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Sample GSM2436561 Query DataSets for GSM2436561
Status Public on Jan 31, 2018
Title 35S::SUP-GR Mock_rep2
Sample type RNA
 
Source name 35S::SUP-GR in Ler wild-type
Organism Arabidopsis thaliana
Characteristics genotype: 35S::SUP-GR in Ler wild-type
treatment: mock
phenotype: control
tissue: inflorescences with flower buds earlier than stage 10
Treatment protocol 10 µm dexamethasone diluted from a 30 mM stock in ethanol were used for the DEX treatment, while the Mock treatment was conducted with the same amount of ethanol, by inverting the plants and submerging the inflorescence for 1 min in solution containing either 10 µm DEX or ethanol, together with 0.015% Silwet L-77.
Growth protocol The seeds of the indicated genotype were planted on soil, and grown at 22°C under continuous light conditions. The inflorescence with flower buds earlier than stage 10 was sampled from Mock and DEX-treated plants.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen).
Label Cy3
Label protocol Labeling was performed following NimbleGen standard operating protocol. See www.nimblegen.com.
 
Hybridization protocol Hybridization was performed following NimbleGen standard operating protocol. See www.nimblegen.com.
Scan protocol Scanning was performed following NimbleGen standard operating protocol. See www.nimblegen.com.
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 Dec 22, 2016
Last update date Jan 31, 2018
Contact name Yifeng XU
E-mail(s) yifeng@tll.org.sg
Phone 68727742
Organization name Temasek Life Sciences Laboratory
Street address 1 Research Link
City Singapore
State/province -
ZIP/Postal code 117604
Country Singapore
 
Platform ID GPL13970
Series (1)
GSE92729 Gene expression analysis of the inflorescence of 35S::SUP-GR after Mock and DEX treatment

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

Data table
ID_REF VALUE
AT1G01020_2 9.224
AT1G01030_1 143.247
AT1G01040_1 975.126
AT1G01046_1 100.207
AT1G01050_1 652.968
AT1G01060_3 0.649
AT1G01100_3 1463.098
AT1G01120_1 836.467
AT1G01140_1 542.478
AT1G01170_2 536.224
AT1G01180_1 6.311
AT1G01183_1 1.678
AT1G01220_1 485.463
AT1G01300_1 1866.51
AT1G01370_1 363.595
AT1G01370_2 343.515
AT1G01400_1 281.659
AT1G01420_1 6.136
AT1G01440_1 319.38
AT1G01450_1 27.386

Total number of rows: 39640

Table truncated, full table size 734 Kbytes.




Supplementary file Size Download File type/resource
GSM2436561_561345A09_140403_450_532.pair.gz 2.2 Mb (ftp)(http) PAIR
Processed data included within Sample table

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