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Sample GSM327413 Query DataSets for GSM327413
Status Public on Jan 15, 2009
Title Populus balsamifera_1006_differentiating_xylem_midday_3
Sample type RNA
Source name Populus balsamifera, clone 1006, differentiating xylem, midday
Organism Populus balsamifera
Characteristics Differentiating xylem – bottom 15 cm of stem - peel off bark and immediately scrape the surface of the exposed wood into micro collection tubes containing liquid nitrogen
Alberta Pacific Forest Industries clone 1006
Clonally-propagated, 8-week-old Populus balsamifera saplings
Differentiating xylem collected in the middle of the light period
Biomaterial provider Alberta Pacific Forest Industries Inc., Boyle, AB, Canada
Growth protocol Plant material was collected from clonally-propagated, 8-week-old Populus balsamifera saplings (1006, Alberta Pacific Forest Industries Inc., Boyle, AB, Canada) grown in a climate-controlled growth chamber. Saplings were grown in Sunshine Mix (Sun Gro Horticulture, Vancouver, BC, Canada) with a 16h photoperiod, a maximum daytime temperature of 22°C and a minimum nighttime temperature of 17°C. All tissues were collected at midday. All tissues were collected from saplings without water limitations. Differentiating xylem was collected from the bottom 6 inches of the stem by peeling off the bark and immediately scraping the surface of the exposed wood into micro collection tubes containing liquid nitrogen. Flash frozen plant tissue was stored at -80°C until RNA was extracted.
Extracted molecule total RNA
Extraction protocol Chang S, Puryear J, Cariney J. 1993. A simple and efficient method for isolating RNA from pine trees. Plant Molecular Biology Reporter. 11:113-116.
Label biotin
Label protocol Affymetrix protocol: Eukaryotic target preparation: One-cycle target labeling assay
Hybridization protocol Affymetrix protocol: Eukaryotic target preparation: Eukaryotic target hybridization
Scan protocol Affymetrix protocol: GeneChip® Scanner 3000 7G Affymetrix 00-0073
Description Affymetrix protol: Fluidics script: EukGE-WS2v5
Data processing MAS5.0, scaled to 500
Submission date Oct 06, 2008
Last update date Dec 16, 2008
Contact name Malcolm M. Campbell
Phone 416-946-0817
Fax 416-978-5878
Organization name University of Toronto
Department Cell & Systems Biology
Lab 3058ESC
Street address 25 Willcocks Street
City Toronto
State/province ON
ZIP/Postal code M5S 3B2
Country Canada
Platform ID GPL4359
Series (1)
GSE13990 Populus balsamifera developmental tissue series

Data table header descriptions
VALUE normalized (scaled) signal count data

Data table
AFFX-BioB-5_at 1916.02 P 0.000581214
AFFX-BioB-M_at 2098.96 P 4.42873e-05
AFFX-BioB-3_at 2039.29 P 4.42873e-05
AFFX-BioC-5_at 6224.46 P 5.16732e-05
AFFX-BioC-3_at 5766.19 P 4.42873e-05
AFFX-BioDn-5_at 8925.4 P 4.42873e-05
AFFX-BioDn-3_at 20688.8 P 4.42873e-05
AFFX-CreX-5_at 51806.2 P 5.16732e-05
AFFX-CreX-3_at 64012.1 P 4.42873e-05
AFFX-DapX-5_at 36150.9 A 0.116113
AFFX-DapX-M_at 67776.2 A 0.147939
AFFX-DapX-3_at 82815.6 P 0.00010954
AFFX-LysX-5_at 8949.96 P 0.00499819
AFFX-LysX-M_at 15484.3 P 0.0113844
AFFX-LysX-3_at 25339.2 P 0.0464816
AFFX-PheX-5_at 13137.7 P 5.16732e-05
AFFX-PheX-M_at 26716.4 P 0.000856509
AFFX-PheX-3_at 15819.6 P 0.00618711
AFFX-ThrX-5_at 17631.6 P 0.0200219
AFFX-ThrX-M_at 24242 A 0.102165

Total number of rows: 61413

Table truncated, full table size 2476 Kbytes.

Supplementary file Size Download File type/resource
GSM327413.CEL.gz 4.6 Mb (ftp)(http) CEL
GSM327413.CHP.gz 338.5 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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