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Sample GSM1542248 Query DataSets for GSM1542248
Status Public on Nov 11, 2014
Title Rice seedlings roots_V Replicate 1
Sample type RNA
 
Channel 1
Source name Roots of rice seedlings were exposed to 1 mM V
Organism Oryza sativa
Characteristics cultivar: TN-67
age: 6 day
treatment: exposed to 1 mM V
Treatment protocol Six-dayold rice samples (100 mg) treated with 1 mM V for 1 and 3 h were harvested for total RNA extraction.
Growth protocol Seeds of rice (O. sativa L. cv. TN67) were surface-disinfected with 2.5% (v/v) sodium hypochlorite (Katayama, Japan) for 15 min, then thoroughly washed in distilled water, and placed in 9-cm Petri dishes containing 25 ml distilled water at 37 ℃ in darkness for 3 days. Then, uniformly germinated seeds were selected and placed on filter paper discs (Advantec No.1) moistened with 10 ml distilled water in Petri dishes. Each Petri dish contained 15 germinated seeds that were grown for 3 days at 26 ℃ in darkness.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from each plant sample using RNeasy Plant Mini kit (QIAGEN, Hilden, Germany) with some modification [40]. The concentrations of total RNA samples were measured by the use of NanodropND 2000 (Nanodrop Technologies, Wilmington, DE, USA). RNA samples >2 g/ l with high purity (OD260/280 > 2, OD260/230 > 2) underwent microarray analysis and semi-quantitative RT-PCR.
Label Cy5
Label protocol Microarray RNA pool was prepared by combining a fixed volume of rice root samples collected at the following time points: 1 and 3 h. Briefly, 0.5 mg total RNAwas amplified by use of a Fluorescent Linear Amplification Kit (Agilent Technologies, USA) and labeled with Cy3-CTP (control samples) or Cy5-CTP (V-treatment) (CyDye, PerkinElmer, USA) during in vitro transcription. RNA was labeled with Cy3 or Cy5.
 
Channel 2
Source name Rice seedlings roots were exposed to water
Organism Oryza sativa
Characteristics cultivar: TN-67
treatment: exposed to water
Treatment protocol Six-dayold rice samples (100 mg) treated with 1 mM V for 1 and 3 h were harvested for total RNA extraction.
Growth protocol Seeds of rice (O. sativa L. cv. TN67) were surface-disinfected with 2.5% (v/v) sodium hypochlorite (Katayama, Japan) for 15 min, then thoroughly washed in distilled water, and placed in 9-cm Petri dishes containing 25 ml distilled water at 37 ℃ in darkness for 3 days. Then, uniformly germinated seeds were selected and placed on filter paper discs (Advantec No.1) moistened with 10 ml distilled water in Petri dishes. Each Petri dish contained 15 germinated seeds that were grown for 3 days at 26 ℃ in darkness.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from each plant sample using RNeasy Plant Mini kit (QIAGEN, Hilden, Germany) with some modification [40]. The concentrations of total RNA samples were measured by the use of NanodropND 2000 (Nanodrop Technologies, Wilmington, DE, USA). RNA samples >2 g/ l with high purity (OD260/280 > 2, OD260/230 > 2) underwent microarray analysis and semi-quantitative RT-PCR.
Label Cy3
Label protocol Microarray RNA pool was prepared by combining a fixed volume of rice root samples collected at the following time points: 1 and 3 h. Briefly, 0.5 mg total RNAwas amplified by use of a Fluorescent Linear Amplification Kit (Agilent Technologies, USA) and labeled with Cy3-CTP (control samples) or Cy5-CTP (V-treatment) (CyDye, PerkinElmer, USA) during in vitro transcription. RNA was labeled with Cy3 or Cy5.
 
 
Hybridization protocol The fragmented labeled cRNA was then pooled and hybridized to the Rice Oligo DNA Microarray 44K RAP-DB (G2519F#15241; Agilent Technologies) at 60 C for 17 h.
Scan protocol After washing and drying by nitrogen gun blowing, microarrays are scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3 and 625 nm for Cy5. Scanned images are analyzed by Feature extraction software 9.5.3 (Agilent Technologies, USA),
Description Biological replicate 1 of 3. Rice seedling roots with or without 1 mM-treated V
Data processing An image analysis and normalization software is used to quantify signal and background intensity for each feature, substantially normalized the data by rank-consistency-filtering LOWESS method.
 
Submission date Nov 10, 2014
Last update date Nov 11, 2014
Contact name Hao-Jen Huang
E-mail(s) haojen@mail.ncku.edu.tw
Organization name National Cheng Kung University
Department Life Sciences
Lab Prof. Huang Hao-Jen
Street address No.1, University Raod,
City Tainan
ZIP/Postal code 701
Country Taiwan
 
Platform ID GPL8852
Series (1)
GSE63152 Transcriptome response to vanadium stress in rice roots

Data table header descriptions
ID_REF
VALUE Normalized log2 ratio (Cy5/Cy3) representing test/reference

Data table
ID_REF VALUE
Os01g0100100|COMBINER_EST|CI448596|0 -0.40193033
Os01g0100200|mRNA|AK059894|CDS+3'UTR 0.5608191
Os01g0100400|mRNA|AK101455|CDS+3'UTR -0.5988012
Os01g0100500|mRNA|AK067316|CDS+3'UTR -0.4788495
Os01g0100600|mRNA|AK121362|CDS+3'UTR -0.17359446
Os01g0100700|mRNA|AK059844|CDS+3'UTR -0.23694046
Os01g0100700|mRNA|AK121523|CDS+3'UTR -0.184454
Os01g0100800|mRNA|AK122012|CDS+3'UTR -0.44787893
Os01g0100900|COMBINER_EST|CI015509|0 -0.10179619
Os01g0101200|mRNA|AK067866|CDS+3'UTR -0.40258798
Os01g0101200|mRNA|AK104517|CDS+3'UTR -1.2700148
Os01g0101200|mRNA|AK104625|CDS+3'UTR -0.84522384
Os01g0101200|mRNA|AK104752|CDS+3'UTR -1.1182128
Os01g0101200|mRNA|AK119457|CDS+3'UTR -0.43518263
Os01g0101300|COMBINER_EST|CI016681|6 -0.37424
Os01g0101600|mRNA|AK099952|CDS+3'UTR -0.00421948
Os01g0101600|mRNA|AK103820|CDS+3'UTR -1.0828773
Os01g0101600|mRNA|AK122118|CDS+3'UTR -1.1953588
Os01g0101700|COMBINER_EST|CI525185|3 -0.25035137
Os01g0101800|mRNA|AK103498|CDS+3'UTR -1.085371

Total number of rows: 42474

Table truncated, full table size 1983 Kbytes.




Supplementary file Size Download File type/resource
GSM1542248_US93703722_251524112860_A1_vs_A2.txt.gz 4.6 Mb (ftp)(http) TXT
Processed data included within Sample table

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