NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1096471 Query DataSets for GSM1096471
Status Public on Jul 01, 2019
Title A.thaliana_Col0_-ABA_rep1
Sample type RNA
 
Source name Whole seedling, 10 day-old
Organism Arabidopsis thaliana
Characteristics treatment: none
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 13.2821
AT1G01020_1 9.4469
AT1G01020_2 8.771
AT1G01030_1 11.44
AT1G01040_1 13.808
AT1G01046_1 11.0906
AT1G01050_1 15.1195
AT1G01060_1 10.426
AT1G01060_3 7.781
AT1G01070_1 12.6443
AT1G01070_2 7.8361
AT1G01073_1 7.9989
AT1G01080_1 15.2088
AT1G01080_2 14.982
AT1G01090_1 15.7297
AT1G01100_1 15.4959
AT1G01100_2 15.616
AT1G01100_3 15.6959
AT1G01110_1 12.7167
AT1G01110_2 12.8622

Total number of rows: 37118

Table truncated, full table size 710 Kbytes.




Supplementary file Size Download File type/resource
GSM1096471_539558A01_WT-R1_532.pair.gz 2.4 Mb (ftp)(http) PAIR
GSM1096471_539558A01_WT-R1_532_RMA.calls.gz 1.4 Mb (ftp)(http) CALLS
GSM1096471_539558A01_WT-R1_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