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Sample GSM1958082 Query DataSets for GSM1958082
Status Public on Dec 01, 2015
Title 540121A10_(10)Col 0 (NO) 15 min Rep 3
Sample type RNA
 
Source name A. thaliana Col-0 15 min after NO
Organism Arabidopsis thaliana
Characteristics ecotype: Col-0
developmental stage: 12-d-old
tissue: seedling
Treatment protocol The pulse of NO was performed by incubating plants in a tightly sealed transparent box after injection of 300 ppm of pure NO gas (Linde AG, Germany) during 5 min.
Growth protocol Samples were harvested 12 h after dawn of day 12 after sowing and seedlings were grown under long days (16 h light / 8 h darkness) photoperiodic conditions.
Extracted molecule total RNA
Extraction protocol Total RNA from wild type and NO-deficient plants was isolated and purified by the Micro-to-Midi Total RNA Purification System from Invitrogen (Carlsbad, CA, USA).
Label Cy3
Label protocol Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
 
Hybridization protocol Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.
Scan protocol Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
Description It is the third of three independent wild-type biological replicates treated with NO for 15 min.
Data processing The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).
 
Submission date Nov 30, 2015
Last update date Dec 01, 2015
Contact name Jose Leon
E-mail(s) jleon@ibmcp.upv.es
Phone +34 963877882
Organization name IBMCP (CSIC-UPV)
Street address CPI Edificio 8E, Ingeniero Fausto Elio s/n
City Valencia
ZIP/Postal code 46022
Country Spain
 
Platform ID GPL13970
Series (1)
GSE75509 IBMCP JLeon lab NO-exposed (15, 30 and 60 min after pulse of 300 ppm NO during 5 min) wt Col-0 versus untreated wt Col -0

Data table header descriptions
ID_REF
VALUE RMA-normalized, averaged gene-level signal intensity

Data table
ID_REF VALUE
AT1G01010_1 13.3528
AT1G01020_1 8.3011
AT1G01020_2 9.3717
AT1G01030_1 11.4397
AT1G01040_1 13.4574
AT1G01046_1 9.8886
AT1G01050_1 15.3239
AT1G01060_1 13.708
AT1G01060_3 7.462
AT1G01070_1 13.2208
AT1G01070_2 7.685
AT1G01073_1 6.7435
AT1G01080_1 15.28
AT1G01080_2 15.1346
AT1G01090_1 15.6145
AT1G01100_1 15.1055
AT1G01100_2 15.5568
AT1G01100_3 15.587
AT1G01110_1 12.2054
AT1G01110_2 11.9446

Total number of rows: 37118

Table truncated, full table size 708 Kbytes.




Supplementary file Size Download File type/resource
GSM1958082_540121A10_10_Col_0_NO_15_min_Rep_3_532.pair.gz 2.4 Mb (ftp)(http) PAIR
GSM1958082_540121A10_10_Col_0_NO_15_min_Rep_3_532_RMA.calls.gz 1.4 Mb (ftp)(http) CALLS
Processed data included within Sample table
Processed data provided as supplementary file

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