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| Status |
Public on Jan 09, 2013 |
| Title |
Sample 7 shoot mRNA LSS_1 As(III) 20 uM 6 h |
| Sample type |
SRA |
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| Source name |
shoot
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| Organism |
Oryza sativa Japonica Group |
| Characteristics |
strain: Nipponbare
tissue: shoot
treatment: As(III) 20 uM
time: 6 h
development stage: 14-day-old
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| Treatment protocol |
For As(III) treatments, 14-d-old rice seedlings were exposed to sodium arsenite (20 and 80 μm) at 9:00, and materials were harvested at 0, 6 and 24 h after treatment.
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| Growth protocol |
Seedlings were grown in 1/2 Hoagland nutrient solution at 28°C day/ 25°C night with a photoperiod of 16 h light (9:00-0:59) and 8 h night (1:00-8:59) in the green house.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using TRIzol reagent (Invitrogen) following the manufacturer’s instructions and was treated with RNase-free DNase I (New England Biolabs) to remove contaminated genomic DNA. mRNA was isolated from total RNA using Dynabeads oligo(dT) (Invitrogen). First- and second-strand cDNA were generated using Superscript II reverse transcriptase (Invitrogen) and random hexamer primers. Double-stranded cDNA was fragmented by nebulization and used for mRNA library construction according to the illuminaIllumina paired-end sample preparation protocol, using custom multiplex indexed Solexa adaptors and sequenced as 75 × 2 using the Illumina GA Genome Analyzer paired-end pipeline.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
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| Data processing |
RNA-Seq tag mapping to the rice reference genome Pair-end mRNA sequence tags were mapped to Nipponbare rice genome by BWA (Li & Durbin, 2009) with the default parameters. Read counts used in expression analyses were based on the subset of uniquely aligned reads that also overlapped the genomic spans of the TIGR6.1 gene model. Gene expression levels within a given sample were normalized using values for a gene's uniquely aligned read counts per kilobase of exon model per million reads (RPKM), uniquely aligning within each sample. Bioinformatics for gene functional annotation Z-score was determined based on the RPKM according to the following formula: Z = (X-μ)/σ, where X is the RPKM of a gene for a specific tissue / timepoint, and μ and σ are the mean transcript expression and standard deviation of a gene across all samples, respectively. All calculations and plots were performed in R language (Severin et al., 2010). DEGseq was used for the identification of differentially expressed genes (P < 0.001) (Wang et al., 2010). In addition, we have made a special effort to compare the GO terms of each gene were annotated based on the integrated information from TIGR6.1 and AgriGo database (Du et al., 2010). Pathway information for gene models was retrieved from Kyoto Encyclopedia of Genes and GenomesKEGG database (KEGG; http://www.genome.jp/kegg/) (Kanehisa & Goto, 2000). miRNA processing miRNA analysis was based on retrieved results from DSAP websites (Huang et al., 2010). Custom R scripts were used for clustering and graphical representation. Rice miRNA-targets pairs information of computational prediction and degradome-seq data was download from RMRD (Lindow et al., 2007; Zhang et al., 2010) and starBase (Yang et al., 2011). Taking into account the fact that miRNA may down-regulate the expressional level of its target mRNA (Rhoades et al., 2002), there should be a negative correlation between miRNA and target mRNA expression profiles. We computed the expressional correlation between the miRNAs and target mRNA (Wang & Li, 2009). The miRNA-mRNA pairs were considered to be biological relevance if Pearson correlation coefficients between them were in the range from -1 to -0.5.
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| Submission date |
Mar 21, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Lujun Yu |
| E-mail(s) |
[email protected]
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| Organization name |
Sun Yat-sen University
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| Lab |
415-114
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| Street address |
xingangxilu 135
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| City |
Guangzhou |
| State/province |
Guandong |
| ZIP/Postal code |
086 |
| Country |
China |
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| Platform ID |
GPL15370 |
| Series (1) |
| GSE36696 |
Comparative transcriptome analysis of transporters, phytohormone and lipid metabolism pathways in response to arsenic stress in rice (Oryza Sativa L.) |
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| Relations |
| SRA |
SRX130831 |
| BioSample |
SAMN00829556 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM898980_mRNA_LLS_RPKM.txt.gz |
192.0 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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