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Sample GSM738228 Query DataSets for GSM738228
Status Public on Dec 31, 2011
Title Whole Tissue_SD 4h Light_Col-0_rep1
Sample type RNA
 
Source name Whole tissue, 10d old in SD
Organism Arabidopsis thaliana
Characteristics cultivar: Col-0
time: 4 hr
Treatment protocol Samples were harvested in dark and after 4h light treatment in SD growth conditions.
Growth protocol Seeds were surface sterilized and plated on Murashige and Skoog growth medium (GM) containing 0.9% agar without Suc (GM - Suc) as described (Shen et al., 2005). After 4 d of stratification at 4oC, seeds were exposed to SD.
Extracted molecule total RNA
Extraction protocol For microarray, total RNA was isolated from 10d-old bhlh93-1 mutant and wild-type Col-0 seedlings grown under SD using the RNeasy plant mini kit (Qiagen). Five µg RNA from 10d old SD grown seedling of Wt and bhlh93-1 mutants was reverse transcribed using the RT-PCR kit from Invitrogen.
Label Cy3
Label protocol Double stranded cDNA was created using the Invitrogen double stranded-cDNA synthesis kit(Cat #11917010) according to Roche Nimblegen instructions (Roche protocol version 2.3) using an oligo-dT primer. Double-stranded cDNA was then labeled using Cy3-labeled nonamers (TriLink, San Diego, CA) and Klenow (large fragment, NEB cat #M0210M) also according to the Roche protocol version 2.3).
 
Hybridization protocol Microarray hybridization experiment was performed according to user manual of Roche Nimbelgen Arabidopsis thaliana 12x135K Array (090717 Athal TAIR9 exp HX12; Cat No. 05543746001). 4 micrograms of labeled product were resuspended in sample tracking control, applied to the arrays, and hybridized overnight in a Maui 4-position hybridization chamber, according to Roche Nimblegen protcol version 2.3. The arrays were then washed and dried according to the same protocol.
Scan protocol Arrays were scanned and analyzed according to Roche Nimblegen protcol version 2.3. Briefly, the arrays were scanned on an Axon 4000B scanner set at 5 micron resolution with 100% laser power and PMT gain between 500 and 600. The resulting TIF images were post-processed using Nimblescan version 2.3 to identify probe locations and each array was visually inspected for proper grid alignment.
Description 394517_A02_22Feb10_532.pair
394517_A02_22Feb10_532_RMA.calls
Data processing The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).
 
Submission date Jun 07, 2011
Last update date Dec 31, 2011
Contact name Enamul Huq
E-mail(s) huq@mail.utexas.edu
Phone 5124716658
Organization name University of Texas at Austin
Department MCDB
Lab Huq lab
Street address 24th St. and Whitis BIO labs ,
City Austin
State/province TX
ZIP/Postal code 78712
Country USA
 
Platform ID GPL13697
Series (1)
GSE29786 Role of bHLH93 in controlling flowering time in Arabidopsis

Data table header descriptions
ID_REF
VALUE Log scale gene expression values were calculated using a robust multiarray analysis (RMA).

Data table
ID_REF VALUE
AT1G01010_1 526.613246
AT1G01020_1 318.1580909
AT1G01020_2 122.1491488
AT1G01030_1 164.7117882
AT1G01040_1 1062.023519
AT1G01046_1 76.46353531
AT1G01050_1 1055.418894
AT1G01060_1 1321.261213
AT1G01060_3 84.4894909
AT1G01070_1 138.3040889
AT1G01070_2 77.66539382
AT1G01073_1 91.54441711
AT1G01080_1 1796.782417
AT1G01080_2 814.1777582
AT1G01090_1 13938.61891
AT1G01100_1 2237.853688
AT1G01100_2 3552.945886
AT1G01100_3 4105.379855
AT1G01110_1 482.9064758
AT1G01110_2 1112.739367

Total number of rows: 37118

Table truncated, full table size 865 Kbytes.




Supplementary file Size Download File type/resource
GSM738228.calls.gz 342.3 Kb (ftp)(http) CALLS
GSM738228.pair.gz 2.2 Mb (ftp)(http) PAIR
Processed data included within Sample table
Processed data provided as supplementary file

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