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Sample GSM2674583 Query DataSets for GSM2674583
Status Public on Jun 20, 2017
Title Col0_3MB_flg22_rep1
Sample type RNA
 
Source name Arabidopsis thaliana Col-0 wild-type, 10 day old whole seedlings
Organism Arabidopsis thaliana
Characteristics genotype: Wild-type
phenotype: normal
accession: CS[ ]
tissue: whole seedling
Growth protocol Each biological replicate included 48, 10 day-old Arabidopsis thaliana seedlings pooled for each treatment. Col-0 seedlings were pre-treated for 2 hours with either 60% DMSO, 250mM 3AB (dissolved in 60% DMSO), or 250mM 3MB (dissolved in 60% DMSO). Col-0 seedlings were then treated for one hour with either ddH2O or 1uM flg22, or 1uM elf18, and parg1 seedlings were treated for one hour with either ddH2O or 1uM elf18.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using Rneasy Mini Kit (Qiagen), and DNA was removed by DNase digestion with the RNase-free DNase Set (Qiagen) RNA quality and concentration was determined using an Agilent 2100 bioanalyzer at the Gene Expression Center at University of Wisconsin-Madison Biotechnology Center, Madison, WI, USA).
Label Cy3
Label protocol Labeling was performed by the Gene Expression Center, Madison, WI USA, following Nimblegen's standard operating protocol. See www.nimblegen.com.
 
Hybridization protocol Hybridization was performed by the Gene Expression Center, Madison, WI USA, following Nimblegen's 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 This sample is of wild-type Arabidopsis thaliana, treated with the PARP inhibitor 3-methyl benzamide (3MB) and the MAMP flg22. It is the first of three biological replicates.
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 Jun 19, 2017
Last update date Jan 23, 2018
Contact name Amy Graham Briggs
E-mail(s) briggsa@beloit.edu
Phone 6083632349
Organization name Beloit College
Department Biology
Street address 700 College St.
City Beloit
State/province WI
ZIP/Postal code 53511
Country USA
 
Platform ID GPL23603
Series (1)
GSE100205 Expression analysis of Arabidopsis thaliana Col-0 and parg1 with and without PARP inhibitor (3AB, 3MB), with and without MAMP (flg22, elf18)

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

Data table
ID_REF VALUE
AT1G01010_BLOCK1 4757.7095
AT1G01010_BLOCK2 4694.0999
AT1G01020_BLOCK1 1222.0154
AT1G01020_BLOCK2 1294.6855
AT1G01030_BLOCK1 264.4028
AT1G01030_BLOCK2 274.3491
AT1G01040_BLOCK1 2097.5587
AT1G01040_BLOCK2 1960.2658
AT1G01050_BLOCK1 8652.1862
AT1G01050_BLOCK2 8714.3967
AT1G01060_BLOCK1 442.0596
AT1G01060_BLOCK2 401.4097
AT1G01070_BLOCK1 573.7903
AT1G01070_BLOCK2 582.4258
AT1G01080_BLOCK1 624.9967
AT1G01080_BLOCK2 723.1468
AT1G01090_BLOCK1 33354.2108
AT1G01090_BLOCK2 36324.8776
AT1G01100_BLOCK1 13529.0717
AT1G01100_BLOCK2 14745.7937

Total number of rows: 60770

Table truncated, full table size 1553 Kbytes.




Supplementary file Size Download File type/resource
GSM2674583_33249202_532.pair.gz 5.4 Mb (ftp)(http) PAIR
GSM2674583_33249202_FR1_RMA.calls.gz 2.2 Mb (ftp)(http) CALLS
Processed data included within Sample table
Processed data provided as supplementary file
Processed data are available on Series record

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