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Sample GSM328275 Query DataSets for GSM328275
Status Public on Jan 31, 2009
Title Populus x canescens leaf hypoxia_rep_03
Sample type RNA
Source name poplar leaf tissue flooded up to 168h
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 5 µg of leaf 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 Source leaves of Grey poplar 168 h hypoxia treated
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 1469.37 P 0.00010954
AFFX-BioB-M_at 1690.46 P 4.42873e-05
AFFX-BioB-3_at 1315.06 P 4.42873e-05
AFFX-BioC-5_at 3680.89 P 4.42873e-05
AFFX-BioC-3_at 3645.82 P 4.42873e-05
AFFX-BioDn-5_at 6631.87 P 4.42873e-05
AFFX-BioDn-3_at 13575.9 P 4.42873e-05
AFFX-CreX-5_at 39290.7 P 5.16732e-05
AFFX-CreX-3_at 45349.4 P 4.42873e-05
AFFX-DapX-5_at 376.965 P 8.14279e-05
AFFX-DapX-M_at 899.569 P 0.000169227
AFFX-DapX-3_at 1294.9 P 5.16732e-05
AFFX-LysX-5_at 88.0595 P 0.000662269
AFFX-LysX-M_at 170.713 P 0.0138105
AFFX-LysX-3_at 308.354 P 6.99729e-05
AFFX-PheX-5_at 121.78 P 0.00010954
AFFX-PheX-M_at 134.704 P 0.0113785
AFFX-PheX-3_at 168.561 P 0.000340305
AFFX-ThrX-5_at 86.1886 A 0.0726824
AFFX-ThrX-M_at 164.35 P 8.14279e-05

Total number of rows: 61413

Table truncated, full table size 2528 Kbytes.

Supplementary file Size Download File type/resource
GSM328275.CEL.gz 4.5 Mb (ftp)(http) CEL
GSM328275.CHP.gz 338.7 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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