The Seed Biology Place

The Plant Cell 23: 2045-2063 (2011)

A Guideline to Family-wide Comparative State-of-the-art qRT-PCR Analysis Exemplified with a Brassicaceae Cross-species Seed Germination Case Study ^[W][OA]

Kai Graeber*, Ada Linkies*, Andrew T.A. Wood, Gerhard Leubner-Metzger
* Both authors contributed equally to this work

University of Freiburg, Faculty of Biology, Institute for Biology II, Botany / Plant Physiology, D-79104 Freiburg, Germany, Web: 'The Seed Biology Place' http://www.seedbiology.de (K.G., A.L., G.L.-M.)
The University of Nottingham, Division of Statistics, School of Mathematical Sciences, University Park, Nottingham NG7 2RD, United Kingdom (A.T.A.W.)

Received February 8, 2011; revised May 6, 2011; accepted May 27, 2011; published June 10, 2011.
www.plantcell.org/cgi/doi/10.1105/tpc.111.084103

Supplemental Table 1. Sequence similarities to Arabidopsis and accession numbers of Lepidium sativum FR14 reference gene cDNA sequences.

Lepidium sativum reference genes cDNA sequence name	GenBank accession numbers	AGI code of putative Arabidopsis ortholog	e-value	% sequence similarity between the two species
LesaG17210	`HQ912755`	At1G17210	0	92
LesaG04660	`HQ912754`	At2G04660	0	92
LesaG19980	`HQ912756`	At2G19980	1e-71	77
LesaG20000	`HQ912757`	At2G20000	4e-160	92
LesaG04320	`HQ912753`	At4G04320	8e-90	91
LesaCYP1	`HS981851`	At4G38740	7e-42	94
LesaACT7	`HS981849`	At5G09810	8e-32	100
LesaACT8	`HS981850`	At1G49240	8e-33	96
LesaEF1-α	`HS981853`	At5G60390	6e-20	94
LesaCYP5	`HS981852`	At2G29960	9e-33	93
LesaUBQ11	`HS981854`	At4G05050	2e-34	92

Synopsis: Developmental processes like seed germination are characterised by massive transcriptome changes. This study compares seed transcriptome datasets of different Brassicaceae to identify stable expressed reference genes for cross-species qRT-PCR normalisation. A workflow is presented for improving RNA quality, qRT-PCR performance, and normalisation when analysing expression changes across species.

Article in PDF format (1.2 MB)
Supplemental data file (156 KB)

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Hyperlink to
Supplemental
Datasets 1 to 3

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The Plant Cell 23: 2045-2063 (2011)

A Guideline to Family-wide Comparative State-of-the-art qRT-PCR Analysis Exemplified with a Brassicaceae Cross-species Seed Germination Case Study [W][OA]

A Guideline to Family-wide Comparative State-of-the-art qRT-PCR Analysis Exemplified with a Brassicaceae Cross-species Seed Germination Case Study ^[W][OA]