Screening Coral Tissue Samples (Colpophyllia natans) Collected From the Florida Keys Using a Quantitative Polymerase Chain Reaction (qPCR) Antibiotic Resistance Gene Microarray – Raw Data

The files in this data release are those referenced in the journal article by Neely and others (2026) entitled “Assessment of antibiotic resistance genes in Caribbean corals, including those treated with amoxicillin.” They represent the raw fluorescence data and threshold cycle (Ct) data generated from quantitative polymerase chain reaction (qPCR) microarray runs using deoxyribonucleic acid (DNA) extractions from 12 coral (Colpophyllia natans) samples as templates. These files are produced by the Applied Biosystems StepOnePlus™ Real-Time PCR System Software (version 2.2.2). The coral tissue samples were collected on November 17th, 2022, from Cheeca Rocks in the Florida Keys from depths ranging from 9 to 13 feet (2.7 to 4.0 meters). The samples were collected for the purpose of determining whether there is a higher incidence or diversity of microbial antibiotic resistance genes (ARG) in corals that have previously been treated for stony coral tissue loss disease (SCTLD) with amoxicillin base2B as compared to untreated coral. Tissue samples were preserved in RNAlater, and frozen until shipped for processing.

The frozen coral samples were sent from Nova Southeastern University (Fort Lauderdale, Florida) and received on November 23rd 2022, by the U.S. Geological Survey St. Petersburg Coastal and Marine Science Center (USGS SPCMSC) Coral Microbial Ecology Laboratory in St. Petersburg, Florida (FL), USA, and immediately frozen at minus twenty degrees Celsius (-20°C) until processing. Microbial DNA extractions from the coral samples were performed on December 13th, 2022, using a Qiagen Dneasy PowerBiofilm kit. All qPCR runs were performed between January and February 2023 on an Applied Biosystems StepOnePlus™ Real-Time PCR System, using Qiagen Microbial DNA qPCR Arrays ARG (BAID-1901ZRC-24), and data files were exported as Microsoft Excel files (.xls) and converted into comma-separated values (.csv) files. The data files were then edited to remove columns that contained no values, or that did not apply to this dataset.

Neely, K.L., Kellogg, C.A., Voelschow, J.J., Cauvin, A.R., Reed, S.A.M., Rubin, E., and Meyer, J.L., 2026, Assessment of antibiotic resistance genes in Caribbean corals, including those treated with amoxicillin: Coral Reefs, https://doi.org/10.1007/s00338-026-02832-z.

本数据集发布包含的全部文件，均对应Neely及其合作者2026年发表于学术期刊的论文《加勒比珊瑚中抗生素抗性基因评估——含阿莫西林处理组珊瑚》。该数据集涵盖以12份珊瑚（Colpophyllia natans）样本的脱氧核糖核酸（deoxyribonucleic acid，DNA）提取物为模板，通过定量聚合酶链式反应（quantitative polymerase chain reaction，qPCR）微阵列实验获得的原始荧光数据与阈值循环（Ct）值数据。上述文件由应用生物系统公司（Applied Biosystems）StepOnePlus™ 实时荧光定量PCR系统软件（版本2.2.2）生成。
本次实验所用珊瑚组织样本采集于2022年11月17日，采样点为佛罗里达群岛的Cheeca Rocks海域，采样深度介于9至13英尺（2.7至4.0米）。本研究旨在对比经阿莫西林（amoxicillin base2B）处理的石珊瑚组织脱落病（stony coral tissue loss disease，SCTLD）患株，与未处理珊瑚体内微生物抗生素抗性基因（antibiotic resistance genes，ARG）的发生率及多样性差异。样本采集后以RNAlater试剂保存，并冷冻储存直至送样处理。

这批冷冻珊瑚样本由佛罗里达州劳德代尔堡的诺瓦东南大学寄出，于2022年11月23日被美国地质调查局圣彼得堡沿海与海洋科学中心（USGS SPCMSC）珊瑚微生物生态实验室接收，接收后即刻置于-20℃环境冷冻保存，直至开展实验处理。2022年12月13日，研究人员采用凯杰（Qiagen）Dneasy PowerBiofilm试剂盒完成所有珊瑚样本的微生物DNA提取。
所有qPCR实验于2023年1月至2月间，在Applied Biosystems StepOnePlus™ 实时荧光定量PCR系统上完成，所用芯片为Qiagen Microbial DNA qPCR Arrays ARG（BAID-1901ZRC-24）。数据文件最初以微软Excel（.xls）格式导出，随后转换为逗号分隔值（.csv）格式。后续研究人员对数据文件进行了编辑，移除了无有效数值或与本数据集无关的列。

参考文献：Neely, K.L.、Kellogg, C.A.、Voelschow, J.J.、Cauvin, A.R.、Reed, S.A.M.、Rubin, E.及Meyer, J.L.，2026年，《加勒比珊瑚中抗生素抗性基因评估——含阿莫西林处理组珊瑚》，《珊瑚礁》，https://doi.org/10.1007/s00338-026-02832-z.