Snapshots of gene expression in rice: limitations for allelic expression imbalance determination
In an initial investigation of differential expression of genes caused by cis-acting regulatory elements in rice, the lack of reproducibility led us to question the basic premise of allelic expression imbalance determination: namely that departures of cDNA expression ratios from those observed in ge...
| Autores principales: | , , , , , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Canadian Science Publishing
2012
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/165777 |
| _version_ | 1855543386478477312 |
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| author | Akkinepalli, Harika Ereful, Nelzo Liu, Yan Malabanan, Kaye Howells, Rhian Stamati, Konstantina Powell, Wayne Leung, Hei Greenland, Andy Mackay, Ian Lee, David |
| author_browse | Akkinepalli, Harika Ereful, Nelzo Greenland, Andy Howells, Rhian Lee, David Leung, Hei Liu, Yan Mackay, Ian Malabanan, Kaye Powell, Wayne Stamati, Konstantina |
| author_facet | Akkinepalli, Harika Ereful, Nelzo Liu, Yan Malabanan, Kaye Howells, Rhian Stamati, Konstantina Powell, Wayne Leung, Hei Greenland, Andy Mackay, Ian Lee, David |
| author_sort | Akkinepalli, Harika |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | In an initial investigation of differential expression of genes caused by cis-acting regulatory elements in rice, the lack of reproducibility led us to question the basic premise of allelic expression imbalance determination: namely that departures of cDNA expression ratios from those observed in genomic DNA provide unequivocal evidence of cis-acting polymorphisms. This paper describes experiments designed to demonstrate that stochastic variation in low copy number of targets in PCR reactions give variable allelic ratios even when starting with the same copy numbers of the two alleles. These significant departures from an expected 1:1 ratio provide an explanation to the lack of reproducibility observed for our cDNA measurements. |
| format | Journal Article |
| id | CGSpace165777 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2012 |
| publishDateRange | 2012 |
| publishDateSort | 2012 |
| publisher | Canadian Science Publishing |
| publisherStr | Canadian Science Publishing |
| record_format | dspace |
| spelling | CGSpace1657772025-12-08T09:54:28Z Snapshots of gene expression in rice: limitations for allelic expression imbalance determination Akkinepalli, Harika Ereful, Nelzo Liu, Yan Malabanan, Kaye Howells, Rhian Stamati, Konstantina Powell, Wayne Leung, Hei Greenland, Andy Mackay, Ian Lee, David alleles complementary dna gene expression genes polymerase chain reaction In an initial investigation of differential expression of genes caused by cis-acting regulatory elements in rice, the lack of reproducibility led us to question the basic premise of allelic expression imbalance determination: namely that departures of cDNA expression ratios from those observed in genomic DNA provide unequivocal evidence of cis-acting polymorphisms. This paper describes experiments designed to demonstrate that stochastic variation in low copy number of targets in PCR reactions give variable allelic ratios even when starting with the same copy numbers of the two alleles. These significant departures from an expected 1:1 ratio provide an explanation to the lack of reproducibility observed for our cDNA measurements. 2012-05 2024-12-19T12:55:27Z 2024-12-19T12:55:27Z Journal Article https://hdl.handle.net/10568/165777 en Canadian Science Publishing Akkinepalli, Harika; Ereful, Nelzo; Liu, Yan; Malabanan, Kaye; Howells, Rhian; Stamati, Konstantina; Powell, Wayne; Leung, Hei; Greenland, Andy; Mackay, Ian and Lee, David. 2012. Snapshots of gene expression in rice: limitations for allelic expression imbalance determination. Genome, Volume 55 no. 5 p. 400-406 |
| spellingShingle | alleles complementary dna gene expression genes polymerase chain reaction Akkinepalli, Harika Ereful, Nelzo Liu, Yan Malabanan, Kaye Howells, Rhian Stamati, Konstantina Powell, Wayne Leung, Hei Greenland, Andy Mackay, Ian Lee, David Snapshots of gene expression in rice: limitations for allelic expression imbalance determination |
| title | Snapshots of gene expression in rice: limitations for allelic expression imbalance determination |
| title_full | Snapshots of gene expression in rice: limitations for allelic expression imbalance determination |
| title_fullStr | Snapshots of gene expression in rice: limitations for allelic expression imbalance determination |
| title_full_unstemmed | Snapshots of gene expression in rice: limitations for allelic expression imbalance determination |
| title_short | Snapshots of gene expression in rice: limitations for allelic expression imbalance determination |
| title_sort | snapshots of gene expression in rice limitations for allelic expression imbalance determination |
| topic | alleles complementary dna gene expression genes polymerase chain reaction |
| url | https://hdl.handle.net/10568/165777 |
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