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Sample GSM328562 Query DataSets for GSM328562
Status Public on Jan 31, 2009
Title Populus x canescens root hypoxia_rep_04
Sample type RNA
 
Source name poplar root tissue flooded up to 24h
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 24 h hypoxia
Data processing GCOS1,4 (Affymetrix)
 
Submission date Oct 08, 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 1189.64 P 5.16732e-05
AFFX-BioB-M_at 1751.08 P 4.42873e-05
AFFX-BioB-3_at 1204.69 P 4.42873e-05
AFFX-BioC-5_at 3512.77 P 5.16732e-05
AFFX-BioC-3_at 3766.21 P 4.42873e-05
AFFX-BioDn-5_at 6505.38 P 4.42873e-05
AFFX-BioDn-3_at 12599 P 4.42873e-05
AFFX-CreX-5_at 40090.2 P 5.16732e-05
AFFX-CreX-3_at 41878.3 P 4.42873e-05
AFFX-DapX-5_at 7785.83 P 4.42873e-05
AFFX-DapX-M_at 11452.5 P 4.42873e-05
AFFX-DapX-3_at 13673.6 P 4.42873e-05
AFFX-LysX-5_at 965.569 P 4.42873e-05
AFFX-LysX-M_at 1309.77 P 4.42873e-05
AFFX-LysX-3_at 2857.56 P 5.16732e-05
AFFX-PheX-5_at 1692.51 P 4.42873e-05
AFFX-PheX-M_at 2355.34 P 4.42873e-05
AFFX-PheX-3_at 1994.68 P 4.42873e-05
AFFX-ThrX-5_at 1879.89 P 4.42873e-05
AFFX-ThrX-M_at 2958.41 P 4.42873e-05

Total number of rows: 61413

Table truncated, full table size 2525 Kbytes.




Supplementary file Size Download File type/resource
GSM328562.CEL.gz 4.3 Mb (ftp)(http) CEL
GSM328562.CHP.gz 342.6 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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