Data Upload and Annotation

FastBMD accepts tab-delimited text files (.txt) that contain a matrix of gene expression values as input. There is a standard format that needs to be followed - see the Data Upload section of the FAQs for more details.

Bromobenzene (rats; microarray)
This dataset demonstrates how FastBMD can be used to analyze microarray data from a well-annotated species. (DOI 10.1007/s00204-016-1886-5)
Chemical: Bromobenzene (CAS number: 108-86-1). Doses: 25, 100, 200, 300, and 400 mkd. Tissue: Liver. Organism Rattus norvegicus (F344 rats). Sex: Male. Duration: 2 weeks.
TCDD (Mouse; RNAseq)
This dataset demonstrates how FastBMD can be used to analyze RNA sequencing data from a well-annotated species. (DOI 10.1186/s12864-015-1527-z)
Chemical: TCDD (CAS number: ). Doses: 0.01, 0.03, 0.1, 0.3, 1, 3, 10, and 30 ug/kg. Tissue: Liver. Organism Mus musculus. Sex: Female. Duration: 4 weeks.
Trenbolone (Japanese medaka; microarray)
This dataset demonstrates how FastBMD can be used to analyze microarray data from an ecological species with limited genome annotation using the annotation-free pipeline. (DOI 10.1002/tox.22158)
Chemical: Trenbolone (CAS number: 10161-33-8). Doses: 2, 6, 20, 60, 100, and 200 ng/L. Tissue: Pooled whole larvae. Organism Larval Oryzias latipes (Japanese medaka). Sex: Both male and female. Duration: 7 days.
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