ddRAD-seq of Microcebus myoxinus: Sample JMR077 - SRA

Links from BioSample

SRX1728086: ddRAD-seq of Microcebus myoxinus: Sample JMR077
2 ILLUMINA (NextSeq 500) runs: 14.5M spots, 2.1G bases, 1.1Gb downloads

Design: ddRAD-seq. Restriction-site-associated DNA libraries were prepared following the methods of Peterson et al. 2012 and Blair et al. 2015. Briefly, starting DNA was digested with restriction enzymes (SphI and MluCI) and ligated to modified Illumina P1 & P2 adapters containing 5bp unique barcodes. A pool of 30 individuals was size selected to 525bp by Pippin Prep (Sage Science). The pool was paired-end sequenced (150 bp) on an Illumina NextSeq 550. The software package trimmomatic (http://www.usadellab.org/cms/?page=trimmomatic) was used to curate the data for overall quality, with the requirement that 80% of a sequence read contain a q-score of 20 or higher. Paired-End reAd mergeR (http://sco.h-its.org/exelixis/web/software/pear/) was used to identify overlapping paired end reads, which were then discarded from further analysis. The process_radtags module of Stacks (http://catchenlab.life.illinois.edu/stacks/) was used for demultiplexing. Only the demultiplexed read 1 data was used for analysis and is uploaded here as a single read.

Submitted by: Duke University

Study: Double-digest Restriction-site associated DNA sequencing (ddRAD-seq) of wild mouse lemurs (genus Microcebus)

PRJNA318921 • SRP073945 • All experiments • All runs

show Abstracthide Abstract

We generated ddRAD-seq data from several species of Madagascar's mouse lemurs (genus Microcebus) to investigate their evolutionary histories. ddRAD-seq was conducted with enzymes SphI and MluCIon 30 samples across 6 species within the genus Microcebus (M. berthae, M. lehilahytsara, M. marohita, M. mittermeieri, M. myoxinus, and M. rufus). Previously these species had only been sequenced at a handful of nuclear and mitochondrial loci. Whole genome RAD-seq data will serve to elucidate speciation processes within the genus and will help to elucidate phylogeographic patterns within Madagascar.

Sample: Microcebus myoxinus JMR077

SAMN04875715 • SRS1412876 • All experiments • All runs

Organism: Microcebus myoxinus

Library:

Name: JMR077

Instrument: NextSeq 500

Strategy: WGS

Source: GENOMIC

Selection: Restriction Digest

Layout: SINGLE

Runs: 2 runs, 14.5M spots, 2.1G bases, 1.1Gb

Run	# of Spots	# of Bases	Size	Published
SRR3496221	8,458,091	1.2G	635.6Mb	2016-06-09
SRR3496251	6,088,050	867.1M	464.2Mb	2016-06-09

ID:: 2472635

SRA

Sequence Read Archive

Result Filters

Send to:

Links from BioSample

Supplemental Content

Related information

Recent activity