This article is part of the supplement: Ninth Annual MCBIOS Conference. Dealing with the Omics Data Deluge

Open Access Proceedings

Transcriptome profile of a bovine respiratory disease pathogen: Mannheimia haemolytica PHL213

Joseph S Reddy1, Ranjit Kumar2, James M Watt3, Mark L Lawrence1, Shane C Burgess4 and Bindu Nanduri1*

Author Affiliations

1 College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762, USA

2 Center for Clinical and Translational Science, University of Alabama at Birmingham, Birmingham, AL 35294, USA

3 Eagle Applied Sciences LLC, San Antonio, TX 78248, USA

4 College of Agriculture and Life Sciences, University of Arizona, Tucson, AZ 85721, USA

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BMC Bioinformatics 2012, 13(Suppl 15):S4  doi:10.1186/1471-2105-13-S15-S4

Published: 11 September 2012

Additional files

Additional file 1:

Complete description of suggested corrections to existing annotation, and identified frameshift mutations. Sheet 1 labeled 'Annotation Errors' contains corrections to annotated genes in M. haemolytica PHL213, previously annotated gene locus and length, suggested correction to its locus. RNA-Seq expression based observed gene and protein length along with description of the exception in the genome that led to the annotation error; in case of mutated start, the mutated amino acid; BLASTX hit used to correct the annotation and its description. Sheet 2 labeled 'Frameshift' contains the two frameshift mutations identified, their frame locus and the BLASTX hit used to identify the frameshift.

Format: XLSX Size: 12KB Download file

Open Data

Additional file 2:

RNA-Seq based expression profile of annotated genes. The sheet labeled as 'MH_Expressed' consists of annotated genes identified as expressed in the RNA-Seq experiment, the observed coverage, average reads per base for each gene and the description of the gene, Sheet 2 labeled as 'MH_NotExpressed' contains annotated genes identified as not expressed in RNA-Seq experiment, the observed coverage, average reads per base for each gene and the description of the gene.

Format: XLSX Size: 124KB Download file

Open Data

Additional file 3:

Comparison of co-expressed gene pairs identified by RNA-Seq and operons predicted by DOOR. Sheet 1 labeled 'MH_DOOR' has a list of operons predicted by DOOR. Sheet 2 labeled 'MH_DOOR_Pairwise' contains a list of co-expressed gene pairs predicted by DOOR. Sheet 3 labeled 'MH_JR' contains a list of operons identified in our RNA-Seq experiment. Sheet 4 labeled 'MH_JR_Pairs' contains a list of co-expressed gene pairs identified by RNA-Seq. Sheet 6 labeled 'MH_Pairwise_Common' contains a list of co-expressed gene pairs common to both DOOR and RNA-Seq. Sheet 7 labeled 'MH_DOOR_Unique' contains a list of co-expressed gene pairs unique to DOOR. Sheet 8 labeled 'MH_JR_Unique' contains a list of co-expressed gene pairs unique to our RNA-Seq experiment.

Format: XLSX Size: 115KB Download file

Open Data

Additional file 4:

Results of M. haemolytica PHL213 sRNA searched against sRNAdb. Putative sRNA identified by RNA-Seq were searched against other bacterial sRNA in small non-coding RNA database (sRNAdb) by conducting BLASTN searches.

Format: XLSX Size: 61KB Download file

Open Data