Ixobrychus_dubius_AMNH_DOT17848_UCE - SRA

SRX9001799: Ixobrychus_dubius_AMNH_DOT17848_UCE
1 ILLUMINA (Illumina HiSeq 3000) run: 2.2M spots, 670.3M bases, 267.2Mb downloads

Design: We standardized our extractions by including 250 ng of DNA in a 50 L aliquots, which were subsequently fragmented with a Covaris S220 focus-ultrasonicator with the following settings: 175 W peak incident power, a duty factor of 2%, and 200 cycles per bust for 44-45 seconds. We targeted fragments of 500-600 bp in length. We then prepared libraries using Kapa Biosystems Library Hyper Prep Kits (# KK2602), following manufacturers protocol, with some minor modifications: 25 l per sample, at a concentration of 10 ng/l, was subjected to end repair and A-tailing on a thermal cycler, followed by the ligation of two universal iTru stubs (iTru Stub Oligo 1 & iTru Stub Oligo 2) and incorporation of iTru dual-indexes (Glenn et al. 2016). Following ligation, we purified samples with Agencourt AMPure XP beads, at a volume of 0.8X. We then amplified libraries using the manufacturers recommended PCR protocol, which included 10 cycles for the denaturation, annealing, and extension steps. We then performed an additional 1X Agencourt AMPure XP bead cleanup, followed by a quantification of the amplified libraries using a Qubit dsDNA HS Assay Kit on a Qubit 2.0 Fluorometer (Life Technologies). Pools of eight amplified libraries were then grouped and enriched for 5,060 UCE loci using 5,742 baits in the MYbaits Tetrapods-UCE-5kv1-96 library capture kit (sequences available at ultraconserved.org) (Faircloth et al. 2012), following the Mycroarray myBaits 3.01 Kit manufacturers protocol. After enrichment, we subsequently amplified capture-reaction products using 18 PCR cycles, followed by a 1.2X Agencourt AMPure XP bead cleanup. Lastly, we quantified enriched, pooled libraries using a Qubit dsDNA HS Assay Kit on a Qubit 2.0 Fluorometer (Life Technologies). Prior to sequencing, pools consisting of equimolar libraries were combined.

Submitted by: Texas Tech University

Study: Herons (Aves:Ardeidae) Raw sequence reads

PRJNA658323 • SRP278663 • All experiments • All runs

show Abstracthide Abstract

Species-level phylogeny using ultraconserved elements (UCEs).

Sample:

SAMN15872376 • SRS7267303 • All experiments • All runs

Organism: Ixobrychus dubius

Library:

Name: Targeted enrichment of Ixobrychus_dubius_AMNH_DOT17848 UCEs

Instrument: Illumina HiSeq 3000

Strategy: Targeted-Capture

Source: GENOMIC

Selection: Reduced Representation

Layout: PAIRED

Runs: 1 run, 2.2M spots, 670.3M bases, 267.2Mb

Run	# of Spots	# of Bases	Size	Published
SRR12511054	2,219,649	670.3M	267.2Mb	2021-09-30

ID:: 11698613

SRA

Sequence Read Archive

Result Filters

Send to:

Supplemental Content

Related information

Search details

Recent activity