NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1096474 Query DataSets for GSM1096474
Status Public on Jul 01, 2019
Title A.thaliana_Col0_+ABA_rep2
Sample type RNA
 
Source name Whole seedling, 10 day-old
Organism Arabidopsis thaliana
Characteristics treatment: ABA
cultivar: Col-0
genotype: Wild-type
Treatment protocol Treatment with ABA (100 μM) was carried out for two hours.
Growth protocol A. thaliana plants (Col-0) were grown on 0.8% agar plates supplemented with MS salts medium and 1% sucrose under a 16h/8h ligth/dark photoperiod, at 22 ºC and 70% relative humidity.
Extracted molecule total RNA
Extraction protocol RNA was extracted using Trizol reagent (Invitrogen) and purified with RNeasy Plant Kit columns (Qiagen).
Label Cy3
Label protocol cDNA amplified from 10 μg of total RNA was labeled with Cy3 fluorophore.
 
Hybridization protocol Material was hybridized to Nimblegen 12x135K array slides, in duplicate, that cover the expression of 39,042 genes of A. Thaliana (4 60mer probes per gene)
Scan protocol Slides were scanned in a DNA Micorarray Scanner G2505C (Agilent Technologies) at 532 nm and at a 3 um resolution, and TIF images imported into NimbleSan v2.6 for quantification of signal intensity
Description NA
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 NimbleSann v 2.6. (Roche NimbleGen, Inc.)
 
Submission date Mar 12, 2013
Last update date Jul 01, 2019
Contact name Crisanto Gutierrez
E-mail(s) cgutierrez@cbm.csic.es
Phone +34 911964638
Organization name Centro de Biologia Molecular Severo Ochoa
Department Genome Dynamics and Function
Street address Nicolas Cabrera 1
City Madrid
ZIP/Postal code 28049
Country Spain
 
Platform ID GPL13970
Series (1)
GSE45038 Expression analysis of plants with altered GEM mRNA levels, with and without ABA treatment (2 hours).

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

Data table
ID_REF VALUE
AT1G01010_1 12.3562
AT1G01020_1 10.133
AT1G01020_2 8.4751
AT1G01030_1 10.7021
AT1G01040_1 13.9965
AT1G01046_1 11.1844
AT1G01050_1 14.9133
AT1G01060_1 12.0927
AT1G01060_3 7.7542
AT1G01070_1 11.6292
AT1G01070_2 8.0508
AT1G01073_1 8.5447
AT1G01080_1 15.1453
AT1G01080_2 15.0277
AT1G01090_1 15.7905
AT1G01100_1 15.4013
AT1G01100_2 15.6018
AT1G01100_3 15.7498
AT1G01110_1 11.5889
AT1G01110_2 11.8401

Total number of rows: 37118

Table truncated, full table size 710 Kbytes.




Supplementary file Size Download File type/resource
GSM1096474_539558A04_WT+R2_532.pair.gz 2.4 Mb (ftp)(http) PAIR
GSM1096474_539558A04_WT+R2_532_RMA.calls.gz 1.4 Mb (ftp)(http) CALLS
GSM1096474_539558A04_WT+R2_532_norm_RMA.pair.gz 2.4 Mb (ftp)(http) PAIR
Processed data included within Sample table
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap