Amplification biases: possible differences among deviating gene expressions

doi:10.1186/1471-2164-9-46

BMC Genomics

Volume 9

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Degrelle SA
Hennequet-Antier C
Chiapello H
Piot-Kaminski K
Piumi F
Robin S
Renard JP
Hue I

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Hennequet-Antier C
Chiapello H
Piot-Kaminski K
Piumi F
Robin S
Renard JP
Hue I
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Research article

Amplification biases: possible differences among deviating gene expressions

Séverine A Degrelle¹ , Christelle Hennequet-Antier²^,5 , Hélène Chiapello² , Karine Piot-Kaminski²^,6 , Francois Piumi³^,7 , Stéphane Robin⁴ , Jean-Paul Renard¹ and Isabelle Hue¹

¹Biologie du Développement et Reproduction UMR 1198; ENVA; CNRS, FRE 2857, Institut National de la Recherche Agronomique, F-78350 Jouy-en-Josas, France

²Mathématique, Informatique et Génome UR1077, Institut National de la Recherche Agronomique, F-78350 Jouy-en-Josas, France

³Radiobiologie et Etude du Génome UMR INRA/CEA, Institut National de la Recherche Agronomique, F-78350 Jouy-en-Josas, France

⁴Mathématiques et Informatique Appliquées UMR INAPG/ENGREF/INRA 518, F-75005 Paris, France

⁵Station de Recherches Avicoles, Institut National de la Recherche Agronomique, F-37380 Nouzilly, France

⁶Modélisation et Ingénierie des Systèmes Complexes pour le Diagnostic FRE3009 CNRS/BIO-RAD, F-34184 Montpellier Cedex 4, France

⁷Biologie des Champignons Filamenteux UFR ESIL, F-13288Marseille Cedex 09, France

author email corresponding author email

BMC Genomics 2008, 9:46doi:10.1186/1471-2164-9-46


Published:	28 January 2008

Additional files

Additional file 1:

Optimisation of each amplification procedure. Southern (A) and Northern (B) blots performed on cDNA (A) and aRNA (B) after increasing PCR cycle numbers or increasing in vitro transcription times were hybridised with a ³²P-labelled DNA probe encoding the exogenous CG03 transcript. A band of the expected size (1 kb) was observed on southern blots after 9, 12 and 15 cycles for the 1^rstand 2^ndrounds of PCR amplifications (A). The negative controls including RT- and mock did not give any signal. A band of the expected size was also observed on Northern blots after 8, 10 or 12 h of in vitro transcription (B). Its intensity increased with the increasing transcription time. Only brain data are illustrated here, but similar results were obtained with ovary and embryos.

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Additional file 2:

Characteristics of the amplified targets from brain and ovary. aRNA and cDNA targets were analysed on RNA 6000 lab-chips and DNA 7500 lab-chips, respectively (BioAnalyser 2100; Agilent Technologies). These populations of amplified molecules displayed slightly different profiles of size distribution depending on the protocol (A, B) or the tissue (C). Each target replicate (1 to 3) has been amplified independently from the same pool of total RNA. The molecular ladders are represented in nucleotides (nt) on the x axis.

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Additional file 3:

List of the 109 EST from Panel 1. Name of the EST from the 1 K array (or core array), GenBank accession numbers (CR), identifiers in TIGR gene index (TC) and Unigene index (Bt.) as well as short names (Gene ID) are provided here.

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Additional file 4:

List of the 45 EST from Panel 2. Name of the EST from the 1 K array (or core array), GenBank accession numbers (CR), identifiers in the TIGR gene index (TC) and the Unigene index (Bt.) as well as short names (Gene ID) are provided here.

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