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Sample GSM1254794 Query DataSets for GSM1254794
Status Public on Aug 31, 2014
Title jmj30 jmj32, rep1
Sample type RNA
 
Source name jmj30 jmj32, 13 DAG, 29°C LD
Organism Arabidopsis thaliana
Characteristics genetic background: Col-0
tissue: seedling
genotype: jmj30-2 jmj32-1
phenotype: Flowered earlier than WT grown at similar condition
Treatment protocol Plants were shift to elevated temperature conditions (29°C, LD) at 3 DAG. Samples were harvested at 13 DAG.
Growth protocol The seeds of the indicated genotype were planted on soil, and grown at 22°C under long day (LD, 16 hour light, 8 hour dark) conditions until treatment.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and DNA was removed by on-column DNaseI 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.
Description Total RNA from jmj30 jmj32 plants were used in this experiment. This is the first sample of the two biological replicates.
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 Oct 30, 2013
Last update date Aug 31, 2014
Contact name Toshiro Ito
E-mail(s) itot@tll.org.sg
Organization name Temasek Life Sciences Laboratory
Lab Plant Systems Biology
Street address 1 Research Link, National University of Singapore
City Singapore
ZIP/Postal code 117604
Country Singapore
 
Platform ID GPL13970
Series (2)
GSE51897 Gene expression analysis of jmj30 jmj32 mutant grown at 29°C under long day conditions
GSE51898 Gene expression analysis of overexpression and loss-of-function at JUMONJI30

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

Data table
ID_REF VALUE
AT1G01010_1 53.7157
AT1G01020_1 4.4454
AT1G01020_2 6.6964
AT1G01030_1 27.9074
AT1G01040_1 155.2948
AT1G01046_1 12.8787
AT1G01050_1 320.5093
AT1G01060_1 23.1187
AT1G01060_3 3.3985
AT1G01070_1 25.5721
AT1G01070_2 3.4477
AT1G01073_1 3.1568
AT1G01080_1 772.3867
AT1G01080_2 627.884
AT1G01090_1 1596.7577
AT1G01100_1 622.1437
AT1G01100_2 747.8229
AT1G01100_3 945.7116
AT1G01110_1 35.365
AT1G01110_2 35.6773

Total number of rows: 37118

Table truncated, full table size 720 Kbytes.




Supplementary file Size Download File type/resource
GSM1254794_561313A09_130627_400_532_532.pair.gz 2.1 Mb (ftp)(http) PAIR
Processed data included within Sample table

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