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Sample GSM790059 Query DataSets for GSM790059
Status Public on Mar 01, 2012
Title RCc3_NAC1_Root_rep_2
Sample type RNA
 
Source name RCc3OsNAC1 plant_Root
Organism Oryza sativa
Characteristics cultivar: Nipponbare
genotype/variation: RCc3:OsNAC1 Transgenic
tissue source: 14d-old seedlings
phenotype: normal
accession: AK067690
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 R_NAC1_R_2
This sample is total RNAs of RCc3:OsNAC1 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 10890.00
3tileprobe_249632 26319.14
3tileprobe_249633 33487.35
3tileprobe_249634 33253.59
3tileprobe_249635 28594.83
3tileprobe_249636 16910.83
3tileprobe_249637 13582.92
3tileprobe_249638 4739.04
3tileprobe_249639 258.20
3tileprobe_249640 126.68
3tileprobe_113383 2174.46
3tileprobe_113384 1695.93
3tileprobe_113385 1110.38
3tileprobe_113386 662.09
3tileprobe_113387 977.68
3tileprobe_113388 769.27
3tileprobe_113389 748.89
3tileprobe_113390 781.61
3tileprobe_113391 953.83
3tileprobe_113392 1146.02

Total number of rows: 389211

Table truncated, full table size 9204 Kbytes.




Supplementary file Size Download File type/resource
GSM790059_R_NAC1_R2.probe.gz 5.9 Mb (ftp)(http) PROBE
GSM790059_R_NAC1_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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