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Sample GSM790057 Query DataSets for GSM790057
Status Public on Mar 01, 2012
Title NT_Root_rep2_1
Sample type RNA
 
Source name Nontransgenic plant (NT)_Root
Organism Oryza sativa
Characteristics cultivar: Nipponbare
genotype/variation: Nontransgenic
tissue source: 14d-old seedlings
phenotype: normal
Growth protocol Transgenic and non-transgenic (NT) rice (Oryza sativa cv Nipponbare) seeds were germinated in half-strength MS solid medium in a growth chamber in the dark at 28C for 4 d, transplanted into soil and then grown in a greenhouse (16-h-light/8-h-dark cycles) at 28-30C for two weeks.
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 by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
 
Hybridization protocol Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.
Scan protocol Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
Description NT_R_2
This sample is total RNAs of Nontransgenic plant Root
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 Sep 02, 2011
Last update date Mar 01, 2012
Contact name Jin Seo Jeong
E-mail(s) jsjeong74@gmail.com
Organization name Myongji University
Street address San 38-2 Namdong, Cheoin-gu
City Yongin
State/province Gyeonggido
ZIP/Postal code 449-728
Country South Korea
 
Platform ID GPL7344
Series (1)
GSE31855 Expression analysis of RCc3:OsNAC9 and GOS2:OsNAC9 transgenic rice plants

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

Data table
ID_REF VALUE
3tileprobe_249631 8642.92
3tileprobe_249632 22779.28
3tileprobe_249633 32414.92
3tileprobe_249634 30727.68
3tileprobe_249635 23527.42
3tileprobe_249636 12081.67
3tileprobe_249637 7647.89
3tileprobe_249638 2602.02
3tileprobe_249639 256.11
3tileprobe_249640 128.70
3tileprobe_113383 2113.57
3tileprobe_113384 2156.89
3tileprobe_113385 1571.59
3tileprobe_113386 1167.87
3tileprobe_113387 1422.91
3tileprobe_113388 1167.02
3tileprobe_113389 992.50
3tileprobe_113390 1416.83
3tileprobe_113391 1414.42
3tileprobe_113392 1670.00

Total number of rows: 389211

Table truncated, full table size 9204 Kbytes.




Supplementary file Size Download File type/resource
GSM790057_NT_R2.probe.gz 6.0 Mb (ftp)(http) PROBE
GSM790057_NT_R2_nm_RMA.pair.gz 6.3 Mb (ftp)(http) PAIR
Processed data included within Sample table
Processed data provided as supplementary file

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