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An atlas of bovine gene expression reveals novel distinctive tissue characteristics and evidence for improving genome annotation

Gregory P Harhay1*, Timothy PL Smith1, Leeson J Alexander2, Christian D Haudenschild3, John W Keele1, Lakshmi K Matukumalli45, Steven G Schroeder5, Curtis P Van Tassell5, Cathy R Gresham6, Susan M Bridges6, Shane C Burgess7 and Tad S Sonstegard5

Author Affiliations

1 USDA-ARS US Meat Animal Research Center, State Spur 18 D, Clay Center, NE 68901, USA

2 USDA-ARS Fort Keogh Livestock and Range Research Laboratory, 243 Fort Keogh Road, Miles City, MT 59301, USA

3 Illumina, Inc., 25861 Industrial Boulevard, Hayward, CA 94545, USA

4 Department of Bioinformatics and Computational Biology, George Mason University, 10900 University Blvd, Manassas, VA 20110, USA

5 USDA-ARS Bovine Functional Genomics Laboratory, 10300 Baltimore Avenue, Bldg 200 Rm 2A BARC-East, Beltsville, MD 20705, USA

6 Department of Computer Science, Mississippi State University, Mississippi State, MS 39762, USA

7 Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762, USA

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Genome Biology 2010, 11:R102  doi:10.1186/gb-2010-11-10-r102

Published: 20 October 2010

Additional files

Additional file 1:

Tissues sampled and annotation. BRENDA tissue ontology terms are given when known, with the hyphenated number at the end of the column headings specifying level of granularity, where 1 is the lowest level of granularity and the broadest scope. Only tags mapping uniquely to the draft genome that passed our filters (Os-fgU; Figure 2b) were considered. Total Sense TPM Within NM & NR Transcripts: sum of normalized tag counts (tags per million) that mapped on the same strand and within the boundaries of NM and NR transcripts. On 3' terminus: sum of normalized tag abundance of those tags that mapped on the same strand and at the 3'-most and next to 3'-most DpnII sites on the NM or NR transcript (Figure 2a). Not on 3' terminus: sum of normalized tag abundance of those tags that did not map to the 3'-most and next to 3'-most DpnII sites on the NM or NR transcript (Figure 2a): Count Sense GeneID: total number of unique GeneIDs associated with the loci that the tags mapped to on the same strand and within the boundaries of the annotated genes. Count Sense Tags within Loci: number of unique tag sequences that mapped within the boundaries of annotated genes. Total Sense TPM within Loci: sum of normalized tag abundance of those tags that mapped on the same strand and within the boundaries of all annotated genes. The headings including the word 'AntiSense' are similarly defined, except that these tags mapped to the strand opposite to that of the annotated gene.

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Additional file 2:

(a) Association of the number of unique sense tag sequences within protein-coding loci with the number of unique protein coding loci for each tissue library. CSTL_PC: count unique sense tag sequence within protein-coding loci. CSG_PC: count sense protein-coding loci from Additional file 1. Each data point represents a single tissue library. The top pane shows that number of sense tags found with protein coding loci varies quadratically with the number of protein coding loci. The bottom pane shows the residuals from the fit of the data to the quadratic above. (b) Association of the number of unique antisense tag sequences within loci with the number of unique loci for each tissue library. CATL_PC: count unique antisense tag sequence within protein-coding loci. CAG_PC: count antisense protein-coding loci from Additional file 1. Each data point represents a single tissue library. The top pane shows that number of antisense tags found with protein coding loci varies quadratically with the number of protein coding loci. The bottom pane shows the residuals from the fit of the data to the quadratic above.

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Additional file 3:

Housekeeping genes. Loci that were observed to be ubiquitously expressed were ordered according to the coefficient of variation in the sum of the observed normalized tag abundance (TPM) of all tags mapping on the same strand and within the boundaries of the gene. Only tags mapping uniquely to the draft genome that passed our filters (Os-fgU; Figure 2b) were considered.

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Open Data

Additional file 4:

Classification of non-genome mapping tags with respect to the number of libraries they were present in and their mapping behavior with respect to EST and genome mismatches. This figure shows that the dominant class of non-genome mapping tags are those that are found in nearly every tissue and that most of these map to ESTs or exhibit a single base mismatch from genome mapping tags.

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