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Sample GSM176879 Query DataSets for GSM176879
Status Public on Dec 31, 2007
Title AWP_Control_1
Sample type RNA
Source name Arabidopsis seedlings, removed from agar plates, 16 h treatment
Organism Arabidopsis thaliana
Characteristics Arabidopsis cv columbia
Biomaterial provider Fisher Scientific
Treatment protocol Seedlings with 2- to 3 cm root length were removed from agar plates and submerged in 1000 ml flasks containing 500 ml of modified one-sixth MS liquid medium containing 50 micromolar aluminum and 1% sucrose added as a carbon source for 16 hr.
Extracted molecule total RNA
Extraction protocol 100 seedlings were harvested at following 16 hr Al or mock treatment.Tissue was ground to a fine powder in liquid nitrogen using a pestle and mortar and total RNA was extracted using the following method. Each 0.5 to 1 g of powdered tissue were added to 5 cm3 of STAT-60 (Tel-Test, TX). The mixture was homogenized and stored on ice for 10 min. Chloroform/isoamyl (24:1, v:v) ETOH was added to the homogenate and centrifuged at 12000g for 30 min (40C). Following the transfer of the aqueous phase to a fresh tube, RNA was precipitated with isopropanol overnight at –200C, pelleted by centrifugation at 12000g for 30 min (40C), and resuspended 0.1 cm3 of RNase-free water. Total RNA was quantified using Beckman Spectrophotometer, and qualified by running 1 μg cm-1 of each sample onto a RNA Lab-On-A-Chip using a Agilent Bioanalyzer 2100 (Agilent technologies, Mountain View, CA).
Label Enzo Biotin-labeled in vitro transcribed (IVT)
Label protocol Briefly, total RNA (8 mg) was synthesized to cDNA using the Superscript Double-Stranded cDNA synthesis kit (Invitrogen Corp, Carlsbad, CA) and poly dT-nucleotide primers that contain a sequence recognized by T7 RNA polymerase. The newly synthesized cDNA was used as a template to generate biotin-labeled invitro transcribed (IVT) cRNA using the Bio-Array High Yield RNA transcript labeling kit (Enzo Diagnostics, Inc, Farmingdale, NY).
Hybridization protocol Twenty micrograms of the cRNA was fragmented to strands of 35 to 200 bases in length. The fragment cRNA was hybridized to and Affymetrix ATH1 array GeneChip at 450C with rotation for 16 h (Affymetrix GeneChip Hybridization Oven 320). The GeneChip arrays were washed and stained (streptavidin phycoerythrin) on an Affymetrix Fluidics Station 400, followed by scanning.
Scan protocol Scanned using Affymetrix 3000 GeneChip scanner
Description The mRNA levels were measured using Affymetrix ATH1 chips (containing 22,810 probe sets) according to standard GeneChip Expression assay protocol. Total RNA was extracted from 100 pooled Arabidopsis seedlings for each GeneChip, control and Al-treated. A total of four chips were used in this experiment, representing two biological replicates to measure expression of whole plant material.
Data processing After hybridization, the chips were scanned using a GeneChip Scanner and raw hybridization data from microarray experiments were imported directly into Affymetrix GeneChip Operating software (GCOS) v1.2 for normalization and to determine the probe intensities and “Present” (P) or “Absent” (A) calls for each chip. The scanned image results for all 4 chips were quantified and analyzed using, dChip (Li and Wong, 2001) and RMA software (Irizarry et al., 2003). The gene list generated in dchip was uploaded into gene ontology consortium website ( to further determine the functional categories of up- and down regulated gene expression.
Submission date Mar 22, 2007
Last update date Aug 28, 2018
Contact name Shirlean B Goodwin
Phone 901-678-1440
Fax 901-678-2458
Organization name University of Memphis
Department Biology
Lab Feinstone Center for Genomic Research
Street address 3774 Walker Ave
City Memphis
State/province TN
ZIP/Postal code 38152
Country USA
Platform ID GPL198
Series (1)
GSE7334 Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
Reanalyzed by GSE119083

Data table header descriptions
VALUE Normalized data using RMA and dchip
ABS_CALL the call in an absolute analysis that indicates if the transcript was present (P), absent (A), marginal (M), or reverse present (RP)
DETECTION P-VALUE 'detection p-value', p-value that indicates the significance level of the detection call

Data table
AFFX-BioB-5_at 12120.1 P 0.000146581
AFFX-BioB-M_at 15778.7 P 4.42873e-05
AFFX-BioB-3_at 13384.9 P 5.16732e-05
AFFX-BioC-5_at 32677.7 P 7.00668e-05
AFFX-BioC-3_at 16354.4 P 5.16732e-05
AFFX-BioDn-5_at 17440.1 P 4.42873e-05
AFFX-BioDn-3_at 107553 P 4.42873e-05
AFFX-CreX-5_at 202790 P 4.42873e-05
AFFX-CreX-3_at 342307 P 4.42873e-05
AFFX-DapX-5_at 444.961 A 0.275146
AFFX-DapX-M_at 111.343 A 0.659339
AFFX-DapX-3_at 203.025 A 0.860518
AFFX-LysX-5_at 200.412 A 0.645547
AFFX-LysX-M_at 41.9761 A 0.969024
AFFX-LysX-3_at 88.4476 A 0.659339
AFFX-PheX-5_at 59.185 A 0.9273
AFFX-PheX-M_at 323.327 A 0.60308
AFFX-PheX-3_at 118.824 A 0.834139
AFFX-ThrX-5_at 76.346 A 0.814869
AFFX-ThrX-M_at 261.064 A 0.574038

Total number of rows: 22810

Table truncated, full table size 644 Kbytes.

Supplementary file Size Download File type/resource
GSM176879.CEL.gz 2.8 Mb (ftp)(http) CEL
GSM176879.CHP.gz 5.2 Mb (ftp)(http) CHP
Raw data provided as supplementary file
Processed data provided as supplementary file

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