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Sample GSM184838 Query DataSets for GSM184838
Status Public on Apr 24, 2008
Title Arabidopsis, root, longitudinal zone 4, standard conditions, replicate 8
Sample type RNA
Source name root tissue
Organism Arabidopsis thaliana
Characteristics Ecotype: Columbia
Age: Seedling roots, 5 days after germination
Growth Media: Standard media
Treatment protocol Seedlings were grown for 5 days before transfer to standard media or standard media supplemented with 140mM NaCl. One hour after transferring seedlings to media, roots were cut into 4 regions using a razor blade.
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 in a single row at a density of ~2/cm for all experiments.
Extracted molecule total RNA
Extraction protocol Approximately 15 sections were dissected for each replicate and pooled. Samples were collected into RNA extraction buffer and briefly sonicated to disrupt the tissue. 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 longitudinal zone 4 isolated from roots grown under standard conditions for 5 days then transferred to standard media for 1hr
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)
GSE7639 Expression analysis of root developmental zones 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 165.901 P 0.000509415
AFFX-BioB-M_at 147.474 P 5.16732e-05
AFFX-BioB-3_at 104.282 P 7.00668e-05
AFFX-BioC-5_at 428.563 P 5.16732e-05
AFFX-BioC-3_at 379.626 P 4.42873e-05
AFFX-BioDn-5_at 830.886 P 4.42873e-05
AFFX-BioDn-3_at 1458.47 P 4.42873e-05
AFFX-CreX-5_at 4806.72 P 4.42873e-05
AFFX-CreX-3_at 7158.89 P 4.42873e-05
AFFX-DapX-5_at 7.77176 A 0.250796
AFFX-DapX-M_at 7.07392 A 0.52976
AFFX-DapX-3_at 3.59595 A 0.51489
AFFX-LysX-5_at 3.46718 A 0.749204
AFFX-LysX-M_at 4.10724 A 0.645547
AFFX-LysX-3_at 2.76996 A 0.440641
AFFX-PheX-5_at 1.05269 A 0.986189
AFFX-PheX-M_at 1.68314 A 0.937071
AFFX-PheX-3_at 6.61912 A 0.382599
AFFX-ThrX-5_at 0.978095 A 0.868639
AFFX-ThrX-M_at 2.84231 A 0.834139

Total number of rows: 22810

Table truncated, full table size 675 Kbytes.

Supplementary file Size Download File type/resource
GSM184838.CEL.gz 3.4 Mb (ftp)(http) CEL
GSM184838.CHP.gz 123.5 Kb (ftp)(http) CHP
Raw data provided as supplementary file
Processed data provided as supplementary file

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