[ensembl-dev] Mouse reference genome

Ben Moore bmoore at ebi.ac.uk
Thu Sep 28 13:08:03 BST 2017


Hi Pankaj,

Yes, the mouse reference genome assembly presented in Ensembl is based on the C57BL/6J strain:
http://www.ensembl.org/Mus_musculus/Info/Annotation <http://www.ensembl.org/Mus_musculus/Info/Annotation>

The genome assembly is called GRCm38 as was produced by the Genome Reference Consortium (GRC):
https://www.ncbi.nlm.nih.gov/grc/mouse <https://www.ncbi.nlm.nih.gov/grc/mouse>

Best wishes

Ben
Ensembl Helpdesk


> On 28 Sep 2017, at 12:38, Pankaj Agarwal <p.agarwal at duke.edu> wrote:
> 
> Hi,
> I was writing to ask if the mouse reference genome is based on the Black 6 (C57BL/6J) strain or some other or it is a combination.
> There is a cell line genomic data set from C57BL/6J strain that I need to align to the reference and I wanted to check if the latest available reference in Ensembl would be the best.
> Thanks,
> - Pankaj
>  
> -----------------------------
> Pankaj Agarwal, M.S
> Bioinformatician
> Data Analyst
> Applied Therapeutics
> Div. of Surgical Sciences
> Dept. of Surgery
> Duke University
> M: 919-244-6389
> O: 919-681-2251
> p.agarwal at duke.edu <mailto:p.agarwal at duke.edu>
>  
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Ben Moore
Ensembl Outreach Officer

European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge
CB10 1SD
UK

bmoore at ebi.ac.uk
+44 (0)1223 494265

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