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Sample GSM1254792 Query DataSets for GSM1254792
Status Public on Aug 31, 2014
Title Col WT, rep1
Sample type RNA
Source name Col WT, 13 DAG, 29°C LD
Organism Arabidopsis thaliana
Characteristics genetic background: Col-0
tissue: seedling
genotype: wild-type
phenotype: High-temperature-induced early flowering
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
Hybridization protocol Hybridization was performed following NimbleGen standard operating protocol. See
Scan protocol Scanning was performed following NimbleGen standard operating protocol. See
Description Total RNA from wild-type 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
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
VALUE RMA-normalized, averaged gene-level signal intensity

Data table
AT1G01010_1 68.0969
AT1G01020_1 5.6569
AT1G01020_2 3.8879
AT1G01030_1 59.1525
AT1G01040_1 189.9773
AT1G01046_1 11.4131
AT1G01050_1 268.3888
AT1G01060_1 30.99
AT1G01060_3 4.4179
AT1G01070_1 32.069
AT1G01070_2 4.6893
AT1G01073_1 4.354
AT1G01080_1 963.39
AT1G01080_2 936.566
AT1G01090_1 1139.5087
AT1G01100_1 509.244
AT1G01100_2 617.8534
AT1G01100_3 750.4313
AT1G01110_1 42.3024
AT1G01110_2 49.2822

Total number of rows: 37118

Table truncated, full table size 720 Kbytes.

Supplementary file Size Download File type/resource
GSM1254792_561313A04_130627_400_532_532.pair.gz 2.1 Mb (ftp)(http) PAIR
Processed data included within Sample table

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