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Sample GSM1254791 Query DataSets for GSM1254791
Status Public on Aug 31, 2014
Title 35S-JMJ30-HA, rep2
Sample type RNA
Source name 35S::JMJ30-HA, 13 DAG
Organism Arabidopsis thaliana
Characteristics genetic background: Col-0
tissue: seedling
genotype: 35S::JMJ30-HA
phenotype: Late flowering
Treatment protocol No treatment applied.
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. 13 DAG seedlings were harvested.
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 35S::JMJ30-HA transgenic plants were used in this experiment. This is the second 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 Oct 19, 2016
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)
GSE51896 Gene expression analysis of 35S::JMJ30-HA overexpression transgenic lines grown at 22°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 28.5525
AT1G01020_1 5.5203
AT1G01020_2 4.9467
AT1G01030_1 48.4681
AT1G01040_1 130.785
AT1G01046_1 18.793
AT1G01050_1 220.738
AT1G01060_1 11.0664
AT1G01060_3 5.1229
AT1G01070_1 13.6924
AT1G01070_2 3.4893
AT1G01073_1 2.7631
AT1G01080_1 443.7677
AT1G01080_2 408.3498
AT1G01090_1 1031.6043
AT1G01100_1 377.46
AT1G01100_2 560.0982
AT1G01100_3 699.4061
AT1G01110_1 32.6378
AT1G01110_2 32.9751

Total number of rows: 37118

Table truncated, full table size 717 Kbytes.

Supplementary file Size Download File type/resource
GSM1254791_561301A12_130502_370_532.pair.gz 2.2 Mb (ftp)(http) PAIR
Processed data included within Sample table

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