Email updates

Keep up to date with the latest news and content from BMC Microbiology and BioMed Central.

Open Access Research article

Experimental annotation of the human pathogen Histoplasma capsulatum transcribed regions using high-resolution tiling arrays

Mark Voorhies1, Catherine K Foo2 and Anita Sil13*

Author Affiliations

1 Department of Microbiology & Immunology, University of California San Francisco, San Francisco, California, 94143, USA

2 Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, 94143, USA

3 Howard Hughes Medical Institute, University of California San Francisco, San Francisco, California, 94143, USA

For all author emails, please log on.

BMC Microbiology 2011, 11:216  doi:10.1186/1471-2180-11-216

Published: 29 September 2011

Additional files

Additional file 1:

Table S1. CSV formatted table of gene validation results, corresponding to the classification n Figure 7. Columns: gene - GSC predicted gene name, NAm1ortholog - BROAD gene name for the INPARANOID identified ortholog in H. capsulatum WU24, repeat, wgtaValid, exprValid, and orthoValid - 1 if a gene was classified as repeat or validations by tiling, expression, or homology respectively; 0 otherwise. Sequences (G217B_predicted.fasta) and gene structures (G217B_predicted.gff3) of the GSC predictions are mirrored at http://histo.ucsf.edu/downloads/ webcite.

Format: CSV Size: 668KB Download file

Open Data

Additional file 2:

Table S2. CSV formatted table giving GSC predicted gene names corresponding to H. capsulatum G217B genes referenced in the text. As noted in the results section, the predicted gene structures are not necessarily identical to experimentally characterized transcripts.

Format: CSV Size: 1KB Download file

Open Data

Additional file 3:

Table S3. GFF3 formatted (tab delimited) table of detected TAR genomic coordinates. Coordinates are given relative to the 11/30/2004 GSC G217B assembly, which is mirrored at http://histo.ucsf.edu/downloads/F_HCG217B.fasta.041130.gz webcite.

Format: GFF3 Size: 474KB Download file

Open Data

Additional file 4:

Data S4. WIG formatted plus strand tiling probe intensities mapped to the 11/30/2004 GSC G217B assembly, suitable for viewing in Gbrowse2 http://gmod.org/wiki/GBrowse webcite.

Format: WIG Size: 8.7MB Download file

Open Data

Additional file 5:

Data S5. WIG formatted minus strand tiling probe intensities mapped to the 11/30/2004 GSC G217B assembly, suitable for viewing in Gbrowse2 http://gmod.org/wiki/GBrowse webcite.

Format: WIG Size: 8.7MB Download file

Open Data

Additional file 6:

Data S6. FASTA formatted DNA sequences for the 264 novel TARs. Coordinates relative to the 11/30/2004 GSC G217B assembly are given in the FASTA header lines.

Format: FASTA Size: 282KB Download file

Open Data