Open Access Highly Accessed Methodology article

Multi-targeted priming for genome-wide gene expression assays

Aleksandra B Adomas1, Francesc Lopez-Giraldez1, Travis A Clark1, Zheng Wang1 and Jeffrey P Townsend2*

Author Affiliations

1 Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect St, New Haven, CT 06511, USA

2 Department of Ecology and Evolutionary Biology, Program in Computational Biology and Bioinformatics, and Microbiology Graduate Program, Yale University, 165 Prospect St, New Haven, CT 06511, USA

For all author emails, please log on.

BMC Genomics 2010, 11:477  doi:10.1186/1471-2164-11-477

Published: 17 August 2010

Additional files

Additional File 1:

Number of MTP priming sites in S. cerevisiae genes. Table of the number of MTP priming sites in S. cerevisiae genes

Format: XLS Size: 1.9MB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional File 2:

Microarray profiling results comparing S. cerevisiae grown in nitrogen rich (SC) or poor (MM) conditions using oligo(dT) and multi-targeted primers (MTPs) for reverse transcription. Table of microarray profiling results comparing S. cerevisiae grown in nitrogen rich (SC) or poor (MM) conditions using oligo(dT) and multi-targeted primers (MTPs) for reverse transcription. For each priming method for each gene, relative gene expression levels in SC and MM, the additions and subtractions for those levels to demarcate 95% credible intervals, and the p-value for the direction of difference observed are reported.

Format: XLS Size: 2.5MB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional File 3:

Comparison of oligo(dT) and MTP priming in terms of number of genes significantly differentially expressed in specific biological processes and metabolic pathways. Table listing biological processes and metabolic pathways with the highest number of genes significantly differentially expressed (P ≤ 0.05) in S. cerevisiae and N. crassa, the number of genes differentially expressed as detected by oligo(dT)-primed and MTP-primed reverse transcription and microarray hybridization, the number of additional genes identified by MTP, and the percent improvement by MTP.

Format: XLS Size: 28KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional File 4:

Number of aligned reads recorded for each gene with oligo(dT)-primed and MTP-primed RNA tag sequencing of S. cerevisiae grown in nitrogen rich (SC) or poor (MM) conditions. Table listing each ORF, the number of oligo(dT) primed reads aligning from nitrogen poor (MM) conditions, the number of oligo(dT) primed reads aligning from nitrogen rich (SC) conditions, the number of multi-target primed reads aligning from nitrogen poor (MM) conditions, and the number of multi-target primed reads aligning from nitrogen rich (SC) conditions

Format: XLS Size: 448KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional File 5:

Comparison of transcript profiling of S. cerevisiae grown in nitrogen rich (SC) or poor (MM) medium obtained with microarray or RNA tag sequencing using MTP or oligo(dT) primers. Table listing S. cerevisiae ORFs and results of both microarray and RNA tag sequencing by both MTP and oligo(dT) priming. Results listed for each platform and priming methodology are the fold change of MM/SC and the p-value.

Format: XLS Size: 1.1MB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional File 6:

Microarray profiling results for N. crassa undergoing sexual development when multi-targeted primers or oligo(dT) primers were used for reverse transcription. Table listing the Broad ID and MIPS ID of well-measured genes in N. crassa protoperithecia (PP) and mycelium (Myc), relative expression levels, additions and subtractions for 95% credible intervals, and p-value, when multi-targeted primers (MTP) or oligo(dT) primers were used for reverse transcription.

Format: XLS Size: 515KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional File 7:

Comparison of expression levels of ribosomal genes in Neurospora crassa. Table of ribosomal genes and their fold change in expression in protoperithecia over mycelium, as measured by two-color microarray hybridization of oligo(dT)-primed cDNA and multi-target-primed cDNA.

Format: DOC Size: 67KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional File 8:

Sequences of primers used for Real Time RT-PCR. Table listing the gene measured, and the forward primer and reverse primer used.

Format: DOC Size: 41KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data