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Sample GSM265411 Query DataSets for GSM265411
Status Public on Apr 24, 2008
Title Arabidopsis, whole roots, -Fe, replicate 1
Sample type RNA
 
Source name Whole roots
Organism Arabidopsis thaliana
Characteristics Ecotype: Columbia
Age: Seedling roots, 6 days after germination
Growth Media: Standard media, transferred to -Fe media for 24 hours prior to harvesting tissue
Treatment protocol Samples were prepared as in Birnbaum et al. (2005) except that roots were transferred to -Fe media for 24 hours before protoplasting or harvested without protoplasting. Protoplasted cells were passed through the FACS device with all cells being collected.
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 whole roots after 24 hours of treatment with -Fe media
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)
GSE10496 Expression analysis of the effect of protoplasting and FACS sorting in roots exposed to iron deficiency (-Fe)
GSE10576 Iron deficiency (-Fe) effect: Arabidopsis roots
Relations
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 55.7579 P 0.000856509
AFFX-BioB-M_at 99.564 P 4.42873e-05
AFFX-BioB-3_at 78.6617 P 0.000195116
AFFX-BioC-5_at 173.683 P 5.16732e-05
AFFX-BioC-3_at 142.82 P 5.16732e-05
AFFX-BioDn-5_at 633.958 P 4.42873e-05
AFFX-BioDn-3_at 956.297 P 4.42873e-05
AFFX-CreX-5_at 2803.92 P 4.42873e-05
AFFX-CreX-3_at 3935.51 P 4.42873e-05
AFFX-DapX-5_at 2.9309 A 0.574038
AFFX-DapX-M_at 0.769294 A 0.876428
AFFX-DapX-3_at 0.632849 A 0.969024
AFFX-LysX-5_at 3.06197 A 0.574038
AFFX-LysX-M_at 1.25164 A 0.978098
AFFX-LysX-3_at 3.08455 A 0.470241
AFFX-PheX-5_at 0.984774 A 0.945787
AFFX-PheX-M_at 0.567687 A 0.963431
AFFX-PheX-3_at 2.74346 A 0.559354
AFFX-ThrX-5_at 0.699114 A 0.932322
AFFX-ThrX-M_at 0.495414 A 0.987453

Total number of rows: 22810

Table truncated, full table size 685 Kbytes.




Supplementary file Size Download File type/resource
GSM265411.CEL.gz 2.2 Mb (ftp)(http) CEL
GSM265411.CHP.gz 122.5 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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