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Sample GSM328277 Query DataSets for GSM328277
Status Public on Jan 31, 2009
Title Populus x canescens root control_rep_01
Sample type RNA
Source name Untreated control poplar root tissue at t=0
Organism Populus tremula x Populus alba
Characteristics Experiments were performed with 3-month-old hybrid poplar plants (Populus x canescens). At the beginning of the experiment, the shoots of the trees had a size of 20 to 25 cm. To induce root hypoxia 52 trees were transferred into large plastic containers. The containers were filled with tap water until the water level exceeded the soil surface by 2-3 cm. Shoots were exposed to ambient air.
Extracted molecule total RNA
Extraction protocol For total RNA extraction the Plant RNeasy kit (Qiagen) was used according to the manufacturer’s instructions with some minor modifications. Aliquots of 90 mg of frozen plant powder were added to 900 µl RLT buffer supplemented with 1% ß-mercaptoethanol, 1% PVPP and 2% (w/v) polyethylenglycol (PEG 10,000), and then incubated for 10 min at 58°C. The samples were further processed according to the manufacturer’s protocol. Total RNA was treated with DNase during (RNase free DNase kit, Qiagen) and after (DNA-free TM kit, Ambion) the extraction procedure.
The quality of the isolated total RNA was tested using an Agilent Bioanalyzer and spectrophotometric analysis (NanoDrop® ND-1000, NanoDrop Technologies) to determine the A260 to A280 ratio.
Label Biotin
Label protocol Labelling of cRNA from 3.5 µg of root total RNA was performed exactly as described in the Affymetrix GeneChip Expression Analysis Technical Manual.
Hybridization protocol standard Affymetrix protocol (see GeneChip Expression Analysis Technical Manual)
Scan protocol standard Affymetrix protocol (see GeneChip Expression Analysis Technical Manual)
Description Roots of Grey poplar 0 h control
Data processing GCOS1,4 (Affymetrix)
Submission date Oct 07, 2008
Last update date Oct 17, 2008
Contact name Juergen Kreuzwieser
Phone +49 761 203 8311
Fax +49 761 203 8302
Organization name University of Freiburg
Department Chair of Tree Physiology
Street address Georges-Koehler-Allee
City Freiburg
ZIP/Postal code 79110
Country Germany
Platform ID GPL4359
Series (1)
GSE13109 Effect of hypoxia on gene expression in Grey poplar

Data table header descriptions
VALUE Scaled expression value
ABS_CALL A qualitative measurement indicating if the probe set is detected (Present; P), not detected (Absent; A), or marginally detected (Marginal;M)
DETECTION P-VALUE A p-value indicating the significance of the Detection call

Data table
AFFX-BioB-5_at 755.585 P 7.00668e-05
AFFX-BioB-M_at 941.716 P 4.42873e-05
AFFX-BioB-3_at 722.097 P 4.42873e-05
AFFX-BioC-5_at 1730.22 P 4.42873e-05
AFFX-BioC-3_at 2135.87 P 4.42873e-05
AFFX-BioDn-5_at 3773.33 P 4.42873e-05
AFFX-BioDn-3_at 7690.57 P 4.42873e-05
AFFX-CreX-5_at 27818.2 P 4.42873e-05
AFFX-CreX-3_at 26528.4 P 4.42873e-05
AFFX-DapX-5_at 5475.39 P 4.42873e-05
AFFX-DapX-M_at 7949.8 P 5.16732e-05
AFFX-DapX-3_at 9305.64 P 4.42873e-05
AFFX-LysX-5_at 550.904 P 4.42873e-05
AFFX-LysX-M_at 864.581 P 4.42246e-05
AFFX-LysX-3_at 2277 P 4.42873e-05
AFFX-PheX-5_at 1183.41 P 4.42873e-05
AFFX-PheX-M_at 1445.9 P 4.42873e-05
AFFX-PheX-3_at 1193.61 P 4.42873e-05
AFFX-ThrX-5_at 1131.73 P 5.16732e-05
AFFX-ThrX-M_at 1860.62 P 4.42873e-05

Total number of rows: 61413

Table truncated, full table size 2537 Kbytes.

Supplementary file Size Download File type/resource
GSM328277.CEL.gz 4.7 Mb (ftp)(http) CEL
GSM328277.CHP.gz 335.3 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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