This article is part of the supplement: Ninth Annual MCBIOS Conference. Dealing with the Omics Data Deluge
Transcriptome profile of a bovine respiratory disease pathogen: Mannheimia haemolytica PHL213
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
BMC Bioinformatics 2012, 13(Suppl 15):S4 doi:10.1186/1471-2105-13-S15-S4Published: 11 September 2012
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
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
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
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