Plant genome dna extraction kit

Manufactured by Tiangen Biotech

Sourced in China

The Plant Genome DNA Extraction Kit is a laboratory equipment designed for the isolation and purification of genomic DNA from a variety of plant species. The kit provides a simple and efficient method for extracting high-quality DNA suitable for further molecular biology applications, such as PCR, sequencing, and genotyping.

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Lab products found in correlation

Hiseq platform, by Illumina (2 mentions) Nanodrop 2000, by Thermo Fisher Scientific (2 mentions) Mgiseq 2000rs, by MGI Tech (1 mentions) Truseq dna pcr free sample preparation kit, by Illumina (1 mentions) Hiseq 2500 sequencer, by Illumina (1 mentions)

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Plant Genome Extraction Kit Plant Genome DNA Kit Genome DNA Extraction Kit Genome extraction kit DNA extraction kit

7 protocols using plant genome dna extraction kit

QTL Mapping for Brassica napus Traits

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A total of 217 F₂ individuals were investigated, of which 30 individuals with WP and YP were selected for BSA. The genomic DNA of selected individuals was extracted using a Plant Genome DNA Extraction Kit (Tiangen, Beijing, China) and balanced–mixed to construct the two pools of WP and YP. The WP and YP then underwent next-generation sequencing (NGS, MGISEQ-2000RS, MGI Tech Co., Ltd., Shenzhen, China) together with the genomic DNA of 16214 and 16287, respectively.
The raw data were filtered and mapped to the Darmor_bzh B. napus genome using Bowtie2 software [56 (link)]. The significant loci were mapped to the ZS11 genome with a higher sequenced quality ZS11 genome released [57 (link)]. The SNPs and InDels between 16214 and 16287 were filtered using Genome Analysis Toolkit software [58 (link)], and the SNP index as well as the Δ(SNP-index) of the WP and YP were calculated subsequently. The AGR was defined according to the average value of Δ(SNP-index), the sliding window was set as 1 Mb, and the step size was set as 1 kb. A threshold significance of 0.99 was selected.

Ding Y., Li H., Liu X., Cheng X., Chen W., Wu M., Chen L., He J., Chao H., Jia H., Fu C, & Li M. (2024). Multi-Omics Analysis Revealed the AGR-FC.C3 Locus of Brassica napus as a Novel Candidate for Controlling Petal Color. Plants, 13(4), 507.

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Microbiome Profiling by 16S Amplicon Sequencing

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Total DNA was extracted from swab samples by Plant Genome DNA Extraction Kit (Tiangen Biotech Co., Ltd., Beijing.,China). 16S rDNA amplicon sequencing was performed on the Illumina HiSeq2500 sequencer (Illumina, Inc., San Diego, CA, US). Sequencing libraries were generated using TruSeq® DNA PCR-Free Sample Preparation Kit (Illumina, Inc., San Diego, CA, United States). Using FLASH v1.2.7 and QIIME v1.7.0, the high-quality clean tags from the raw sequence data were obtained (Caporaso et al., 2010 (link)). Chimeras were removed using UCHIME algorithm (Edgar et al., 2011 (link)). Using Uparse v7.0.1001 (with default sequence similarity of 97%), Operational Taxonomic Units (OTU) classification was determined (Edgar, 2013 (link)). The raw sequencing datasets are available at NCBI SRA repository (accession PRJNA942587).

Zhang M., Ma Y., Xu H., Wang M, & Li L. (2023). Surfaces of gymnastic equipment as reservoirs of microbial pathogens with potential for transmission of bacterial infection and antimicrobial resistance. Frontiers in Microbiology, 14, 1182594.

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Quantifying Vibrio parahaemolyticus in Shrimp

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To explore the dynamic changes in V. parahaemolyticus in shrimp, DNA from the hepatopancreas samples was extracted using the Plant Genome DNA Extraction Kit (TIANGEN, Beijing, China) according to the manufacturer’s protocols. The concentration and purity of DNA was measured by NanoDrop 2000 (Thermo Fisher Scientific, Waltham, MA, USA), and the DNA integrity was measured by 1% agarose gel electrophoresis. Then, the extracted DNA was screened for the presence of the PirA^Vp sequence using the TaqMan-probe fluorescence real-time PCR. The copy number of PirA^Vp was calculated according to the standard curves, which were constructed by measuring the presence of the PirA^Vp and PirB^Vp. The primers used in RT-qPCR are shown in Table S1.

Miao M., Li S., Liu Y., Yu Y, & Li F. (2023). Transcriptome Analysis on Hepatopancreas Reveals the Metabolic Dysregulation Caused by Vibrio parahaemolyticus Infection in Litopenaeus vannamei. Biology, 12(3), 417.

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Genome-wide SNP discovery and genotyping of peanut RILs

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Genomic DNA of the parents and 212 RILs was extracted from young leaf tissues using the Plant genome DNA extraction kit (TIANGEN) and randomly sheared by sonication. The DNA fragments with the length of 300 bp were recovered by electrophoresis. After ligating DNA fragments with adapters, libraries were paired-end sequenced using the Illumina Hi-seq platform with read length of 150 bp.
After trimming adapters and low quality reads, clean data was used for aligning to the reference genome, allowing SNP identification and genotyping. In detail, the assembly of Arachis hypogaea cv. Tifrunner was used as the reference genome [4]. The aln command in the software bwa-0.7.10 was used to align clean data to the reference genome, and unique reads were used for subsequent SNP variation detection by the software GATK3.3.0. The obtained SNP sets of two parents were filtered used the missing values, heterozygosis, depth and GQ value and the homozygous and polymorphic loci were used for the RIL population. The binary alignment mapping (BAM) files obtained in this study have been submitted to the BioProject database at NCBI under the BioProject ID: PRJNA602098.

Liu H., Sun Z., Zhang X., Qin L., Qi F., Wang Z., Du P., Xu J., Zhang Z., Han S., Li S., Gao M., Zhang L., Cheng Y., Zheng Z., Huang B, & Dong W. (2020). QTL mapping of web blotch resistance in peanut by high-throughput genome-wide sequencing. BMC Plant Biology, 20, 249.

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Fungal DNA Extraction and Phylogenetic Analysis

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Total genomic DNA was extracted from the 7-day fresh mycelia using the plant genome DNA extraction kit (Tiangen Biochemical Technology Co., Ltd.). The regular PCR extension was implemented by primer ITS1-F: 5’-CTTGGTCATTTTAGAGGAAGTAA-3’; and ITS4-B: 5’ -CAGGAGACTTGTACACGGTCCAG-3’. The PCR program was as follows: 5 min at 94°C; 30 rounds of 30 s at 94°C, 30 s at 55°C, and 40 s at 72°C; and final extension for 10 min at 72°C. The fragments were submitted to a sequencing service (General Biosystems, Inc., China). The sequence was aligned using the BLAST software in the NCBI database. Based on the results of the Blast search, 15 sequences with the highest similarity were selected to perform the phylogenetic analysis and construction of an unrooted tree using the software MEGA version 7.0.

Wang Q., Qian Y., Ma Y, & Zhu C. (2018). A Preliminary Study on the Newly Isolated High Laccase-producing Fungi: Screening, Strain Characteristics and Induction of Laccase Production. Open Life Sciences, 13, 463-469.

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Transgenic Arabidopsis Expressing Peanut FAD Genes

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Genomic DNA was prepared from peanut plants using a Plant Genome DNA Extraction kit (TIANGEN Biotechnology Co., Beijing, China). The primer pairs FAD3-1-F/-R, FAD3-2-F/-R, FAD3-3-F/-R and FAD3-4-F/-R (Table S1) were used to amplify the up-stream sequence of each of the four FAD genes. The fragments were inserted to the MCS site of the pCAMBIA1381Z plasmid which also harbors the GUS. The resulting constructs were transformed into A. tumefaciens strain LBA4404, and from thence into A. thaliana, as described above. Progeny of putative transformants were raised on half strength MS medium containing 100 mg/L kanamycin to select for T 1 plants carrying the transgene, and the same selection procedure was repeated in the T 2 and T 3 generations. Whole plants, flowers, pods and seeds of transgene homozygous T 3 plants were subjected to GUS staining (Jefferson et al. 1987) . All primer sequences are given in Table S1.

Peng Z., Ruan J., Tian H., Shan L., Meng J., Guo F., Zhang Z., Ding H., Wan S., & Li X. (2020). The Family of Peanut Fatty Acid Desaturase Genes and a Functional Analysis of Four ω-3 AhFAD3 Members. Plant Molecular Biology Reporter, 38(2), 209-221.

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Whole Genome Sequencing of Peanut RILs

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Genomic DNA of the parents and 212 RILs was extracted from young leaf tissues using the Plant genome DNA extraction kit (TIANGEN) and randomly sheared by sonication. The DNA fragments with the length of 300 bp were recovered by electrophoresis.
After ligating DNA fragments with adapters, libraries were paired-end sequenced using the Illumina Hi-seq platform with read length of 150 bp.
After trimming adapters and low quality reads, clean data was used for aligning to the reference genome, allowing SNP identification and genotyping. In detail, the assembly of Arachis hypogaea cv. Tifrunner was used as the reference genome [4] . The aln command in the software bwa-0.7.10 was used to align clean data to the reference genome, and unique reads were used for subsequent SNP variation detection by the software GATK3.3.0. The obtained SNP sets of two parents were filtered used the missing values, heterozygosis, depth and GQ value and the homozygous and polymorphic loci were used for the RIL population. The binary alignment mapping (BAM) files obtained in this study have been submitted to the BioProject database at NCBI under the BioProject ID: PRJNA602098.

Liu H., Sun Z., Zhang X., Qin L., Qi F., Wang Z., Du P., Xu J., Zhang Z., Han S., Li S., Gao M., Zhang L., Cheng Y., Zheng Z., Huang B., & Dong W. (2020). QTL Mapping of Web Blotch Resistance in Peanut by High-throughput Genome-wide Sequencing.

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