RAZOR Database: PCR Primers and Gel Electrophoresis Images

Name: RAZOR Database: PCR Primers and Gel Electrophoresis Images
Creator: figshare
Published: 2025-12-02 06:13:19
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DataCite Commons2025-12-02 更新2026-02-09 收录

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Overview Zipped contents for the RAZOR database. RAZOR is a catalog of predicted and experimentally-validated PCR and qPCR primers designed against 20 different respiratory viruses and was created at the Janga Lab at Indiana University Indianapolis. ContentsThe zip file contains: primers.tsv (file) | a delimited file of all RAZOR primers, including viral targets, genomic coordinates, sequences, and physiochemical metadata. Explanations for each column are provided in the Column Descriptions section below. razor_primers_filtered_pair_penalty_0.5.csv (file) | a subset of primers.tsv; filtered to include only primer pairs whose Primer3 pair penalty score is less than 0.5. Represents an optimal set of PCR primers. validated_primer_images (folder) | a folder of 8 gel electrophoresis images. Shows results for 4 SARS-CoV-2 PCR primers and 4 SARS-CoV-2 qPCR primers. Column Descriptionsid | the unique id of the PCR primer pair accession | NCBI accession code for the target virusvirus_genome_abbreviated_name | short unique identifier for the virus namevirus_genome_full_name | complete name of the virusvirus_genome_isolate | isolate of the virus genome_length | length of the virus genome (nt)product_start | genomic start coordinate of the PCR product (amplicon)product_end | end coordinate of the PCR product product_size | length of the PCR product (nt)product_melting_temp | melting temperature of the PCR product (°C)primer_pair_self_complementarity_anywhere | Tendency of forward and reverse PCR primers to bind to each other at any position in the primer sequencesprimer_pair_self_complementarity_3' | Tendency of forward primer to bind reverse in its 3' regionannealing_temp | temperature at which both primers bind to the template sequence (°C)primer_pair_tm_difference | difference in forward and reverse primer melting temperatures (°C)primer_pair_penalty_score | Primer3 weighted penalty score for forward - reverse primer pairforward_primer_start | start coordinate of the forward primerforward_primer_end | end coordinate of the forward primerforward_primer_size | length of the forward primer (nt)forward_primer_seq | sequence of the forward primer forward_primer_melting_temp | melting temperature of the forward primer (°C)forward_primer_gc% | Guanine (G) - Cytosine (C) content of the forward primer sequence (%)forward_primer_self_complementarity_anywhere | Tendency of the forward primer to self-bind anywhereforward_primer_self_complementarity_3' | Tendency of the forward primer to self-bind in its 3' regionforward_primer_hairpin_stability | Penalty weight of the most stable expected forward primer hairpin structureforward_primer_delta_g | Gibbs free energy required to break the most stable expected forward primer hairpin structure (kJ/mol)forward_primer_penalty_score | Primer3 penalty score for the forward primerreverse_primer_start | start coordinate of the reverse primerreverse_primer_end | end coordinate of the reverse primer reverse_primer_size | length of the reverse primer (nt)reverse_primer_seq | sequence of the reverse primerreverse_primer_melting_temp | melting temperature of the reverse primer (°C)reverse_primer_gc% | Guanine (G) - Cytosine (C) content of the reverse primer sequence (%)reverse_primer_self_complementarity_anywhere | Tendency of the reverse primer to self-bind anywherereverse_primer_self_complementarity_3' | Tendency of the reverse primer to self-bind in its 3' regionreverse_primer_hairpin_stability | Penalty weight of the most stable expected reverse primer hairpin reverse_primer_delta_g | Gibbs free energy required to break the most stable expected reverse primer hairpin structure (kJ/mol)reverse_primer_penalty_score | Primer3 penalty score for the reverse primerexperimental_validation | bool indicating whether or not the predicted primer pair has been experimentally validatedexperimal_validation_image | gel electrophoresis image or an equivalent demonstrating the experimental validation of the PCR primer pair validation_group | the organization credited for the validation experiment

数据集概览 本文件为RAZOR数据库的压缩打包内容。RAZOR数据库是针对20种不同呼吸道病毒设计的、经预测与实验验证的聚合酶链式反应（PCR）及实时定量聚合酶链式反应（qPCR）引物目录，由印第安纳波利斯印第安纳大学Janga实验室构建。 数据集内容 该压缩包包含以下文件与文件夹： primers.tsv | 涵盖所有RAZOR引物的分隔符格式文件，包含病毒靶标、基因组坐标、序列及理化元数据。各列的详细说明详见下文的列说明部分。 razor_primers_filtered_pair_penalty_0.5.csv | primers.tsv的子集文件，仅筛选出Primer3引物对罚分分值低于0.5的引物对，代表一套最优的PCR引物组合。 validated_primer_images（文件夹） | 包含8张凝胶电泳图像的文件夹，展示了4种严重急性呼吸综合征冠状病毒2（SARS-CoV-2）PCR引物及4种SARS-CoV-2 qPCR引物的实验结果。 列说明 id | PCR引物对的唯一标识符 accession | 靶标病毒的美国国家生物技术信息中心（NCBI）登录号 virus_genome_abbreviated_name | 病毒名称的简短唯一标识符 virus_genome_full_name | 病毒的完整名称 virus_genome_isolate | 病毒分离株 genome_length | 病毒基因组长度（单位：核苷酸，nt） product_start | PCR扩增产物（扩增子，amplicon）的基因组起始坐标 product_end | PCR扩增产物的基因组终止坐标 product_size | PCR扩增产物长度（单位：核苷酸） product_melting_temp | PCR扩增产物的解链温度（单位：摄氏度，°C） primer_pair_self_complementarity_anywhere | 正、反向PCR引物在引物序列任意位置发生互补结合的倾向 primer_pair_self_complementarity_3' | 正向引物在其3'端区域与反向引物发生互补结合的倾向 annealing_temp | 两条引物与模板序列结合的退火温度（单位：摄氏度） primer_pair_tm_difference | 正、反向引物解链温度的差值（单位：摄氏度） primer_pair_penalty_score | Primer3正、反向引物对的加权罚分分值 forward_primer_start | 正向引物的基因组起始坐标 forward_primer_end | 正向引物的基因组终止坐标 forward_primer_size | 正向引物长度（单位：核苷酸） forward_primer_seq | 正向引物的序列 forward_primer_melting_temp | 正向引物的解链温度（单位：摄氏度） forward_primer_gc% | 正向引物序列的鸟嘌呤（G）-胞嘧啶（C）含量（百分比） forward_primer_self_complementarity_anywhere | 正向引物自身在任意位置发生互补结合的倾向 forward_primer_self_complementarity_3' | 正向引物在其3'端区域发生自身互补结合的倾向 forward_primer_hairpin_stability | 正向引物最稳定预期发夹结构的罚分权重 forward_primer_delta_g | 破坏正向引物最稳定预期发夹结构所需的吉布斯自由能（单位：千焦每摩尔，kJ/mol） forward_primer_penalty_score | 正向引物的Primer3罚分分值 reverse_primer_start | 反向引物的基因组起始坐标 reverse_primer_end | 反向引物的基因组终止坐标 reverse_primer_size | 反向引物长度（单位：核苷酸） reverse_primer_seq | 反向引物的序列 reverse_primer_melting_temp | 反向引物的解链温度（单位：摄氏度） reverse_primer_gc% | 反向引物序列的鸟嘌呤（G）-胞嘧啶（C）含量（百分比） reverse_primer_self_complementarity_anywhere | 反向引物自身在任意位置发生互补结合的倾向 reverse_primer_self_complementarity_3' | 反向引物在其3'端区域发生自身互补结合的倾向 reverse_primer_hairpin_stability | 反向引物最稳定预期发夹结构的罚分权重 reverse_primer_delta_g | 破坏反向引物最稳定预期发夹结构所需的吉布斯自由能（单位：千焦每摩尔） reverse_primer_penalty_score | 反向引物的Primer3罚分分值 experimental_validation | 布尔型字段，用于标识该预测引物对是否经过实验验证 experimal_validation_image | 用于展示该PCR引物对实验验证结果的凝胶电泳图像或等效验证图像 validation_group | 负责该验证实验的机构

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figshare

创建时间：

2025-09-23