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Sample GSM244434 Query DataSets for GSM244434
Status Public on Nov 22, 2008
Title Mlp infected tissue, biological rep2
Sample type RNA
 
Source name poplar leaf tissues infected with Mlp
Organism Populus maximowiczii x Populus nigra
Characteristics Fully expanded leaves from leaf plastochron index (LPI) five and six were detached and infected with Mlp at a density of 2,000 spores per cm2.
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 Melampsora larici poplulina
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 8.239
AFFX-BioB-5_at 7.994
AFFX-BioB-M_at 8.329
AFFX-BioC-3_at 9.259
AFFX-BioC-5_at 9.355
AFFX-BioDn-3_at 11.616
AFFX-BioDn-5_at 10.564
AFFX-CreX-3_at 13.020
AFFX-CreX-5_at 12.942
AFFX-DapX-3_at 9.326
AFFX-DapX-5_at 8.167
AFFX-DapX-M_at 9.046
AFFX-LysX-3_at 6.909
AFFX-LysX-5_at 4.794
AFFX-LysX-M_at 5.866
AFFX-PheX-3_at 6.428
AFFX-PheX-5_at 5.782
AFFX-PheX-M_at 5.996
AFFX-Ptp-actin-3_s_at 10.594
AFFX-Ptp-actin-5_a_at 10.293

Total number of rows: 61413

Table truncated, full table size 1693 Kbytes.




Supplementary file Size Download File type/resource
GSM244434.CEL.gz 4.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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