|Aspergillus fumigatus Datasets|
|Source: Data supplied to AspGD by Natalie Fedorova, JCVI. This project has been funded in whole or part with federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services under contract numbers N01-AI30071 and / or HHSN272200900007C.|
|Notes: A. fumigatus isolates: 4 "reference" and 19 "target" Aspergillus fumigatus strains have been sequenced using the Illumina platform. The list of sequenced strains includes (i) 7 drug resistant isolates, selected to facilitate the identification of new mechanisms of antifungal drug resistance (F series); (ii) 12 genotypically linked isolates from 2 hospital outbreaks, included to validate the discriminatory power of existing genotyping markers (B series).
SRA submission and metadata can be found here:
For SNP analysis, the following parameters were used:
This reference file used in the alignments (also available for download from link below, AF293_REF.fasta) is the same sequence that was submitted to GenBank:
To remove false positives, the VCFs were further filtered using the following parameters:
The GFF files corresponding to each VCF file were generated at AspGD by converting formats and mapping scaffolds to chromosomes.
|DOWNLOAD these data from AspGD:|
Reference sequence used in the alignments
Fedorova, N., et al.
|Aspergillus oryzae Datasets|
|Wang et al., 2010|
|Source: A. oryzae RNA-Seq was performed by Wang B, Guo G, Wang C, Lin Y, Wang X, Zhao M, Guo Y, He M, Zhang Y, and Pan L, at the School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, Guangdong, China. Data were downloaded from NCBI by AspGD.|
|Notes: This A. oryzae RNA-Seq dataset is published in:|
Wang B, et al. 2010.
Data were downloaded from NCBI:
This publicly available A. oryzae RNA-Seq dataset comprises eight experiments. Paired-end RNA-sequencing (RNA-Seq), using the Illumina platform, was conducted on polyadenylated-enriched mRNA isolated from four different culture conditions.
|DOWNLOAD these data from AspGD:|
Wang B, Guo G, Wang C, Lin Y, Wang X, Zhao M, Guo Y, He M, Zhang Y, Pan L. Survey of the transcriptome of Aspergillus oryzae via massively parallel mRNA sequencing. Nucleic Acids Res. 2010 Aug;38(15):5075-87. Epub 2010 Apr 14.
|If you would like to suggest datasets or
citations to add to this list,
please send a
message to AspGD curators with details.|
|Return to AspGD||Send a Message to the AspGD Curators|
AspGD Copyright © 2008-2013 The Board of Trustees, Leland Stanford Junior University, and Broad Institute.
Permission to use the information contained in this database was given by the researchers/institutes who contributed or published the information. Users of the database are solely responsible for compliance with any copyright restrictions, including those applying to the author abstracts. Documents from this server are provided "AS-IS" without any warranty, expressed or implied.
To cite AspGD, please use the following reference: Cerqueira GC, Arnaud MB, Inglis DO, Skrzypek MS, Binkley G, Simison M, Miyasato SR, Binkley J, Orvis J, Shah P, Wymore F, Sherlock G, Wortman JR (2013). The Aspergillus Genome Database (AspGD): multispecies curation and incorporation of RNA-Seq data to improve structural gene annotations. Nucleic Acids Res. 42(Database issue):D705-D710; see How to cite AspGD.