IC4R005-lncRNA-2016-19769571 - Revision history

Liman: /* Research Findings */

2016-07-17T05:22:57Z

‎Research Findings

2016-07-17T05:17:48Z

‎Research Findings

2016-07-17T05:16:01Z

‎Research Findings

2016-07-17T05:14:30Z

‎Research Findings

2016-07-17T05:12:02Z

‎Research Findings

2016-07-16T14:46:34Z

‎Research Findings

2016-07-16T14:38:58Z

‎Plant Culture & Treatment

2016-07-16T14:38:43Z

‎The Background of This Project

2016-07-16T14:37:36Z

‎Plant Culture & Treatment

2016-07-16T14:35:57Z

‎Illumina Sequencing

← Older revision		Revision as of 05:22, 17 July 2016
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	[[File:IC4R005-lncRNA-2016-19769571-t3.png \|center \|thumb \|800px \|'''Table 3. Drought-responsive novel long noncoding RNAs. Fold change is the ratio of expression level at 0–6 h''']]		[[File:IC4R005-lncRNA-2016-19769571-t3.png \|center \|thumb \|800px \|'''Table 3. Drought-responsive novel long noncoding RNAs. Fold change is the ratio of expression level at 0–6 h''']]
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		+	* As shown in Fig. 2, the novel miRNA and an existing miRNA, osa-miR169 g, are arranged in phase in a hairpin sequence. This result is consistent with the previous research in Arabidopsis where multiple small RNAs originated and are arranged in phase within a hairpin sequence. The expression level of os-miR9898 was down-regulated by 5.5-fold at 6 h compared to 0 h (Fig. 3). As a result, we selected one novel miRNA for validation via qRT-PCR (Fig. 2).
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		+	[[File:IC4R005-lncRNA-2016-19769571-f2.png \|center \|thumb \|800px \|'''Figure 2. Hairpin structure of novel un-annotated droughtresponsive miRNA hairpin structure. Color represents the folding intensity between match pairs''']]
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		+	[[File:IC4R005-lncRNA-2016-19769571-f3.png \|center \|thumb \|800px \|'''Figure 3. Novel miRNA transcript qRT-PCR.''']]

	==Labs working on this Project==		==Labs working on this Project==

← Older revision		Revision as of 05:17, 17 July 2016
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	[[File:IC4R005-lncRNA-2016-19769571-t2.png \|center \|thumb \|800px \|'''Table 2. Novel/function-unknown drought-stress responsive coding transcripts.''']]		[[File:IC4R005-lncRNA-2016-19769571-t2.png \|center \|thumb \|800px \|'''Table 2. Novel/function-unknown drought-stress responsive coding transcripts.''']]
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		+	* The researchers selected 10 novel lncRNAs for validation via qRT-PCR (Table 3).
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		+	[[File:IC4R005-lncRNA-2016-19769571-t3.png \|center \|thumb \|800px \|'''Table 3. Drought-responsive novel long noncoding RNAs. Fold change is the ratio of expression level at 0–6 h''']]

	==Labs working on this Project==		==Labs working on this Project==

← Older revision		Revision as of 05:16, 17 July 2016
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	[[File:IC4R005-lncRNA-2016-19769571-t1.png \|center \|thumb \|800px \|'''Table 1. Enriched functions of activated and suppressed DEGs under drought-stress''']]		[[File:IC4R005-lncRNA-2016-19769571-t1.png \|center \|thumb \|800px \|'''Table 1. Enriched functions of activated and suppressed DEGs under drought-stress''']]
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		+	* After filtering out TFs previously reported in drought-stress studies, we selected 68 TFs as candidates with unknown functions for further study. We performed qRT-PCR on the 68 TFs and validated 18 of them (Table 2). The expression level of all 18 coding TFs was increased after 1 and 6 h drought treatment compared to 0 h control.
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		+	[[File:IC4R005-lncRNA-2016-19769571-t2.png \|center \|thumb \|800px \|'''Table 2. Novel/function-unknown drought-stress responsive coding transcripts.''']]

	==Labs working on this Project==		==Labs working on this Project==

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 * A total of 1080 and 4017 DEGs were found at 0–1 h and 0–6 h data points, respectively. Histograms and volcano plots of expression fold changes are shown in Fig. 1. The DEG analysis showed that the number of DEG increased as drought-stress continued. This observation showed that when the plant was exposed to a longer period of drought-stress, transcriptional changes were bigger for the experiment.
 * Among the 4017 DEGs from the 0-to-6 h data set, 1472 genes were activated and 2545 genes were suppressed. We investigated the known functions of the activated/suppressed differentially expressed genes under drought-stress by Gene Ontology (GO) enrichment analysis. The result is shown in Table 1.
 ==Labs working on this Project==

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 ==Research Findings==
-* The researchers identified 18 TFs, ten lncRNAs and one miRNA as being novel drought-responsive regulatory transcripts.
+* A total of 1080 and 4017 DEGs were found at 0–1 h and 0–6 h data points, respectively. Histograms and volcano plots of expression fold changes are shown in Fig. 1. The DEG analysis showed that the number of DEG increased as drought-stress continued. This observation showed that when the plant was exposed to a longer period of drought-stress, transcriptional changes were bigger for the experiment.
 ==Labs working on this Project==

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 ==Plant Culture & Treatment==
-* Rice plants, O.sativa L. Nipponbare, were acquired from the Rural Development Administration of Korea (RDA). The rice plants were cultured in Yoshida solution at pH 5.8 and maintained in a temperaturecontrolled culture room at 29 �C under 16 h/8 h light/dark conditions. Rice plants at the three-leaf stage were subjected to drought-stress for 1 and 6 h by removal of the culture solution. Untreated plants were used as control. After treatment, entire plants were immediately transferred into liquid nitrogen.
+* Rice plants, O.sativa L. Nipponbare, were acquired from the Rural Development Administration of Korea (RDA). The rice plants were cultured in Yoshida solution at pH 5.8 and maintained in a temperaturecontrolled culture room at 29 ℃ under 16 h/8 h light/dark conditions. Rice plants at the three-leaf stage were subjected to drought-stress for 1 and 6 h by removal of the culture solution. Untreated plants were used as control. After treatment, entire plants were immediately transferred into liquid nitrogen.
 ==Research Findings==

← Older revision		Revision as of 14:38, 16 July 2016
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	==The Background of This Project==		==The Background of This Project==
		+	* Drought-stress can cause major economic loss and is a serious issue to address in agriculture. Defining the molecular pathways in how a plant responds to droughtstress may prove valuable in developing new drought-resistant plants. In this study, the researchers identified several novel drought-responsive regulatory coding and noncoding transcripts in rice, Oryza sativa L., using the next generation sequencing (NGS) technique and bioinformatics analyses.

	==Plant Culture & Treatment==		==Plant Culture & Treatment==

← Older revision		Revision as of 14:37, 16 July 2016
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	==Plant Culture & Treatment==		==Plant Culture & Treatment==
		+	* Rice plants, O.sativa L. Nipponbare, were acquired from the Rural Development Administration of Korea (RDA). The rice plants were cultured in Yoshida solution at pH 5.8 and maintained in a temperaturecontrolled culture room at 29 �C under 16 h/8 h light/dark conditions. Rice plants at the three-leaf stage were subjected to drought-stress for 1 and 6 h by removal of the culture solution. Untreated plants were used as control. After treatment, entire plants were immediately transferred into liquid nitrogen.

	==Research Findings==		==Research Findings==