### Data
For further information, please contact: (__hoelzer__ dot __martin__ at __gmail__ dot __com__).
Here, we provide data accompanying our transcriptomic study of the innate immune response of the "microbat" _Myotis daubentonii_ (suborder _Yangochiroptera_). We stimulated _M. daubentonii_ cells either with a strong IFN inducer virus (RVFV Clone 13) or with type I IFN and harvested total RNA in triplicates at two time points (6h, 24h) post infection.
Details can be found in our manuscript:
[Hölzer, M., Schoen, A., Wulle, J., Müller, M.A., Drosten, C., Marz, M., Weber, F., Virus- and interferon alpha-induced transcriptomes of cells from the microbat _Myotis daubentonii_,
iScience 19, 647-661 (2019)](https://doi.org/10.1016/j.isci.2019.08.016)
The raw RNA-Seq reads (Illumina HiSeq2500, single-end, 50bp) can be found here:
[Gene Expression Omnibus: GSE12130](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE121301)
Our manuscript is further accompanied by a [electronic supplement](https://www.rna.uni-jena.de/supplements/mda/) including an [interactive gene observer](https://www.rna.uni-jena.de/supplements/mda/report.html). The full electronic supplement can be also downloaded here: ``supp_mda.zip``
__We provide the following data:__
* the combined _M. lucifugus_ (Myoluc2.0, release 86) and RVFV (NC014397.1, NC014395.1, NC014396.1) genome used for mapping (`fasta`)
* the extended Ensembl annotation for _M. lucifugus_ (based on Ensembl Myoluc2.0, release 86) (`gtf`)
* the 18 processed (trimmed and rRNA-cleaned) short-reads used for mapping (`fastq`)
* mappings and indices of all 18 samples produced by [STAR](https://github.com/alexdobin/STAR) vs. the concatenated _M. lucifugus_ and RVFV genome (`bam`, `bai`)
* unique (and multiple) read countings produced by [featureCounts](http://subread.sourceforge.net/) and correspodning TPM values (`txt`)
* _de novo_ transcriptome assemblies of combined triplicates with [Trinity](https://github.com/trinityrnaseq/trinityrnaseq/wiki) (`fasta`)
* a multi-tool _de novo_ transcriptome assembly of all 18 combined RNA-Seq samples combining the output of [SPAdes](http://cab.spbu.ru/software/spades/) in RNA and single-cell mode, [Trinity](https://github.com/trinityrnaseq/trinityrnaseq/wiki), and [SOAPdenovo-Trans](http://soap.genomics.org.cn/SOAPdenovo-Trans.html) (`fasta`)
_Please check our manuscript for details._
__Fig. 1__: Workflow of the experiments and analyses to measure the _M. daubentonii_ transcriptomes in response to virus and IFN.
If you use our data, please cite:
[Hölzer, M., Schoen, A., Wulle, J., Müller, M.A., Drosten, C., Marz, M., Weber, F., Virus- and interferon alpha-induced transcriptomes of cells from the microbat _Myotis daubentonii_,
iScience 19, 647-661 (2019)](https://doi.org/10.1016/j.isci.2019.08.016)
