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Sample GSM1144815 Query DataSets for GSM1144815
Status Public on May 31, 2014
Title Low photosynthetic rate gene pool,L_E,biological rep2
Sample type RNA
Source name Leaves from 5 low photosynthetic rate individuals.
Organism (Populus alba x Populus glandulosa) x Populus tomentosa
Characteristics tissue: leaves
phenotype: low photosynthetic rate
genotype: F1 interspecific population (the female hybrid clone “YX01” (P. alba × P. glandulossa) and the male clone “LM50” (P. tomentosa))
Treatment protocol Photosynthetic characteristics was collected from fully expanded leaves using the LI-6400 portable photosynthesis system (Li-Cor Inc., Lincoln, NE, USA) at 9:00–11:30 on sunny days. Three functional leaves, the fourth to sixth counting from the individual stem head of all of the population were measured. According to the average of the data, fifty individuals which the value was in the peak were measured again to ensure the phenotype was stable. Among them leaves from thirty samples including fifteen individuals of high and fifteen individuals of low photosynthetic rate were selected to construct gene pool and immediately placed into liquid nitrogen in the field and stored at -80°C until used for isolating RNA.
Growth protocol A total of 1200 progeny, which were randomly selected from the F1 interspecific population of 5000 pedigree, were used in this study. They established by controlled crossing between two elite poplar parents, the female hybrid clone “YX01” (P. alba × P. glandulossa) and the male clone “LM50” (P. tomentosa). The progeny was grown in Xiao Tangshan horticulture fields of Beijing Forestry University, Beijing, China (40°2′N, 115°50′E), using a randomized complete block design with three replications in 2008.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the Plant Qiagen RNAeasy kit (Qiagen China, Shanghai) according to the manufacturer’s instructions. Each replicate mixed RNA extractions of 5 individuals to equal quantities (2 mg) for later microarray analysis. All the RNA samples including every individual and the mixed integrities were examined by Agilent 2100 Bioanalyzer (Agilent Technologies, USA) according to the manufacturer’s instructions, and no evidence of degradation was noted. They subsequently were reverse transcribed into cDNA utilizing the SuperScript First-Strand Synthesis system and the supplied polythymine primers (Invitrogen).
Label biotin
Label protocol Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.
Hybridization protocol Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.
Scan protocol Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.
Description Expression data from two years old leaves of F1 interspecific population
Leaves from 5 low photosynthetic rate individuals.
Data processing Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).
Submission date May 20, 2013
Last update date May 31, 2014
Contact name Bowen Wang
Organization name Beijing Forest University
Street address Beijing Forest University
City Beijing
ZIP/Postal code 100083
Country China
Platform ID GPL4359
Series (1)
GSE47105 Expression data from different photosynthetic rate in Populus.

Data table header descriptions
VALUE log2 MAS 5.0 signal

Data table
Ptp.1.1.S1_at 11.469491
Ptp.1.1.S1_s_at 12.429932
Ptp.10.1.A1_at 11.671057
Ptp.100.1.S1_a_at 12.475315
Ptp.100.2.S1_a_at 12.420126
Ptp.100.2.S1_at 8.575546
Ptp.1000.1.A1_at 6.354048
Ptp.1002.1.A1_at 12.550071
Ptp.1003.1.A1_at 9.093111
Ptp.1004.1.S1_at 7.74166
Ptp.1006.1.A1_at 10.675276
Ptp.1007.1.S1_at 13.629835
Ptp.1008.1.A1_at 8.708274
Ptp.1009.1.A1_at 6.3554416
Ptp.101.1.S1_at 8.190603
Ptp.1010.1.A1_at 8.7282095
Ptp.1010.1.A1_s_at 11.024928
Ptp.1011.1.S1_at 9.32586
Ptp.1011.1.S1_s_at 10.209565
Ptp.1011.2.S1_at 6.8383784

Total number of rows: 61313

Table truncated, full table size 1896 Kbytes.

Supplementary file Size Download File type/resource
GSM1144815_L_E.CEL.gz 4.0 Mb (ftp)(http) CEL
Processed data included within Sample table

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