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Sample GSM184923 Query DataSets for GSM184923
Status Public on Apr 24, 2008
Title Arabidopsis, root cells, protophloem, 140 mM NaCl, 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 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 protophloem 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
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
Reanalyzed by GSE118579
Reanalyzed by GSE119083

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

Data table
AFFX-BioB-5_at 238.134 P 0.000146581
AFFX-BioB-M_at 229.927 P 4.42873e-05
AFFX-BioB-3_at 144.047 P 7.00668e-05
AFFX-BioC-5_at 554.589 P 4.42873e-05
AFFX-BioC-3_at 473.138 P 4.42873e-05
AFFX-BioDn-5_at 1295.05 P 4.42873e-05
AFFX-BioDn-3_at 2267.37 P 5.16732e-05
AFFX-CreX-5_at 5460.33 P 4.42873e-05
AFFX-CreX-3_at 8120.61 P 4.42873e-05
AFFX-DapX-5_at 14.9759 P 0.0284465
AFFX-DapX-M_at 15.6025 A 0.275146
AFFX-DapX-3_at 1.26518 A 0.978107
AFFX-LysX-5_at 1.12709 A 0.941556
AFFX-LysX-M_at 8.90833 A 0.672921
AFFX-LysX-3_at 1.12111 A 0.672921
AFFX-PheX-5_at 1.61709 A 0.937071
AFFX-PheX-M_at 1.10378 A 0.824672
AFFX-PheX-3_at 22.0897 A 0.287743
AFFX-ThrX-5_at 1.11994 A 0.910522
AFFX-ThrX-M_at 1.72723 A 0.891041

Total number of rows: 22810

Table truncated, full table size 676 Kbytes.

Supplementary file Size Download File type/resource
GSM184923.CEL.gz 3.3 Mb (ftp)(http) CEL
GSM184923.CHP.gz 123.5 Kb (ftp)(http) CHP
Raw data provided as supplementary file
Processed data provided as supplementary file

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