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Sample GSM184921 Query DataSets for GSM184921
Status Public on Apr 24, 2008
Title Arabidopsis, root cells, stele, 140 mM NaCls, replicate 3
Sample type RNA
 
Source name Protoplasted and FACS sorted root cells
Organism Arabidopsis thaliana
Characteristics Ecotype: Columbia
Age: Seedling roots, 6 days after germination
GFP-reporter: WOL::GFP
Growth Media: Standard media for 6 days, transferred to media supplemented with 140mM NaCl for 1 hour before protoplasting
Treatment protocol Samples were prepared as in Birnbaum et al. (2005) for roots grown under standard conditions. For salt treated samples, roots were transferred to 140 mM NaCl for 1hr before protoplasting. Three replicates were performed per cell type, per condition. In order to test for the effects of sorting, Col-0 roots were protoplasted after being treated for 1 hour with or without salt treatment. Cells were passed through the FACS device with all cells being collected.
Growth protocol Seeds were surface sterilized with 50% Bleach and 0.1% Tween for 5 minutes and then rinsed 3 times with sterile water. Seeds were stratified at 4˚C for 2 days before being planted on standard media. Standard media is 1X concentration Murashige and Skoog salt mixture (Caisson laboratories), 0.5g/L MES, 1% sucrose, 1% agar and adjusted to pH 5.7 with KOH. Salt media is standard media with varying amounts of NaCl added. Nylon mesh was placed on top of the solidified media and seeds were evenly placed on the mesh at a density of ~20 seeds/cm in two rows.
Extracted molecule total RNA
Extraction protocol RNA was extracted using the RNAeasy Micro Kit (Qiagen GmbH).
Label biotin
Label protocol Fragmented cRNA probes were prepared using the two-cycle amplification protocol by Affymetrix.
 
Hybridization protocol Standard Affymetrix protocols. Samples were submitted to Expression Analysis Inc. (Durham, NC) for hybridization to Affymetrix ATH1 microarrays.
Scan protocol Standard Affymetrix protocols. Samples were submitted to Expression Analysis Inc. (Durham, NC) for hybridization to Affymetrix ATH1 microarrays.
Description Gene expression data from isolated stele cells after roots were treated with 140 mM NaCl for 1 hour
Data processing MAS 5
 
Submission date Apr 26, 2007
Last update date Aug 28, 2018
Contact name Jose Ramon Dinneny
E-mail(s) jdinneny@carnegiescience.edu
Organization name Carnegie Institution for Science, Department of Plant Biology
Department Plant Biology
Lab Jose R. Dinneny
Street address 260 Panama St
City Stanford
State/province United States
ZIP/Postal code 94305
Country USA
 
Platform ID GPL198
Series (1)
GSE7641 Expression analysis of root cell-types after treatment with salt
Relations
Reanalyzed by GSE118579
Reanalyzed by GSE119083

Data table header descriptions
ID_REF
VALUE Signal
ABS_CALL indicating whether the transcript was present (P), absent (A), or marginal (M)
DETECTION P-VALUE

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 72.4207 P 0.0032123
AFFX-BioB-M_at 75.092 P 7.00668e-05
AFFX-BioB-3_at 37.5538 P 0.0012475
AFFX-BioC-5_at 230.292 P 6.02111e-05
AFFX-BioC-3_at 126.455 P 9.4506e-05
AFFX-BioDn-5_at 365.748 P 4.42873e-05
AFFX-BioDn-3_at 827.164 P 6.02111e-05
AFFX-CreX-5_at 2538.4 P 4.42873e-05
AFFX-CreX-3_at 3362.11 P 4.42873e-05
AFFX-DapX-5_at 8.10624 A 0.195266
AFFX-DapX-M_at 5.62134 A 0.58862
AFFX-DapX-3_at 1.65209 A 0.9273
AFFX-LysX-5_at 6.22581 A 0.41138
AFFX-LysX-M_at 7.67327 A 0.749204
AFFX-LysX-3_at 6.11391 A 0.5
AFFX-PheX-5_at 1.89255 A 0.932322
AFFX-PheX-M_at 1.45562 A 0.891021
AFFX-PheX-3_at 3.71576 A 0.699394
AFFX-ThrX-5_at 1.77383 A 0.749204
AFFX-ThrX-M_at 4.73587 A 0.455413

Total number of rows: 22810

Table truncated, full table size 680 Kbytes.




Supplementary file Size Download File type/resource
GSM184921.CEL.gz 3.5 Mb (ftp)(http) CEL
GSM184921.CHP.gz 122.5 Kb (ftp)(http) CHP
Raw data provided as supplementary file
Processed data provided as supplementary file

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