title: mtGenome of Ursus spelaeus
design: ancient DNA was extracted according to the method described by Dabney and colleagues. DNA extracts were converted into double-indexed Illumina libraries using the approaches described in Meyer & Kircher 2010 and Kircher et al. 2012. All extractions and pre-amplification steps of the library preparation were performed in a designated ancient DNA clean room facility. Indexed libraries were amplified in 100 l reactions with AccuPrime Pfx and Herculase II Fusion followed by purification. Target enrichment of mitochondrial DNA was performed by in-solution capture of the pooled libraries using baits generated from modern polar bear (Ursus maritimus) mitochondrial DNA as described by Furtwngler and colleagues. Finally, the enriched libraries were multiplex sequenced on an Illumina HiSeq 4000 using 75+8+8 cycles at the Max Planck Institute for Science of Human History, Jena, Germany.