IC4R001-Genome-2002-11935017 - Revision history

Guangyi: /* Corresponding Author */

2016-06-29T08:00:07Z

‎Corresponding Author

Guangyi: /* Research Findings */

2016-06-29T07:53:59Z

‎Research Findings

Guangyi: /* Research Findings */

2016-06-29T07:44:21Z

‎Research Findings

Guangyi: /* Research Findings */

2016-06-29T06:19:51Z

‎Research Findings

Guangyi at 06:12, 29 June 2016

2016-06-29T06:12:35Z

Guangyi: /* Plant Culture & Treatment */

2016-06-29T06:00:19Z

‎Plant Culture & Treatment

Guangyi: /* Plant Culture & Treatment */

2016-06-29T01:09:57Z

‎Plant Culture & Treatment

Guangyi: /* Plant Culture & Treatment */

2016-06-29T01:09:26Z

‎Plant Culture & Treatment

Guangyi at 01:09, 29 June 2016

2016-06-29T01:09:08Z

Guangyi: /* Corresponding Author */

2016-06-28T14:58:58Z

‎Corresponding Author

← Older revision		Revision as of 08:00, 29 June 2016
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	==Corresponding Author==		==Corresponding Author==
	*'''Huanming Yang:'''hyang@genomics.org.cn.		*'''Huanming Yang:'''hyang@genomics.org.cn.
		+	<br>

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 *After the GC contents of individual exons and introns were plotted as a function of genomic length (i.e., the sum of exon and intron lengths), it was apparent that most of the variation was within genes (Fig.4).
 <br>
-[[File:IC4R001-Genome-2002-11935017-f4.png |center |thumb |10000px |'''Fig. 4. GC content for individual exons as a function of their gene size, in A. thaliana, O.sativa, and H. sapiens. All exon and intron sequences were derived from cDNA-to-genomic alignments. Each data point is a single exon.Exons for the same gene are plotted at the same abscissa and connected by a vertical line.The genes are sorted by size, where gene size is defined as the sum of exon and intron lengths.To make the figure legible, we use constant spacing between genes, thus resulting in nonuniform abscissa labels. We show only the 41 largest genes for which the entire cDNA could be aligned to genomic sequence. Given the draft nature of the rice genome, some of the largest rice genes had to be omitted.''']]
+[[File:IC4R001-Genome-2002-11935017-f4.png |center |thumb |10000px |''''''Fig. 4. GC content for individual exons as a function of their gene size, in A. thaliana, O.sativa, and H. sapiens. All exon and intron sequences were derived from cDNA-to-genomic alignments. Each data point is a single exon.Exons for the same gene are plotted at the same abscissa and connected by a vertical line.The genes are sorted by size, where gene size is defined as the sum of exon and intron lengths.To make the figure legible, we use constant spacing between genes, thus resulting in nonuniform abscissa labels. We show only the 41 largest genes for which the entire cDNA could be aligned to genomic sequence. Given the draft nature of the rice genome, some of the largest rice genes had to be omitted.'''''']]
 ==Labs working on this Project==

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 [[File:IC4R001-Genome-2002-11935017-f3.png |center |thumb |10000px |''''''Fig. 3. GC content distribution for exons and introns in A. thaliana, O. sativa, and H. sapiens. All exon and intron sequences were derived from cDNA-to-genomic alignments. '''''']]
 <br>
 ==Labs working on this Project==

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 ==Research Findings==
 *The researchers have found that smaller windows are more informative, because when these windows are larger than a typical gene size, they obscure differences between intergenic DNA and genes. We used a 500-bp window size, to obtain a smaller size than that of most plant genes (Fig. 2)
 [[File:IC4R001-Genome-2002-11935017-f2.png |center |thumb |10000px |''''''Fig. 2. Distributions for genomic GC content in A. thaliana, O. sativa, and H. sapiens, computed over a bin size of 500 bp. Note that for bins/10=100, the number of bins with that GC content is 1000.'''''']]
 <br>
 ==Labs working on this Project==
 *Beijing Genomics Institute/Center of Genomics and Bioinformatics, Chinese Academy of Sciences, Beijing 101300, China.

@@ Line 10: / Line 10: @@
 *The researchers used a “whole-genome shotgun” approach, as successfully applied to Drosophila melanogaster (25) and Homo sapiens (8).The data are complementary to those of the IRGSP, which is sequencing Nipponbare, a cultivar of the subspecies japonica, with a “clone-by-clone” approach. If assuming a euchromatic rice genome size of 430 Mb, and a Phred Q20 (26, 27) read length of 500 base pairs (bp), then 13 coverage would be equivalent to 0.86 million sequence reads, or 1 million reads after the typical success rate of 80 to 85% is factored in. Shotgun libraries were constructed with a variety of methods for clone-insert preparation (28–30), to minimize the likelihood of systematic biases in genome representation. A total of 55 plasmid libraries were constructed for 93-11 and PA64s, with a 2-kb nominal clone-insert size.Overall, we prepared 2.75 million plasmid DNA samples (31, 32). Sequencing was performed on both ends of the inserts. By the 21 October 2001 freeze, there were 4.62 million successful reads, indicating an 84% success rate. The average Q20 read length was 546 bp.
 <br>
+==Research Findings==
 ==Labs working on this Project==
 *Beijing Genomics Institute/Center of Genomics and Bioinformatics, Chinese Academy of Sciences, Beijing 101300, China.

@@ Line 8: / Line 8: @@
 <br>
 ==Plant Culture & Treatment==
-*The researchers used a “whole-genome shotgun” approach, as successfully applied to Drosophila melanogaster (25) and Homo sapiens (8).The data are complementary to those of the IRGSP, which is sequencing Nipponbare, a cultivar of the subspecies japonica, with a “clone-by-clone” approach. If assuming a euchromatic rice genome size of 430 Mb, and a Phred Q20 (26, 27) read length of 500 base pairs (bp), then 13 coverage would be equivalent to 0.86 million sequence reads, or 1 million reads after the typical success rate of 80 to 85% is factored in. Shotgun librarieswere constructed with a variety of methods for clone-insert preparation (28–30), to minimize the likelihood of systematic biases in genome representation. A total of 55 plasmid libraries were constructed for 93-11 and PA64s, with a 2-kb nominal clone-insert size.Overall, we prepared 2.75 million plasmid DNA samples (31, 32). Sequencing was performed on both ends of the inserts. By the 21 October 2001 freeze, there were 4.62 million successful reads, indicating an 84% success rate. The average Q20 read length was 546 bp.
+*The researchers used a “whole-genome shotgun” approach, as successfully applied to Drosophila melanogaster (25) and Homo sapiens (8).The data are complementary to those of the IRGSP, which is sequencing Nipponbare, a cultivar of the subspecies japonica, with a “clone-by-clone” approach. If assuming a euchromatic rice genome size of 430 Mb, and a Phred Q20 (26, 27) read length of 500 base pairs (bp), then 13 coverage would be equivalent to 0.86 million sequence reads, or 1 million reads after the typical success rate of 80 to 85% is factored in. Shotgun libraries were constructed with a variety of methods for clone-insert preparation (28–30), to minimize the likelihood of systematic biases in genome representation. A total of 55 plasmid libraries were constructed for 93-11 and PA64s, with a 2-kb nominal clone-insert size.Overall, we prepared 2.75 million plasmid DNA samples (31, 32). Sequencing was performed on both ends of the inserts. By the 21 October 2001 freeze, there were 4.62 million successful reads, indicating an 84% success rate. The average Q20 read length was 546 bp.
 <br>

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 <br>
 ==Corresponding Author==
-'''Huanming Yang''':hyang@genomics.org.cn.
+*'''Huanming Yang:'''hyang@genomics.org.cn.