Ultraconserved element target capture of Holhymenia tibialis - SRA

SRX5995160: Ultraconserved element target capture of Holhymenia tibialis
1 ILLUMINA (Illumina HiSeq 3000) run: 3.4M spots, 682.5M bases, 288.6Mb downloads

Design: Genomic DNA was extracted using a 1) Gentra Puregene Tissue, 2) Qiagen DNeasy Blood and Tissue kit (see Forthman et al., 2019), or 3) Qiagen DNeasy Blood and Tissue kit coupled with Qiagen QIAquick PCR purification kit (see Knyschov et al., 2019). Libraries were constructed from genomic DNA following Forthman et al. (2019). Cleaned, amplified libraries were quantified with Qubit and subsequently combined in equimolar amounts into 1000 ng pools. A custom MYbaits kit containing a subset of Hemiptera UCE probes designed from pentatomomorphan species (Faircloth, 2017) was used for target enrichment. The hybridization mixture used half volume baits (2.75 uL) with 2.75 uL molecular-grade water. For some samples, we followed Forthman et al. (2019) enrichment protocol (TE protocol), while others were subjected to a modified version of the protocol (TE-touchdown protocol). For the TE protocol, a baits were hybridized with each library pool at 65C for 1624 hours. In the TE-touchdown protocol, baits were to hybridize with library pools at 65C for 18 hours followed by 18 hours at 62C. However, samples were prematurely removed during the TE-touchdown protocol before hybridization was complete. At the recommendation of Arbor Biosciences, we added an additional 2.75 uL baits to these samples and re-ran the hybridization protocol to completion. Bait-target hybrids were bound to Dynabeads M-280 Streptavidin beads, washed, and resuspended in 30 uL IDTE. 2.5 uL each of 5 uM iTru P5/P7 primers (Glenn et al., 2016) for the post-capture PCR amplification mix. 14-17 cycles of post-capture amplification were performed, followed by cleaning. Enriched library pools were pooled in equimolar amounts and sequenced using a single Illumina HiSeq3000 lane (2x100 run) at the University of Florida Interdisciplinary Center for Biotechnology Research (ICBR).

Submitted by: University of Florida

Study: Phylogenomic analysis of the Coreinae

PRJNA546248 • SRP200892 • All experiments • All runs

show Abstracthide Abstract

Phylogenomic analysis of the specious leaf-footed bug subfamily Coreinae (Hemiptera: Heteroptera: Coreidae) using ultraconserved element loci

Sample:

SAMN11956941 • SRS4900069 • All experiments • All runs

Organism: Holhymenia tibialis

Library:

Name: Holhymenia tibialis CMF0801

Instrument: Illumina HiSeq 3000

Strategy: Targeted-Capture

Source: GENOMIC

Selection: Reduced Representation

Layout: PAIRED

Runs: 1 run, 3.4M spots, 682.5M bases, 288.6Mb

Run	# of Spots	# of Bases	Size	Published
SRR9224654	3,378,894	682.5M	288.6Mb	2020-12-01

ID:: 8037558

SRA

Sequence Read Archive

Result Filters

Send to:

Supplemental Content

Related information

Search details

Recent activity