IC4R007-lncRNA-2015-26437919 - Revision history

Guangyi: /* Research Findings */

2016-07-15T14:42:52Z

‎Research Findings

Guangyi: /* Research Findings */

2016-07-15T14:37:29Z

‎Research Findings

Guangyi: /* Research Findings */

2016-07-15T14:37:03Z

‎Research Findings

Guangyi: /* Research Findings */

2016-07-15T14:36:23Z

‎Research Findings

Guangyi: /* Research Findings */

2016-07-15T14:25:48Z

‎Research Findings

Guangyi: /* Research Findings */

2016-07-15T14:19:38Z

‎Research Findings

Guangyi: /* Research Findings */

2016-07-15T14:17:00Z

‎Research Findings

Guangyi: /* Plant Culture & Treatment */

2016-07-15T14:13:20Z

‎Plant Culture & Treatment

Guangyi: /* Plant Culture & Treatment */

2016-07-15T14:10:13Z

‎Plant Culture & Treatment

Guangyi: /* Corresponding Author */

2016-07-15T14:08:38Z

‎Corresponding Author

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 *To confirm the reliability of the identified lncRNA genes,the researchers selected 20 lncRNAs for RT-PCR validation. seventeen lncRNAs were successfully amplified (Additional file 3:Figure S2), suggesting that a high percentage of lncRNAs detected by this pipeline were reliable in terms of expression. The transcription orientation of these 17 lncRNAs were determined by strand-specific RT-PCR. Sixteen out of them were successfully amplified. The results demonstrated that four lncRNAs were transcribed from the sense strand whereas 12 lncRNAs from the antisense strand (Fig. 2).
 <br>
-[[File:IC4R007-lncRNA-2015-26437919-fs2.png |center |thumb |10000px |'''''']]
+[[File:IC4R007-lncRNA-2015-26437919-fs2.png |center |thumb |10000px |''''''Fig. S2 RT-PCR validation of 20 randomly selected lncRNAs. Seventeen lncRNAs were successfully amplified and confirmed by sequencing. The PCR product in lane 15, BPHLNC-unc536, was not correctly amplified. Two lncRNAs, BPHLNC-unc525 and BPHLINC406, were not amplified and were not shown in the figure. Lane 1–18: BPHOGS10028742-AS-RA, BPHLINC074-RA, BPHOGS10028378-AS-RA, BPHOGS10006054-OT-RA, BPHLINC250-RA, BPHOGS10022296-OT-RA, BPHLNC-unc280-RA, BPHLINC164-RA, BPHOGS10026274-IT-RA, BPHOGS10006052-AS-RA, BPHOGS10017161-OT-RA, BPHOGS10027736-OT-RB, BPHOGS10003291-OT-RA, BPHLNC-unc005-RA, BPHLNC-unc536-RA, BPHOGS10000919-OT-RA, BPHOGS10035448-AS-RA, BPHOGS10030139-OT-RA, respectively. (TIFF 4040 kb)'''''']]
 <br>
 [[File:IC4R007-lncRNA-2015-26437919-f2a.png |center |thumb |10000px ]]
-[[File:IC4R007-lncRNA-2015-26437919-f2b.png |center |thumb |10000px |'''''']]
+[[File:IC4R007-lncRNA-2015-26437919-f2b.png |center |thumb |10000px |''''''Fig. 2 Strand-specific PCR of 17 randomly selected lncRNAs to determine the transcription orientation. BPHOGS10035448-AS-RA was not amplified with a correct band. So, 16 lncRNAs were successfully amplified and confirmed by sequencing (see Figure S2 for RT-PCR validation). The results indicated that 12 lncRNA transcribed from the antisense strand, and four from the sense strand. F: forward primer (sense); R: reverse primer (antisense); RT:reverse transcriptase'''''']]
 ==Labs working on this Project==

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 [[File:IC4R007-lncRNA-2015-26437919-t1.png |center |thumb |10000px ]]
 <br>
-*To confirm the reliability of the identified lncRNA genes,the researchers selected 20 lncRNAs for RT-PCR validation. seventeen lncRNAs were successfully amplified (Additional file 3:Figure S2), suggesting that a high percentage of lncRNAs detected by this pipeline were reliable in terms of expression. The transcription orientation of these 17 lncRNAs were determined by strand-specific
+*To confirm the reliability of the identified lncRNA genes,the researchers selected 20 lncRNAs for RT-PCR validation. seventeen lncRNAs were successfully amplified (Additional file 3:Figure S2), suggesting that a high percentage of lncRNAs detected by this pipeline were reliable in terms of expression. The transcription orientation of these 17 lncRNAs were determined by strand-specific RT-PCR. Sixteen out of them were successfully amplified. The results demonstrated that four lncRNAs were transcribed from the sense strand whereas 12 lncRNAs from the antisense strand (Fig. 2).
 <br>
 [[File:IC4R007-lncRNA-2015-26437919-fs2.png |center |thumb |10000px |'''''']]

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 *The individual datasets were analyzed separately using the computational pipeline. In total, 948 and 1562 lncRNA genes were found in the 2-day-old adults of the LFP and HFP populations, respectively, whereas 1324 and 1563 lncRNAs were identified in the fifth instar larvae of the LFP and HFP populations. A higher number of lncRNAs(1798–2081) were discovered in the fat body, salivary gland,and antennae of the virulence-associated Mudgo and TN1 populations. 1618, 1806, and 1721 lncRNAs were found in the wild, I87i, and C89i populations, respectively (Table 1).
 <br>
-[[File:IC4R007-lncRNA-2015-26437919t1.png |center |thumb |10000px ]]
+[[File:IC4R007-lncRNA-2015-26437919-t1.png |center |thumb |10000px ]]
 <br>
-*To confirm the reliability of the identified lncRNA genes,the researchers selected 20 lncRNAs for RT-PCR validation. seventeen
+*To confirm the reliability of the identified lncRNA genes,the researchers selected 20 lncRNAs for RT-PCR validation. seventeen lncRNAs were successfully amplified (Additional file 3:Figure S2), suggesting that a high percentage of lncRNAs detected by this pipeline were reliable in terms of expression. The transcription orientation of these 17 lncRNAs were determined by strand-specific
 RT-PCR. Sixteen out of them were successfully amplified. The results demonstrated that four lncRNAs were transcribed from the sense strand whereas 12 lncRNAs from the antisense strand (Fig. 2).
 <br>
 [[File:IC4R007-lncRNA-2015-26437919-fs2.png |center |thumb |10000px |'''''']]
 <br>
-[[[File:IC4R007-lncRNA-2015-26437919-f2a.png |center |thumb |10000px ]]
+[[File:IC4R007-lncRNA-2015-26437919-f2a.png |center |thumb |10000px ]]
 [[File:IC4R007-lncRNA-2015-26437919-f2b.png |center |thumb |10000px |'''''']]

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 [[File:IC4R007-lncRNA-2015-26437919-fs2.png |center |thumb |10000px |'''''']]
 <br>
-[[File:IC4R007-lncRNA-2015-26437919-f2.png |center |thumb |10000px |'''''']]
+[[[File:IC4R007-lncRNA-2015-26437919-f2a.png |center |thumb |10000px ]]
 ==Labs working on this Project==

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 [[File:IC4R007-lncRNA-2015-26437919t1.png |center |thumb |10000px ]]
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 ==Labs working on this Project==

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 <br>
 [[File:IC4R007-lncRNA-2015-26437919-f1.png |center |thumb |10000px |''''''Fig. 1 The computational pipeline for identifying lncRNA genes in N. lugens from RNA-seq data.'''''']]
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← Older revision		Revision as of 14:17, 15 July 2016
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	==Research Findings==		==Research Findings==
		+	*A computational pipeline was developed to identify lncRNA genes from the N. lugens transcriptome (Fig. 1).This pipeline was applied on 12 different N. lugens transcriptome datasets and yielded 2439 transcript isoforms corresponding to 1882 loci from 12 N. lugens RNA-seq datasets.
		+	<br>
		+	[[File:IC4R007-lncRNA-2015-26437919-f1.png \|center \|thumb \|10000px \|''''''Fig. 1 The computational pipeline for identifying lncRNA genes in N. lugens from RNA-seq data.'''''']]
		+	<br>

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

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 ==Plant Culture & Treatment==
-*A computational pipeline was developed to identify lncRNA genes in the rice brown planthopper,Nilaparvata lugens, a destructive rice pest causing huge yield losses. Strand specific RT-PCR were used to determine the transcription orientation of lncRNAs.
+*The rice brown planthoppers were collected from rice fields in Nanjing area, Jiangsu Province, China and maintained on rice seedlings at 27 ± 1 °C, under a 16-h light/8-h dark photoperiod and 70–80 % relative humidity. The insects were transferred to fresh seedlings every 5–7 days to ensure sufficient nutrition.
 <br>

← Older revision		Revision as of 14:10, 15 July 2016
Line 7:		Line 7:

	==Plant Culture & Treatment==		==Plant Culture & Treatment==
		+	*A computational pipeline was developed to identify lncRNA genes in the rice brown planthopper,Nilaparvata lugens, a destructive rice pest causing huge yield losses. Strand specific RT-PCR were used to determine the transcription orientation of lncRNAs.
		+	<br>

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

← Older revision		Revision as of 14:08, 15 July 2016
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	==Corresponding Author==		==Corresponding Author==
		+	*lifei18@zju.edu.cn
		+	<br>