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Sample GSM265422 Query DataSets for GSM265422
Status Public on Apr 24, 2008
Title Arabidopsis, root, longitudinal zone 3, standard conditions, rep1
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 -Fe media. 24 hours after transferring seedlings to media, roots were cut into 4 regions using a razor blade.
Growth protocol Seeds were surface sterilized for 2 minutes in 70% ethanol, the ethanol was removed, then replaced with 30% Bleach and 0.02% Triton X-100 for 15 minutes. Seeds were rinsed 3 times with sterile water, stratified for 4˚C for 2 days, then placed on standard media. Standard media is 1X Murashige and Skoog salt mixture in which ferrous sulfate is replaced with 100mM Fe(III)-EDTA, 0.5g/L MES, 1% sucrose, 1% agar and adjusted to pH 5.7 with KOH. –Fe media is 1X Murashige and Skoog salt mixture in which ferrous sulfate is replaced with 0.3mM Ferrozine. 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 roots 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 Samples were submitted to Expression Analysis Inc. (Durham, NC) for hybridization to Affymetrix ATH1 microarrays.
Scan protocol Samples were submitted to Expression Analysis Inc. (Durham, NC) for hybridization to Affymetrix ATH1 microarrays.
Description Gene expression data from longitudinal zone 3 isolated from roots grown under standard conditions for 5 days then transferred to standard media for 1hr
Data processing MAS5.0
 
Submission date Feb 12, 2008
Last update date Aug 28, 2018
Contact name Terri Anita Long
E-mail(s) tlong@duke.edu
Phone 919-613-8202
Fax 919-613-8177
Organization name Duke University
Department Biology
Lab Philip Benfey
Street address Box 90338
City Durham
State/province NC
ZIP/Postal code 27707
Country USA
 
Platform ID GPL198
Series (2)
GSE10497 Expression analysis of root developmental zones after iron deficiency (-Fe) treatment
GSE10576 Iron deficiency (-Fe) effect: Arabidopsis roots
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 85.6407 P 0.036569
AFFX-BioB-M_at 100.339 P 0.00141043
AFFX-BioB-3_at 93.1463 P 0.00401721
AFFX-BioC-5_at 261.872 P 0.00010954
AFFX-BioC-3_at 203.605 P 4.42873e-05
AFFX-BioDn-5_at 546.988 P 4.42873e-05
AFFX-BioDn-3_at 959.431 P 7.00668e-05
AFFX-CreX-5_at 2848.86 P 4.42873e-05
AFFX-CreX-3_at 4355.08 P 4.42873e-05
AFFX-DapX-5_at 18.0326 M 0.0629293
AFFX-DapX-M_at 11.887 A 0.440646
AFFX-DapX-3_at 7.67944 A 0.737173
AFFX-LysX-5_at 1.28469 A 0.969024
AFFX-LysX-M_at 3.05547 A 0.989683
AFFX-LysX-3_at 3.25288 A 0.327079
AFFX-PheX-5_at 1.66185 A 0.814869
AFFX-PheX-M_at 2.29653 A 0.868639
AFFX-PheX-3_at 5.63584 A 0.843268
AFFX-ThrX-5_at 3.2416 A 0.953518
AFFX-ThrX-M_at 10.8706 A 0.617401

Total number of rows: 22810

Table truncated, full table size 673 Kbytes.




Supplementary file Size Download File type/resource
GSM265422.CEL.gz 3.5 Mb (ftp)(http) CEL
GSM265422.CHP.gz 124.2 Kb (ftp)(http) CHP
Raw data provided as supplementary file
Processed data included within Sample table
Processed data provided as supplementary file

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