IC4R013-RNA-Seq-2012-22537016 - Revision history

Liman: /* Research Findings */

2016-07-13T09:14:27Z

‎Research Findings

Liman: /* Research Findings */

2016-07-13T09:12:35Z

‎Research Findings

Liman: /* Research Findings */

2016-07-13T07:55:02Z

‎Research Findings

Liman: /* Research Findings */

2016-07-13T07:54:11Z

‎Research Findings

Liman: /* Research Findings */

2016-07-13T07:29:01Z

‎Research Findings

Liman: /* Research Findings */

2016-07-13T07:24:32Z

‎Research Findings

Liman: /* Research Findings */

2016-07-13T07:23:38Z

‎Research Findings

Liman: /* Research Findings */

2016-07-13T07:14:09Z

‎Research Findings

Liman: /* Illumina Sequencing */

2016-07-13T06:40:40Z

‎Illumina Sequencing

Liman: /* Illumina Sequencing */

2016-07-13T06:40:21Z

‎Illumina Sequencing

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 [[File:IC4R013-RNA-Seq-2012-22537016-f3.png |center |thumb |800px |'''Figure 3. Differential expression of rice microRNAs (miRNAs) and their target mRNAs under As(III) stress.''']]
-* In the mRNA-seq data, 1477 (60.9%) TF genes were detected and 468 (19.3%) TFs were differentially expressed. Consistent with the
+* In the mRNA-seq data, 1477 (60.9%) TF genes were detected and 468 (19.3%) TFs were differentially expressed. Consistent with the whole genome gene expression patterns, HSR and HLS expressed the lowest number of TF genes (1005 and 955), but with the highest super-high expression gene numbers (65 and 44). Of the 468 (42 subfamilies) differentially expressed TFs, 230 (36 subfamilies) were in the roots, 103 (31 subfamilies) were in the shoots and 135 (22 subfamilies) were in both the roots and shoots.Clustering analyses were performed to further explore the relationship between the As(III)-responsive TFs and DEGs. Results showed that the differentially expressed TF genes were grouped into two clusters, and that four groups were well correlated with the same topology of DEGs. Therefore, the dynamics of accumulation of TFs after As(III) stress were particularly well resolved in the mRNA-seq data, and specific subfamilies of TFs were preferentially expressed after As(III) treatment.
 ==Labs working on this Project==

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 [[File:IC4R013-RNA-Seq-2012-22537016-f2.png |center |thumb |800px |'''Figure 2. Expression profile of transporter genes under As(III) stress.''']]
+* From the KEGG, the researchers observed that 3628 As(III)-responsive genes could be annotated to 228 pathways. Among them, phytohormone (specifically JA) and lipid metabolism pathways were two of the most significant pathways identified.
+* From the sequencing data, the researchers identified 97–146 miRNAs belonging to 41–50 miRNA families as predicted by the miRBase database. The miRNA data were further analyzed to identify As(III)-responsive miRNAs. In general, the expression of 36 miRNAs showed significant alterations in response to As(III) treatments. Twenty-five miRNAs (22 families) were observed in the roots (Fig. 3a), whereas 30 miRNAs (23 families) were observed in the shoots (Fig. 3c). Using the computational prediction and degradome-Seq data, the researchers further computed the expression correlation between the miRNAs and their predicted mRNA targets. Among the 2467 candidate miRNA–mRNA pairs identified, only 237 and 128 pairs in the roots and shoots, respectively, were found to be biologically relevant. In particular, the correlation coefficients of two transporter–miRNA pairs, two lipid–miRNA pairs and three JA–miRNA pairs in the roots (Fig. 3b), and five transporter– miRNA pairs, one lipid–miRNA pair and one JA–miRNA pair in the shoots (Fig. 3d) ranged from -1 to -0.5.
+[[File:IC4R013-RNA-Seq-2012-22537016-f3.png |center |thumb |800px |'''Figure 3. Differential expression of rice microRNAs (miRNAs) and their target mRNAs under As(III) stress.''']]
 ==Labs working on this Project==

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 [[File:IC4R013-RNA-Seq-2012-22537016-f1.png |center |thumb |800px |'''Figure 1. Global patterns of differentially expressed genes (DEGs) under As(III) stress.''']]
-* To elucidate the molecular mechanisms of As(III) uptake and transportation in rice, we analyzed the expression profiles of rice genes encoding various types of transporter (Fig. 2a). The hierarchical clustering showed that 273 out of 473 transporter genes were regulated upon As(III) treatment in either roots or shoots (Fig. 2b). In general, 106 As(III)-responsive transporter DEGs were deemed to be significantly different after As(III) treatments, including 62 DEGs in the roots, 21 in the shoots and 23 in both roots and shoots (Fig. 2c,d).
+* To elucidate the molecular mechanisms of As(III) uptake and transportation in rice, the researchers analyzed the expression profiles of rice genes encoding various types of transporter (Fig. 2a). The hierarchical clustering showed that 273 out of 473 transporter genes were regulated upon As(III) treatment in either roots or shoots (Fig. 2b). In general, 106 As(III)-responsive transporter DEGs were deemed to be significantly different after As(III) treatments, including 62 DEGs in the roots, 21 in the shoots and 23 in both roots and shoots (Fig. 2c,d).
 [[File:IC4R013-RNA-Seq-2012-22537016-f2.png |center |thumb |800px |'''Figure 2. Expression profile of transporter genes under As(III) stress.''']]

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 * After comparisons between untreated and As(III)-treated samples, two main groups with four clusters of samples were identified by their transcriptome similarity, indicating that the transcriptomes of different treatments within shoots or roots were clustered together (Fig. 1a). The effect of dosage on the root samples was more significant than that of time, whereas the situation was reversed for the shoots, which was further confirmed by the principal component analysis (PCA) analysis (Fig. 1b).
-[[File:IC4R013-RNA-Seq-2012-22537016-f1.png |center |thumb |800px |'''Figure 1 Global patterns of differentially expressed genes (DEGs) under As(III) stress.''']]
+[[File:IC4R013-RNA-Seq-2012-22537016-f1.png |center |thumb |800px |'''Figure 1. Global patterns of differentially expressed genes (DEGs) under As(III) stress.''']]
-* To elucidate the molecular mechanisms of As(III) uptake and transportation in rice, we analyzed the expression profiles of rice genes encoding various types of transporter (Fig. 2a).
+* To elucidate the molecular mechanisms of As(III) uptake and transportation in rice, we analyzed the expression profiles of rice genes encoding various types of transporter (Fig. 2a). The hierarchical clustering showed that 273 out of 473 transporter genes were regulated upon As(III) treatment in either roots or shoots (Fig. 2b). In general, 106 As(III)-responsive transporter DEGs were deemed to be significantly different after As(III) treatments, including 62 DEGs in the roots, 21 in the shoots and 23 in both roots and shoots (Fig. 2c,d).
+*

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 ==Research Findings==
-* After comparisons between untreated and As(III)-treated samples, two main groups with four clusters of samples were identified by their transcriptome similarity, indicating that the transcriptomes of different treatments within shoots or roots were clustered together (Fig. 1a and Table S3). The effect of dosage on the root samples was more significant than that of time, whereas the situation was reversed for the shoots, which was further confirmed by the principal component analysis (PCA) analysis (Fig. 1b).
+* After comparisons between untreated and As(III)-treated samples, two main groups with four clusters of samples were identified by their transcriptome similarity, indicating that the transcriptomes of different treatments within shoots or roots were clustered together (Fig. 1a). The effect of dosage on the root samples was more significant than that of time, whereas the situation was reversed for the shoots, which was further confirmed by the principal component analysis (PCA) analysis (Fig. 1b).
 [[File:IC4R013-RNA-Seq-2012-22537016-f1.png |center |thumb |800px |'''Figure 1 Global patterns of differentially expressed genes (DEGs) under As(III) stress.''']]
+* To elucidate the molecular mechanisms of As(III) uptake and transportation in rice, we analyzed the expression profiles of rice genes encoding various types of transporter (Fig. 2a).
+*

← Older revision		Revision as of 07:14, 13 July 2016
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	==Research Findings==		==Research Findings==
		+	* Using Illumina high-throughput sequencing, 3.4–9.2 million 75 bp paired-endmRNA reads were generated in the analyzed samples, and 1.01–2.54 million unique-type reads were mapped uniquely to the rice genomic location, with 67.1–86.0% of the mapped reads located in the annotated genic regions . The expression of 31 441 (54.6%) genes was detected in at least one sample, and 13 893 (24.1%) and 3665 (6.4%) genes were detected in all samples and one of the samples, respectively (Fig. S3b), indicating that the expressed genes were comparable among samples.
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		+	[[File:.png \|center \|thumb \|800px \|'''Figure 1 Accumulation of 36-bp reads to cover whole transcripts.''']]
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	==Labs working on this Project==		==Labs working on this Project==

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 ==Illumina Sequencing==
-* Total RNA was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer’s instructions and was treated with RNase-free DNase I (New England Biolabs, Inc. Ipswich, MA, USA) to remove contaminated genomic DNA. mRNA was isolated from total RNA using Dynabeads oligo(
+* Total RNA was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer’s instructions and was treated with RNase-free DNase I (New England Biolabs, Inc. Ipswich, MA, USA) to remove contaminated genomic DNA. mRNA was isolated from total RNA using Dynabeads oligo(dT) (Invitrogen). First- and second-strand cDNA was 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 Illumina paired-end sample preparation protocol, using custom multiplex-indexed Solexa adaptors and sequenced as 75x2 using the Illumina GA Genome Analyzer paired-end pipeline. The original data set was deposited in the NCBI GEO database (access no. GSE36696).
 ==Research Findings==

← Older revision		Revision as of 06:40, 13 July 2016
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	==Illumina Sequencing==		==Illumina Sequencing==
		+	* Total RNA was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer’s instructions and was treated with RNase-free DNase I (New England Biolabs, Inc. Ipswich, MA, USA) to remove contaminated genomic DNA. mRNA was isolated from total RNA using Dynabeads oligo(
		+	dT) (Invitrogen). First- and second-strand cDNA was 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 Illumina paired-end sample preparation protocol, using custom multiplex-indexed Solexa adaptors and sequenced as 75x2 using the Illumina GA Genome Analyzer paired-end pipeline. The original data set was deposited in the NCBI GEO database (access no. GSE36696).

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