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Sample GSM596124 Query DataSets for GSM596124
Status Public on Oct 01, 2010
Title WW-ctrl for mDr Day01, Rep2
Sample type RNA
 
Source name Young leaf samples from plants subjected to 1 day of well-watered conditions after 30 DAS
Organism Arabidopsis thaliana
Characteristics ecotype: Columbia
tissue: young leaves
treatment: well-watered control
treatment time: 1 day
Treatment protocol For drought treatment, pellets were weighed before sowing to determine the amount of water in pellets at the beginning of the experiment. Controlled moderate drought (mDr) was maintained by giving plants water to keep the soil moisture level at 30% of field capacity, which is 200% or 2 g H2O g-1 dry soil. Water was withheld at 30 days after sowing (DAS). For progressive drought (pDr) treatment, plants were grown in a growth room as described above, water was withheld at 35 DAS, and pellets were allowed to dry and monitored by weighing the pellets until the required pDr level was reached.
Growth protocol Arabidopsis (Columbia) seeds were sown in moistened peat pellets, stratified at 4°C for 2 days, and then transferred to a growth room kept at 10 hours light (100 µmole m-2 s-1) and 22°C.
Extracted molecule total RNA
Extraction protocol For RNA isolation, two biological replicate samples of 5 pooled plants were collected at early (day1) and late stage (day10) for mDr, and first day of wilting for pDr, along with controls for mDr and pDr. RNA was isolated using RNeasy Kit (Qiagen, USA). After that, genomic DNA was eliminated using DNase kit (Qiagen, USA).
Label biotin
Label protocol RNA preparation/labeling was done using the Affymetrix 3' IVT Express kit, with biotin as label. The cRNA (or aRNA) is purified via beads and fragmented before hybridization.
 
Hybridization protocol 4 µg RNA samples were hybridized to the Affymetrix (ATH1 25K) GeneChip. The hybridization protocol was done using the GeneChip Hybridization, Wash, and Stain kit. The cocktail includes 12.5 ug aRNA, control oligo B2, 20x hyb controls of bioB, bioC, bioD, and cre, 2X hyb mix, and DMSO. The hybridization mix was heated at 99C for 5 min, 45C for 5 min, and then hybridized for 16h at 45C.
Scan protocol Arrays were stained using the Affymetrix FS450 fluidics station with FS450_0001 fluidics protocol. Afterwards, arrays were scanned with the Affymetrix Gene Chip Scanner 3000 with HR (high resolution).
Description mDr-Day01_WW-ctrl_Rep2
Well-watered control for mDr Day01.
Data processing For each of the drought experiments, mDr-Day1, mDr-Day10 and pDr, raw data were background corrected, normalized and summarized according to the custom CDF using RMA (Irizarry et al., 2003). RMA was implemented in the 'affy' Bioconductor package within the R statistical computing environment.

Each of the mDr-Day01, mDr-Day10 and pDr sample groups (along with their controls, for a total of 4 samples per group) were normalized separately.

The custom CDF was built by uniquely mapping 232,697 probe sequences to 21,389 Arabidopsis (TAIR8) gene-based probe sets in the following manner: (i) probes that have perfect sequence identity with a single target gene were selected, (ii) probes mapping to reverse complements of genes were annotated separately as antisense probes (not used in the above counts), and finally, (iii) probes were grouped into probe sets, each corresponding to a single gene, and probe sets having at least 3 unique sequences were retained (>99% probe sets have >=5 probes). Note that these stringent criteria used to construct the CDF make it possible to reliably measure expression values of members of multigene families (free from cross-hybridization between paralogs showing high sequence similarity).
 
Submission date Sep 20, 2010
Last update date Sep 24, 2010
Contact name Andy Pereira
E-mail(s) pereiraa@vbi.vt.edu
Phone 540-231-3784
Organization name Virginia Tech
Department Virginia Bioinformatics Institute
Lab Plant Stress Systems Biology
Street address Washington Street MC0477
City Blacksburg
State/province VA
ZIP/Postal code 24061
Country USA
 
Platform ID GPL10948
Series (1)
GSE24177 Gene expression changes in response to drought stress in Arabidopsis reveal early responses leading to acclimation in plant growth

Data table header descriptions
ID_REF
VALUE RMA log2 expression value

Data table
ID_REF VALUE
AT1G01010_at 3.740216652
AT1G01030_at 4.068945282
AT1G01040_at 7.79860472
AT1G01050_at 8.791424219
AT1G01060_at 6.161459315
AT1G01070_at 4.5483566
AT1G01080_at 8.587670415
AT1G01090_at 9.922447339
AT1G01100_at 11.15489698
AT1G01110_at 4.370279665
AT1G01120_at 8.842749245
AT1G01130_at 4.153509456
AT1G01140_at 8.139742645
AT1G01150_at 2.779270406
AT1G01160_at 6.533477426
AT1G01170_at 9.579545505
AT1G01180_at 3.790178625
AT1G01190_at 5.170921213
AT1G01200_at 4.230302194
AT1G01220_at 7.234560922

Total number of rows: 21517

Table truncated, full table size 523 Kbytes.




Supplementary file Size Download File type/resource
GSM596124.CEL.gz 2.0 Mb (ftp)(http) CEL
Processed data included within Sample table

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