ddRADseq data of California Gnatcatcher (Polioptila californica) - SRA

SRX15660509: ddRADseq data of California Gnatcatcher (Polioptila californica)
1 ILLUMINA (Illumina HiSeq 4000) run: 5.2M spots, 497.5M bases, 158.8Mb downloads

Design: We collected ddRADseq data using the Peterson et al. 2012 protocol modified to use separate indexing reads. We digested genomic DNA with EcoRI and MseI (New England Biolabs) in a single reaction and used Solid Phase Reversible Immobilization (SPRI) beads (Beckman Coulter) to purify the digestions prior to ligating 10 uniquely bar-coded adapters with T4 ligase (New England Biolabs). Libraries were size-selected between 250 and 400 base pairs (bp) using a Pippin Prep size fractionator (Sage Science). The final library amplification used proofreading Taq and Illumina's indexed primers. The fragment size distribution and concentration of each pool was determined on an Agilent Bioanalyzer and qPCR was performed to determine library concentrations. Sequencing was conducted on two lanes of an Illumina HiSeq 4000 at the Genomics and Cell Characterization Core Facility at the University of Oregon.

Submitted by: United States Geological Survey

Study: California gnatcatcher, Polioptila californica, restriction site-associated DNA sequencing data (ddRADseq) throughout California, USA (2012-2013) and Baja California, Mexico (2018-2019)

PRJNA844114 • SRP379425 • All experiments • All runs

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These data were collected to assess the distribution of genetic diversity within and among occurrences of the endangered California Gnatcatcher (Polioptila californica) and explore its evolutionary relationship to recognized subspecific with adjacent distribution in Baja California, using genome-wide genetic markers. The dataset archived herein can be used to further investigate evolutionary or ecological processes that affect these sampled occurrences of Polioptila californica, or they may be used to reconfirm the patterns reported in Vandergast et al. 2022 (see Larger Work Citation).

Sample: ddRADseq data of Polioptila californica

SAMN28789850 • SRS13359178 • All experiments • All runs

Organism: Polioptila californica californica

Library:

Name: Library_SD03

Instrument: Illumina HiSeq 4000

Strategy: RAD-Seq

Source: GENOMIC

Selection: Reduced Representation

Layout: SINGLE

Runs: 1 run, 5.2M spots, 497.5M bases, 158.8Mb

Run	# of Spots	# of Bases	Size	Published
SRR19609595	5,236,692	497.5M	158.8Mb	2022-06-17

ID:: 22281827

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