.nyu.edu/home/
Organization name New York University
Department Biology
Lab Coruzzi
Street address 100 Washington Square East. 1009 Main Building
City NYC
State/province NY
ZIP/Postal code 10012
Country USA
 
Platform ID GPL198
Series (1)
GSE22966 A systemic view of coordinated root responses to NO3- heterogeneous environment in Arabidopsis
Relations
Reanalyzed by GSE118579

Data table header descriptions
ID_REF
VALUE Normalized gene level expression values from MAS5.0v

Data table
ID_REF VALUE
244901_at 60.38871995
244902_at 111.41773
244903_at 154.186715
244904_at 5.81725094
244905_at 17.57113436
244906_at 192.1666824
244907_at 10.93543294
244908_at 5.098805073
244909_at 24.15145434
244910_s_at 32.53991834
244911_at 19.44628813
244912_at 997.9261472
244913_at 9.127304826
244914_at 2.56110379
244915_s_at 8.423268198
244916_at 5.467684765
244917_at 2.960520514
244918_at 23.36968852
244919_at 14.95410643
244920_s_at 210.39109

Total number of rows: 22810

Table truncated, full table size 490 Kbytes.




Supplementary file Size Download File type/resource
GSM566870.CEL.gz 2.3 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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