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Sample GSM790065 Query DataSets for GSM790065
Status Public on Mar 01, 2012
Title RCc3_NAC5_Root_rep_2
Sample type RNA
 
Source name RCc3OsNAC5 plant_Root
Organism Oryza sativa
Characteristics cultivar: Nipponbare
genotype/variation: RCc3:OsNAC5 Transgenic
tissue source: 14d-old seedlings
phenotype: normal
accession: AK102475
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 (16h-light/8h-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_NAC5_R_2
This sample is total RNAs of RCc3:OsNAC5 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)
GSE31856 Expression analysis of RCc3:OsNAC5 and GOS2:OsNAC5 transgenic rice plants

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

Data table
ID_REF VALUE
3tileprobe_249631 17493.54
3tileprobe_249632 32181.86
3tileprobe_249633 34465.01
3tileprobe_249634 44028.12
3tileprobe_249635 37057.41
3tileprobe_249636 25847.19
3tileprobe_249637 20938.06
3tileprobe_249638 8086.60
3tileprobe_249639 581.53
3tileprobe_249640 516.02
3tileprobe_113383 4847.10
3tileprobe_113384 4567.92
3tileprobe_113385 3625.06
3tileprobe_113386 2419.21
3tileprobe_113387 3208.49
3tileprobe_113388 2662.69
3tileprobe_113389 2734.68
3tileprobe_113390 2880.99
3tileprobe_113391 2490.60
3tileprobe_113392 3181.27

Total number of rows: 389211

Table truncated, full table size 9247 Kbytes.




Supplementary file Size Download File type/resource
GSM790065_R_NAC5_R2.probe.gz 5.9 Mb (ftp)(http) PROBE
GSM790065_R_NAC5_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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