IC4R011-RNA-Seq-2010-21122150 - Revision history

Liman: /* Research Findings */

2016-07-12T08:17:47Z

‎Research Findings

Liman: /* Research Findings */

2016-07-12T08:16:06Z

‎Research Findings

Liman: /* Research Findings */

2016-07-12T08:13:53Z

‎Research Findings

Liman: /* Research Findings */

2016-07-12T08:12:20Z

‎Research Findings

Liman: /* Research Findings */

2016-07-12T07:34:59Z

‎Research Findings

Liman: /* Research Findings */

2016-07-12T07:26:11Z

‎Research Findings

Liman: /* Research Findings */

2016-07-12T07:19:26Z

‎Research Findings

Liman: /* Research Findings */

2016-07-12T07:13:44Z

‎Research Findings

Liman: /* Research Findings */

2016-07-12T07:12:49Z

‎Research Findings

Liman: /* Research Findings */

2016-07-12T07:12:25Z

‎Research Findings

@@ Line 13: / Line 13: @@
 [[File:IC4R011-RNA-Seq-2010-21122150-f1.png |center |thumb |800px |'''Figure 1 Accumulation of 36-bp reads to cover whole transcripts.''']]
 <br>
-<br>
 * Rice transcriptome analysis was based on response to salinity stress. mRNAs were prepared from the tissues of normal rice shoots and roots and from those subjected to 1 h of salinity stress. Of the 27 to 35 million quality-evaluated reads (Table 1; Total filtered reads), 72.0% to 75.2% were mapped uniquely to the rice genome (Table 1; Unique-genome); 5.0% to 5.7% of the reads bridged flanking exons (Table 1; Unique-bridged); 6.0% to 11.2% of the reads were repetitive sequences (Table 1; Multiple); and 10.1% to 16.7% had no match in the genome (Table 1; Unmapped). Thus, a total of 76.9% to 80.9% of the reads were mapped uniquely to the rice genome or to exon-exon junctions (Table 1; Unique-total).
 [[File:IC4R011-RNA-Seq-2010-21122150-t1.png |center |thumb |1000px |'''Tabel 1 Numbers of mapped reads.''']]
+<br>
 * The researchers comprehensively compared the RPKM of each gene in response to salinity stress (r = 0.95 in shoot and 0.94 in root; Figure 2). The researchers used the G-test with a 1% false discovery rate (FDR) and identified 6,469 (in shoot) and 10,321 (in root) differentially expressed RAP2 genes. Of these, 3,050 (up, 1,651; down, 1,399) genes were commonly differentially expressed. The number of highly differentially expressed genes (>32×) was greater in the root (58 genes) than in the shoot (5 genes). Expression of genes previously identified under salinity stress was induced in the root (> 2×). The distribution of mapped reads on the rice genome was graphed on a GBrowse(Figure 3).
 [[File:IC4R011-RNA-Seq-2010-21122150-f2.png |center |thumb |800px |'''Figure 2 Comparison of RPKM of each gene after salinity stress.''']]
 [[File:IC4R011-RNA-Seq-2010-21122150-f3.png |center |thumb |800px |'''Figure 3 Differential expression of genes in a 100-kb region on chromosome 2.''']]
+<br>
 * In the shoot, 51,301 transcripts were predicted (RPKM ≥ 2, length ≥ 100 bp) (Table 2); 94.6% (48,506/51,301) of the predicted transcripts were mapped on previously annotated loci in RAP2; thus, the remaining 2,795 predicted transcripts were unannotated in RAP-DB (Table 2). In the root, 3,082 of the 54,491 predicted transcripts were mapped on unannotated regions(Table 2). The reseachers attempted to predict the functions of unannotated transcripts by BLASTX search and longest-ORF search. In a BLASTX search against the UniProt and RefSeq sequences, of the predicted transcripts, 995 (shoot) and 1,052 (root) had ORFs similar to those encoding the amino acid sequences of functional proteins (Table 2). Of the remaining unannotated transcripts, 1,670 (shoot) and 1,873 (root) had ORFs encoding at least 20 amino acids by longest-ORF search (Table 2). Amino acid length was widely distributed: the mean and median were 125 and 77 amino acids in the shoot, and 123 and 74 in the root (Figure 4).
 [[File:IC4R011-RNA-Seq-2010-21122150-t2.png |left |thumb |500px |'''Table 2 Numbers and ORF predictions of transcripts.''']]

@@ Line 19: / Line 19: @@
 * The researchers comprehensively compared the RPKM of each gene in response to salinity stress (r = 0.95 in shoot and 0.94 in root; Figure 2). The researchers used the G-test with a 1% false discovery rate (FDR) and identified 6,469 (in shoot) and 10,321 (in root) differentially expressed RAP2 genes. Of these, 3,050 (up, 1,651; down, 1,399) genes were commonly differentially expressed. The number of highly differentially expressed genes (>32×) was greater in the root (58 genes) than in the shoot (5 genes). Expression of genes previously identified under salinity stress was induced in the root (> 2×). The distribution of mapped reads on the rice genome was graphed on a GBrowse(Figure 3).
-[[File:IC4R011-RNA-Seq-2010-21122150-f2.png |center |thumb |1000px |'''Figure 2 Comparison of RPKM of each gene after salinity stress.''']]
+[[File:IC4R011-RNA-Seq-2010-21122150-f2.png |center |thumb |800px |'''Figure 2 Comparison of RPKM of each gene after salinity stress.''']]
-[[File:IC4R011-RNA-Seq-2010-21122150-f2.png |center |thumb |1000px |'''Figure 3 Differential expression of genes in a 100-kb region on chromosome 2.''']]
+[[File:IC4R011-RNA-Seq-2010-21122150-f3.png |center |thumb |800px |'''Figure 3 Differential expression of genes in a 100-kb region on chromosome 2.''']]
 * In the shoot, 51,301 transcripts were predicted (RPKM ≥ 2, length ≥ 100 bp) (Table 2); 94.6% (48,506/51,301) of the predicted transcripts were mapped on previously annotated loci in RAP2; thus, the remaining 2,795 predicted transcripts were unannotated in RAP-DB (Table 2). In the root, 3,082 of the 54,491 predicted transcripts were mapped on unannotated regions(Table 2). The reseachers attempted to predict the functions of unannotated transcripts by BLASTX search and longest-ORF search. In a BLASTX search against the UniProt and RefSeq sequences, of the predicted transcripts, 995 (shoot) and 1,052 (root) had ORFs similar to those encoding the amino acid sequences of functional proteins (Table 2). Of the remaining unannotated transcripts, 1,670 (shoot) and 1,873 (root) had ORFs encoding at least 20 amino acids by longest-ORF search (Table 2). Amino acid length was widely distributed: the mean and median were 125 and 77 amino acids in the shoot, and 123 and 74 in the root (Figure 4).

@@ Line 24: / Line 24: @@
 * In the shoot, 51,301 transcripts were predicted (RPKM ≥ 2, length ≥ 100 bp) (Table 2); 94.6% (48,506/51,301) of the predicted transcripts were mapped on previously annotated loci in RAP2; thus, the remaining 2,795 predicted transcripts were unannotated in RAP-DB (Table 2). In the root, 3,082 of the 54,491 predicted transcripts were mapped on unannotated regions(Table 2). The reseachers attempted to predict the functions of unannotated transcripts by BLASTX search and longest-ORF search. In a BLASTX search against the UniProt and RefSeq sequences, of the predicted transcripts, 995 (shoot) and 1,052 (root) had ORFs similar to those encoding the amino acid sequences of functional proteins (Table 2). Of the remaining unannotated transcripts, 1,670 (shoot) and 1,873 (root) had ORFs encoding at least 20 amino acids by longest-ORF search (Table 2). Amino acid length was widely distributed: the mean and median were 125 and 77 amino acids in the shoot, and 123 and 74 in the root (Figure 4).
 [[File:IC4R011-RNA-Seq-2010-21122150-t2.png |left |thumb |500px |'''Table 2 Numbers and ORF predictions of transcripts.''']]
-[[File:IC4R011-RNA-Seq-2010-21122150-f4.png |right |thumb |500px |'''Figure 4 ORF length and number of transcripts.''']]
+[[File:IC4R011-RNA-Seq-2010-21122150-f4.png |center |thumb |500px |'''Figure 4 ORF length and number of transcripts.''']]
 ==Labs working on this Project==

@@ Line 18: / Line 18: @@
 [[File:IC4R011-RNA-Seq-2010-21122150-t1.png |center |thumb |1000px |'''Tabel 1 Numbers of mapped reads.''']]
-The researchers comprehensively compared the RPKM of each gene in response to salinity stress (r = 0.95 in shoot and 0.94 in root; Figure 2). The researchers used the G-test with a 1% false discovery rate (FDR) and identified 6,469 (in shoot) and 10,321 (in root) differentially expressed RAP2 genes. Of these, 3,050 (up, 1,651; down, 1,399) genes were commonly differentially expressed. The number of highly differentially expressed genes (>32×) was greater in the root (58 genes) than in the shoot (5 genes). Expression of genes previously identified under salinity stress was induced in the root (> 2×). The distribution of mapped reads on the rice genome was graphed on a GBrowse(Figure 3).
+* The researchers comprehensively compared the RPKM of each gene in response to salinity stress (r = 0.95 in shoot and 0.94 in root; Figure 2). The researchers used the G-test with a 1% false discovery rate (FDR) and identified 6,469 (in shoot) and 10,321 (in root) differentially expressed RAP2 genes. Of these, 3,050 (up, 1,651; down, 1,399) genes were commonly differentially expressed. The number of highly differentially expressed genes (>32×) was greater in the root (58 genes) than in the shoot (5 genes). Expression of genes previously identified under salinity stress was induced in the root (> 2×). The distribution of mapped reads on the rice genome was graphed on a GBrowse(Figure 3).
 [[File:IC4R011-RNA-Seq-2010-21122150-f2.png |center |thumb |1000px |'''Figure 2 Comparison of RPKM of each gene after salinity stress.''']]
 [[File:IC4R011-RNA-Seq-2010-21122150-f2.png |center |thumb |1000px |'''Figure 3 Differential expression of genes in a 100-kb region on chromosome 2.''']]
 ==Labs working on this Project==

@@ Line 18: / Line 18: @@
 [[File:IC4R011-RNA-Seq-2010-21122150-t1.png |center |thumb |1000px |'''Tabel 1 Numbers of mapped reads.''']]
-The researchers comprehensively compared the RPKM of each gene in response to salinity stress (r = 0.95 in shoot and 0.94 in root; Figure 2). The researchers used the G-test with a 1% false discovery rate (FDR) and identified 6,469 (in shoot) and 10,321 (in root) differentially expressed RAP2 genes. Of these, 3,050 (up, 1,651; down, 1,399) genes were commonly differentially expressed.
+The researchers comprehensively compared the RPKM of each gene in response to salinity stress (r = 0.95 in shoot and 0.94 in root; Figure 2). The researchers used the G-test with a 1% false discovery rate (FDR) and identified 6,469 (in shoot) and 10,321 (in root) differentially expressed RAP2 genes. Of these, 3,050 (up, 1,651; down, 1,399) genes were commonly differentially expressed. The number of highly differentially expressed genes (>32×) was greater in the root (58 genes) than in the shoot (5 genes). Expression of genes previously identified under salinity stress was induced in the root (> 2×). The distribution of mapped reads on the rice genome was graphed on a GBrowse(Figure 3).
 ==Labs working on this Project==

← Older revision		Revision as of 07:26, 12 July 2016
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	[[File:IC4R011-RNA-Seq-2010-21122150-t1.png \|center \|thumb \|1000px \|'''Tabel 1 Numbers of mapped reads.''']]		[[File:IC4R011-RNA-Seq-2010-21122150-t1.png \|center \|thumb \|1000px \|'''Tabel 1 Numbers of mapped reads.''']]
		+
		+	The researchers comprehensively compared the RPKM of each gene in response to salinity stress (r = 0.95 in shoot and 0.94 in root; Figure 2). The researchers used the G-test with a 1% false discovery rate (FDR) and identified 6,469 (in shoot) and 10,321 (in root) differentially expressed RAP2 genes. Of these, 3,050 (up, 1,651; down, 1,399) genes were commonly differentially expressed.

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

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 * As the number of reads increased, the fraction of highly expressed genes(RPKM ≥ 300) close to their final RPKM was almost unchanged, whereas those of genes with relatively low expression (RPKM 3-30) converged more slowly (Figure 1b). With four technical replicates (corresponding to about 27 to 35 million reads), 81.2% of genes with relatively low expression levels (RPKM 3-30) reached to within ± 5% of their final RPKM (Figure 1b).
-[[File:IC4R011-RNA-Seq-2010-21122150-f1.png |center |thumb |800px |'''Figure 1''' ''Accumulation of 36-bp reads to cover whole transcripts.'']]
+[[File:IC4R011-RNA-Seq-2010-21122150-f1.png |center |thumb |800px |'''Figure 1''' '''''Accumulation of 36-bp reads to cover whole transcripts.''''']]
 <br>
 <br>
 * Rice transcriptome analysis was based on response to salinity stress. mRNAs were prepared from the tissues of normal rice shoots and roots and from those subjected to 1 h of salinity stress. Of the 27 to 35 million quality-evaluated reads (Table 1; Total filtered reads), 72.0% to 75.2% were mapped uniquely to the rice genome (Table 1; Unique-genome); 5.0% to 5.7% of the reads bridged flanking exons (Table 1; Unique-bridged); 6.0% to 11.2% of the reads were repetitive sequences (Table 1; Multiple); and 10.1% to 16.7% had no match in the genome (Table 1; Unmapped). Thus, a total of 76.9% to 80.9% of the reads were mapped uniquely to the rice genome or to exon-exon junctions (Table 1; Unique-total).
-[[File:IC4R011-RNA-Seq-2010-21122150-t1.png |center |thumb |1000px |'''Tabel 1''' ''Numbers of mapped reads.'']]
+[[File:IC4R011-RNA-Seq-2010-21122150-t1.png |center |thumb |1000px |'''Tabel 1''' '''''Numbers of mapped reads.''''']]
 ==Labs working on this Project==