Multilocus Sequence Data Collection

Multilocus sequence data were collected at the Center for Anchored Phylogenomics at Florida State University (www.anchoredphylogeny.com) following Lemmon et al. [41 (link)] with some adjustments. Each genomic DNA sample was sonicated to a fragment size of ~175–300 bp using a Covaris E220 Focused-ultrasonicator with Covaris microTUBES. Library preparation and indexing followed Meyer and Kircher [49 (link)]. Indexed libraries were pooled at equal quantities (12 pools of 16 samples each), and the library pools were enriched using a custom Agilent Custom SureSelect kit (Agilent Technologies), with probes designed as described above. The 12 enriched library pools were pooled with equal quantities for sequencing on 4 PE150 Illumina HiSeq2000 lanes with 8 bp indexing. Sequencing was performed at Florida State University in the College of Medicine Translational Science Laboratory.

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Stout C.C., Tan M., Lemmon A.R., Lemmon E.M, & Armbruster J.W. (2016). Resolving Cypriniformes relationships using an anchored enrichment approach. BMC Evolutionary Biology, 16, 244.

Publication 2016

E220 Focused-ultrasonicator microTUBES Agilent Custom SureSelect kit HiSeq2000

Genomic Library Translational

Corresponding Organization : Auburn University

Other organizations : Florida State University

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Variable analysis

independent variables

Fragmentation of genomic DNA samples to a size of ~175–300 bp using a Covaris E220 Focused-ultrasonicator with Covaris microTUBES
Library preparation and indexing using the protocol described in Meyer and Kircher [49]
Enrichment of indexed libraries using a custom Agilent Custom SureSelect kit with probes designed as described

dependent variables

Sequencing of the 12 enriched library pools on 4 PE150 Illumina HiSeq2000 lanes with 8 bp indexing

control variables

Pooling of indexed libraries at equal quantities (12 pools of 16 samples each)
Pooling of the 12 enriched library pools at equal quantities for sequencing

controls

No positive or negative controls were explicitly mentioned in the provided information.

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