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SRX22323348: ddRADseq of anolis sagrei: adult liver tissue
1 ILLUMINA (Illumina NovaSeq 6000) run: 9.5M spots, 892.9M bases, 310.3Mb downloads

Design: Whole specimens were formalin-fixed and livers dissected and preserved in 95% ethanol for DNA extractions. DNA was extracted from all tissues using a Qiagen DNeasy Blood and Tissue Kit (Qiagen, Inc.) and quantified using a Qubit dsDNA BR assay kit (Thermo Fisher, Waltham, MA). We prepared two genomic libraries following a modified double-digest RADseq (ddRAD) protocol of Peterson et al. (2012) (protocol in Barley et al. 2019): we digested 500 ng of each sample for 4 hours using the enzymes Sbfl and NlaIII. After ligation of the illumina adaptors, we pooled equimolar amounts of each samples that each had different adapter sequences and used AmpureX beads to purify the samples. We then quantified these using the Qubit dsDNA BR assay kit and and size selected for fragments between 375 and 475 bp using a Pippin Prep. We then ran PCR for 8-10 cycles using taq and the Illumina index primers for final library amplification. We quantified the final library concentration using the Qubit dsDNA HS assay kit. Prepared libraries were sent to the Oklahoma Medical Research Foundation at for sequencing on the NovaSeq platform, with one library per lane.
Submitted by: University of Hawaii
Study: Anolis sagrei Raw sequence reads
show Abstracthide Abstract
We sought to obtain representative sampling from the brown anoles native range, and a set of areas where large, introduced populations now occur. For the native range, we obtained samples from Cuba through museum loans (MVZ and MCZ) and from the Bahamas and Cayman Islands through a collaboration with Dr. Amber Wright. For the SE US introduced range (Florida and Alabama), we obtained samples through museum loans (LACMA, FLMNH, MVZ), and obtained samples from Tampa, FL through a collaboration with Dr. Amber Wright. Samples were collected in Orange County, California through previous survey efforts (Fisher et al. 2020). We surveyed and sampled the islands of Hawaii, Maui, Molokai, Lanai, Oahu, and Kauai in the Hawaiian Archipelago. In Hawaii, specimens were collected through survey efforts and sites were selected based on personal observations of the species presence or with the help of community science records on the iNaturalist platform. From our field collections, whole specimens were formalin-fixed and livers dissected and preserved in 95% ethanol for DNA extractions. DNA was extracted from all tissues using a Qiagen DNeasy Blood and Tissue Kit (Qiagen, Inc.) and quantified using a Qubit dsDNA BR assay kit (Thermo Fisher, Waltham, MA). We prepared two genomic libraries following a modified double-digest RADseq (ddRAD) protocol of Peterson et al. (2012) (protocol in Barley et al. 2019) and sequenced on an Illumina NovaSeq SP Lane (100SR, 10X chemistry), with one library per lane. We demultiplexed each sample using the process_radtags program in STACKS V.2.514 (Catchen et al. 2013).
Sample:
SAMN37951781 • SRS19373935 • All experiments • All runs
Organism: Anolis sagrei
Library:
Name: 354
Instrument: Illumina NovaSeq 6000
Strategy: RAD-Seq
Source: GENOMIC
Selection: size fractionation
Layout: SINGLE
Runs: 1 run, 9.5M spots, 892.9M bases, 310.3Mb
Run# of Spots# of BasesSizePublished
SRR266226219,498,727892.9M310.3Mb2024-06-01

ID:
30290819

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