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Sample GSM328484 Query DataSets for GSM328484
Status Public on Jan 31, 2009
Title Populus x canescens root hypoxia_rep_01
Sample type RNA
 
Source name poplar root tissue flooded up to 5h
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 5 h hypoxia
Data processing GCOS1,4 (Affymetrix)
 
Submission date Oct 07, 2008
Last update date Oct 17, 2008
Contact name Juergen Kreuzwieser
E-mail(s) juergen.kreuzwieser@ctp.uni-freiburg.de
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
ID_REF
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
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 993.156 P 6.02111e-05
AFFX-BioB-M_at 1280.46 P 4.42873e-05
AFFX-BioB-3_at 758.806 P 4.42873e-05
AFFX-BioC-5_at 2157.93 P 5.16732e-05
AFFX-BioC-3_at 2764.25 P 4.42873e-05
AFFX-BioDn-5_at 5347.75 P 4.42873e-05
AFFX-BioDn-3_at 9152.54 P 4.42873e-05
AFFX-CreX-5_at 30224.3 P 5.16732e-05
AFFX-CreX-3_at 31995.2 P 4.42873e-05
AFFX-DapX-5_at 7120 P 4.42873e-05
AFFX-DapX-M_at 9776.22 P 4.42873e-05
AFFX-DapX-3_at 10981.5 P 4.42873e-05
AFFX-LysX-5_at 767.703 P 4.42873e-05
AFFX-LysX-M_at 1048.49 P 4.42873e-05
AFFX-LysX-3_at 2653.42 P 5.16732e-05
AFFX-PheX-5_at 1607.12 P 4.42873e-05
AFFX-PheX-M_at 1982.74 P 4.42873e-05
AFFX-PheX-3_at 1550.45 P 4.42873e-05
AFFX-ThrX-5_at 1443.95 P 4.42873e-05
AFFX-ThrX-M_at 2222.4 P 4.42873e-05

Total number of rows: 61413

Table truncated, full table size 2533 Kbytes.




Supplementary file Size Download File type/resource
GSM328484.CEL.gz 4.5 Mb (ftp)(http) CEL
GSM328484.CHP.gz 338.5 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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