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Sample GSM176880 Query DataSets for GSM176880
Status Public on Dec 31, 2007
Title AWP_Control_2
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 (http://www.geneontology.org/) 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
E-mail(s) sgoodwin@memphis.edu
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
Relations
Reanalyzed by GSE119083

Data table header descriptions
ID_REF
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
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 872.897 A 0.083592
AFFX-BioB-M_at 1145.99 P 0.0044838
AFFX-BioB-3_at 1350.91 P 0.00401721
AFFX-BioC-5_at 3449.28 P 0.000195116
AFFX-BioC-3_at 2121.28 P 0.000581214
AFFX-BioDn-5_at 1834.95 P 0.000445901
AFFX-BioDn-3_at 15736.2 P 7.00668e-05
AFFX-CreX-5_at 27079.1 P 4.42873e-05
AFFX-CreX-3_at 46986.5 P 4.42873e-05
AFFX-DapX-5_at 37.0507 A 0.916408
AFFX-DapX-M_at 598.594 A 0.262827
AFFX-DapX-3_at 57.4472 A 0.978098
AFFX-LysX-5_at 179.774 A 0.41138
AFFX-LysX-M_at 124.746 A 0.814869
AFFX-LysX-3_at 105.848 A 0.52976
AFFX-PheX-5_at 20.1037 A 0.945787
AFFX-PheX-M_at 49.0677 A 0.843268
AFFX-PheX-3_at 155.194 A 0.843268
AFFX-ThrX-5_at 27.0206 A 0.932322
AFFX-ThrX-M_at 93.993 A 0.659339

Total number of rows: 22810

Table truncated, full table size 645 Kbytes.




Supplementary file Size Download File type/resource
GSM176880.CEL.gz 3.2 Mb (ftp)(http) CEL
GSM176880.CHP.gz 5.7 Mb (ftp)(http) CHP
Processed data provided as supplementary file

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