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Sample GSM184905 Query DataSets for GSM184905
Status Public on Apr 24, 2008
Title Arabidopsis, root cells, protophloem, standard conditions, replicate 2
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: S32
Growth Media: Standard media
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 protophloem cells
Data processing MAS 5
 
Submission date Apr 26, 2007
Last update date Aug 15, 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

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 417.073 P 0.000581214
AFFX-BioB-M_at 376.679 P 5.16732e-05
AFFX-BioB-3_at 356.895 P 4.42873e-05
AFFX-BioC-5_at 1199.83 P 4.42873e-05
AFFX-BioC-3_at 967.325 P 5.16732e-05
AFFX-BioDn-5_at 2257.63 P 4.42873e-05
AFFX-BioDn-3_at 4184.42 P 6.02111e-05
AFFX-CreX-5_at 12846 P 4.42873e-05
AFFX-CreX-3_at 17048.3 P 4.42873e-05
AFFX-DapX-5_at 4.63365 A 0.772364
AFFX-DapX-M_at 19.6363 A 0.262827
AFFX-DapX-3_at 2.19364 A 0.983338
AFFX-LysX-5_at 2.72532 A 0.969024
AFFX-LysX-M_at 12.0246 A 0.824693
AFFX-LysX-3_at 19.3574 A 0.382599
AFFX-PheX-5_at 1.07183 A 0.994435
AFFX-PheX-M_at 1.95892 A 0.916408
AFFX-PheX-3_at 7.12893 A 0.772364
AFFX-ThrX-5_at 3.69198 A 0.904333
AFFX-ThrX-M_at 4.69901 A 0.631562

Total number of rows: 22810

Table truncated, full table size 665 Kbytes.




Supplementary file Size Download File type/resource
GSM184905.CEL.gz 3.3 Mb (ftp)(http) CEL
GSM184905.CHP.gz 123.5 Kb (ftp)(http) CHP
Raw data provided as supplementary file
Processed data provided as supplementary file

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