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Sample GSM266667 Query DataSets for GSM266667
Status Public on Apr 24, 2008
Title Arabidopsis, root cells, columella root cap, -Fe, 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: PET111
Growth Media: Standard media for 6 days, transferred to -Fe media for 24 hours before protoplasting
Treatment protocol Samples were prepared as in Birnbaum et al. (2005) Nat. Methods for roots grown under standard conditions. For -Fe treated samples, roots were transferred to -Fe media for 24 hours before protoplasting.
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 planted at ~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 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 isolated columella root cap cells after roots were treated to -Fe media for 24 hours
Data processing MAS5.0
 
Submission date Feb 15, 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)
GSE10501 Expression analysis of root cell-types 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 239.715 P 0.000972149
AFFX-BioB-M_at 281.404 P 6.02111e-05
AFFX-BioB-3_at 157.308 P 4.42873e-05
AFFX-BioC-5_at 622.492 P 5.16732e-05
AFFX-BioC-3_at 479.612 P 7.00668e-05
AFFX-BioDn-5_at 1255.68 P 4.42873e-05
AFFX-BioDn-3_at 1851.84 P 4.42873e-05
AFFX-CreX-5_at 6744.64 P 4.42873e-05
AFFX-CreX-3_at 7817.8 P 4.42873e-05
AFFX-DapX-5_at 10.5322 A 0.470241
AFFX-DapX-M_at 10.8759 A 0.645547
AFFX-DapX-3_at 4.64579 A 0.891021
AFFX-LysX-5_at 4.27635 A 0.860518
AFFX-LysX-M_at 1.88954 A 0.993129
AFFX-LysX-3_at 3.01393 A 0.455409
AFFX-PheX-5_at 0.668813 A 0.997727
AFFX-PheX-M_at 6.55133 A 0.749204
AFFX-PheX-3_at 17.9805 A 0.216524
AFFX-ThrX-5_at 1.18305 A 0.963431
AFFX-ThrX-M_at 4.46669 A 0.904372

Total number of rows: 22810

Table truncated, full table size 675 Kbytes.




Supplementary file Size Download File type/resource
GSM266667.CEL.gz 3.2 Mb (ftp)(http) CEL
GSM266667.CHP.gz 124.7 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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