Target enrichment of UCEs and exons from Hypocnemis striata (Hypmis_s... - SRA

SRX9044780: Target enrichment of UCEs and exons from Hypocnemis striata (Hypmis_strata_LSUMZ78142)
1 ILLUMINA (Illumina HiSeq 3000) run: 2.7M spots, 553.1M bases, 216.5Mb downloads

Design: We extracted whole genomic DNA from frozen tissues using standard methods and kits (Qiagen, Valencia, CA). Toepad DNA was extracted using a similar strategy, but in an ancient DNA lab where contamination risks were minimized (detailed protocol available at https://github.com/mgharvey/tyranni). We quantified DNA extracts using a Qubit fluorometer and sent them to Rapid Genomics (Gainesville, FL) for library preparation and sequence capture following the general protocol of Faircloth et al. 2012. This protocol involves fragmenting the genomic DNA, ligating barcoded Illumina-compatible adapters, PCR amplification, probe hybridization, and enrichment of hybridized fragments.

Submitted by: Louisiana State University

Study: Targeted enrichment of ultraconserved elements and exons from suboscine passerines

PRJNA655842 • SRP279468 • All experiments • All runs

show Abstracthide Abstract

The tropics are the source of most biodiversity, yet inadequate sampling obscures answers to fundamental questions about how this diversity evolves. We leverage sampling assembled over decades of fieldwork to study diversification of the largest tropical bird radiation, suboscine passerines, by collecting sequence data using targeted enrichment of 2,389 genomic regions (2,321 UCEs and 96 exons) from 1,940 individuals of 1,287 species.

Sample:

SAMN15864769 • SRS7295041 • All experiments • All runs

Organism: Hypocnemis striata

Library:

Name: Hypmis_strata_LSUMZ78142

Instrument: Illumina HiSeq 3000

Strategy: WGS

Source: GENOMIC

Selection: Hybrid Selection

Layout: PAIRED

Runs: 1 run, 2.7M spots, 553.1M bases, 216.5Mb

Run	# of Spots	# of Bases	Size	Published
SRR12555798	2,737,949	553.1M	216.5Mb	2020-12-10

ID:: 11751451

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