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Sample GSM327412 Query DataSets for GSM327412
Status Public on Jan 15, 2009
Title Populus balsamifera_1006_differentiating_xylem_midday_2
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 1501.57 P 0.000753643
AFFX-BioB-M_at 1930.87 P 4.42873e-05
AFFX-BioB-3_at 1754.65 P 4.42873e-05
AFFX-BioC-5_at 4731.9 P 5.16732e-05
AFFX-BioC-3_at 4775.1 P 4.42873e-05
AFFX-BioDn-5_at 6741.52 P 4.42873e-05
AFFX-BioDn-3_at 17349.6 P 4.42873e-05
AFFX-CreX-5_at 41109.3 P 5.16732e-05
AFFX-CreX-3_at 50985.4 P 4.42873e-05
AFFX-DapX-5_at 31858 A 0.139482
AFFX-DapX-M_at 52382.8 A 0.108979
AFFX-DapX-3_at 63934 P 0.00933744
AFFX-LysX-5_at 7682.86 P 0.0044838
AFFX-LysX-M_at 12007.6 M 0.0542134
AFFX-LysX-3_at 20974.3 P 0.0396608
AFFX-PheX-5_at 10786.8 P 0.002867
AFFX-PheX-M_at 21067.1 P 0.0219019
AFFX-PheX-3_at 11291.8 A 0.0726999
AFFX-ThrX-5_at 14892.2 P 0.00844047
AFFX-ThrX-M_at 17707.6 A 0.131361

Total number of rows: 61413

Table truncated, full table size 2474 Kbytes.

Supplementary file Size Download File type/resource
GSM327412.CEL.gz 4.9 Mb (ftp)(http) CEL
GSM327412.CHP.gz 336.2 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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