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Sample GSM244440 Query DataSets for GSM244440
Status Public on Nov 22, 2008
Title Mixed infected tissue, biological rep2
Sample type RNA
 
Source name poplar leaf tissues infected both with Mlp and Mmd
Organism Populus maximowiczii x Populus nigra
Characteristics Fully expanded leaves from leaf plastochron index (LPI) five and six were detached and infected with Mlp and Mmd at a density of 2,000 spores per cm2 each.
Treatment protocol Poplar leaves were detached from trees and seperated to half-leaves. Half-leaves were kept on wet paper on their abaxial side inside Petri dishes prior to infection.
Growth protocol Poplar clone NM6 was grown grown in Promix soil under controlled greenhouse conditions prior to inoculation. NM6 plants were kept under a 16-h photoperiod with weekly fertilizations (20:20:20 N: P: K). Melampsora larici-populina (Mlp) and Melampsora medusae f. sp. deltoidae (Mmd) were maintained on clone Jackii (Populus balsamifera L. x Populus deltoides Marsh.).
Extracted molecule total RNA
Extraction protocol Total RNA were extracted from frozen leaf tissues using the RNAeasy Plant Mini Kit (Qiagen, Mississauga, ON) according to the manufacturer’s instructions. Following a DNase I treatment (Qiagen), 10 μg of total RNA from each biological sample were used for each microarray experiment.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
 
Hybridization protocol Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Poplar Genome Array. GeneChips were washed and stained in the Fluidics protocol EukGE_WS2v5_450
Scan protocol GeneChip scanner
Description Gene expression data from infected tissues with both Melampsora larici poplulina and Melampsora medusae f.sp. deltoides
Data processing The data were analyzed with Robust Multichip Average (RMA)
 
Submission date Nov 23, 2007
Last update date Aug 14, 2011
Contact name Armand Séguin
E-mail(s) Armand.Seguin@rncan.gc.ca
Phone 418-648-2533
Organization name Laurentian forestry Service
Street address 1055 rue de PEPS
City Québec
State/province Québec
ZIP/Postal code G1V4C7
Country Canada
 
Platform ID GPL4359
Series (1)
GSE9673 Comparative transcriptomic reveals signatures specific to various interactions with Melampsora rust fungi

Data table header descriptions
ID_REF
VALUE RMA normalized and logarithmic transformed data (log base2).

Data table
ID_REF VALUE
AFFX-BioB-3_at 7.982
AFFX-BioB-5_at 7.692
AFFX-BioB-M_at 8.156
AFFX-BioC-3_at 9.135
AFFX-BioC-5_at 9.096
AFFX-BioDn-3_at 11.456
AFFX-BioDn-5_at 10.457
AFFX-CreX-3_at 13.026
AFFX-CreX-5_at 12.868
AFFX-DapX-3_at 9.421
AFFX-DapX-5_at 8.131
AFFX-DapX-M_at 9.023
AFFX-LysX-3_at 7.109
AFFX-LysX-5_at 5.226
AFFX-LysX-M_at 5.934
AFFX-PheX-3_at 6.623
AFFX-PheX-5_at 5.792
AFFX-PheX-M_at 5.977
AFFX-Ptp-actin-3_s_at 10.534
AFFX-Ptp-actin-5_a_at 10.239

Total number of rows: 61413

Table truncated, full table size 1693 Kbytes.




Supplementary file Size Download File type/resource
GSM244440.CEL.gz 4.3 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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