Insect fresh DNA was extracted using the Tiangen Genomic DNA Extraction Kit (DP304, Tiangen Biotech Co., Ltd., Beijing, China), and insect powder was extracted using the Ezup Food Genomic DNA Extraction Kit (B518264, Sangon Biotech Co, Ltd., Shanghai, China). COI sequences were recovered, and the origin identification was validated. Thermo Fisher Scientific’s BioMate 3 (Thermo Fisher Scientific, Waltham, MA, USA) was used to calculate the total DNA concentrations. Each of the sample DNA was stocked at −20 °C before use.
Tiangen genomic dna extraction kit
Manufactured by Tiangen Biotech
Sourced in China
The TIANGEN Genomic DNA Extraction Kit is a laboratory tool designed for the efficient extraction and purification of genomic DNA from a variety of biological samples. It provides a straightforward and reliable method to obtain high-quality DNA for various downstream applications, such as PCR, sequencing, and genetic analysis.
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Lab products found in correlation
Quantitect sybr green pcr kit, by Qiagen (2 mentions)
Ezup food genomic dna extraction kit, by Sangon (1 mentions)
Biomate 3, by Thermo Fisher Scientific (1 mentions)
Primescript rt reagent kit, by Takara Bio (1 mentions)
Superscripts 2 first strand cdna synthesis kit, by Thermo Fisher Scientific (1 mentions)
Trizol reagent, by Thermo Fisher Scientific (1 mentions)
Simplechip enzymatic chromatin ip kit, by Cell Signaling Technology (1 mentions)
Cfx connect real time pcr detection system, by Bio-Rad (1 mentions)
5 protocols using tiangen genomic dna extraction kit
1
Insect Fresh and Powder DNA Extraction
2
Bamboo Genome Sequencing and Analysis
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Total genomic DNA was isolated from silica-dried healthy leaves using the TIANGEN Genomic DNA Extraction Kit (TIANGEN, Beijing, China). DNA samples of concentration meeting the standard (≥1 μg) were randomly sheared into fragments using Covaris M220 (Covaris, Woburn, MA, USA). Fragments of 350 bp were enriched using PCR, and the paired-end (2 × 150 bp) reads were generated in Novogene (Beijing, China) using the NovaSeq 6000 platform. As a result, approximately 20 Gb genome skimming data were generated for each sample. Among species with already published bamboo genome data, Bonia amplexicaulis (L.C. Chia, H.L. Fung & Y.L. Yang) N.H. Xia, with a whole genome size of 0.848 Gb (Guo Z.H. et al., 2019 (link)), is the species closest to the taxa included in the present investigation (Zhou M.Y. et al., 2017 (link)). Hence, the expected sequencing coverage for our samples would be approximately 23.58× (20 Gb/0.848 Gb). For confirmation of the actual coverage, Jellyfish 2.2.3 (Marçais and Kingsford, 2011 (link)) and GenomeScope 2.0 (Ranallo-Benavidez et al., 2020 (link)) were used to estimate genome size for each newly sequenced sample (including the outgroup).
3
Comprehensive DNA and RNA Extraction and Quantification
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DNA was isolated using the TIANGEN Genomic DNA Extraction Kit (catalog no. DP304; TIANGEN Biotech, Beijing, China). Total RNA was isolated from the MH7A cells using fast 200 (Fastagen, China) and was reverse-transcribed into cDNA by using the PrimeScript RT Reagent kit (TakaRa, Japan). The qRT-PCR reaction was performed using the QuantiTect SYBR Green PCR Kit (QIAGEN, USA). We used GAPDH as an endogenous control to normalize the differences in samples. Primers of qRT-PCR are shown in Supplementary Table 6 .
4
Deep Genome Skimming of Plant Leaves
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Young leaves at the vegetative growth stage were collected in the field. Total genomic DNA was isolated from silica-dried leaves following the manufacturer’s specifications TIANGEN Genomic DNA Extraction Kit (TIANGEN, Beijing, China). DNA samples of concentration up to standard (≥1 μg) were sheared into fragments using Covaris M220 (Covaris, Woburn, MA). Insert size of 350 bp fragments were enriched by PCR, and the paired-end (2 × 150 bp) libraries were constructed on NovaSeq 6000 platform. About 20G deep genome skimming (DGS ) data were generated. Finally, adapters and low-quality reads were filtered from raw data using Fastp v 0.23.1 (Chen et al. 2018 (link)) software.
5
Chromatin Immunoprecipitation Assay in HEK293T Cells
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ChIP assays were performed in HEK293T cells by using the SimpleChIP Enzymatic Chromatin IP Kit (Cell Signaling Technology), as described previously (31) . A total of 50 mg of sonicated chromatin was incubated with 3 mg of ZNF329 antibody (sc-377455; Santa Cruz Biotechnology, Dallas, TX), the histone H3 rabbit antibody (positive control), or normal rabbit IgG (negative control). Protein-DNA complex was precipitated with agarose beads and reversely cross-linked by 5 mol/L NaCl and proteinase K. The DNA fragments were purified using DNA purification spin columns for subsequent quantitative PCR (qPCR) with allele-specific primers listed in Supplementary Table 1.
DNA and RNA Isolation and Real-Time qPCR DNA was isolated using the TIANGEN Genomic DNA Extraction Kit (catalog no. DP304; TIANGEN Biotech, Beijing, China). RNA was isolated with TRIzol reagent (Invitrogen), and 5 mg of total RNA per reaction was used to synthesize the cDNA with the SuperScripts II First-Strand cDNA Synthesis Kit (Invitrogen). Real-time qPCR was performed with the QuantiTect SYBR Green PCR Kit (QIAGEN, Dusseldorf, Germany) by the CFX Connect Real-Time PCR Detection System (Bio-Rad, Hercules, CA). Samples were tested in a 96-well format in triplicate. For experiments in the SGBS cells, GAPDH was used as an endogenous control.
DNA and RNA Isolation and Real-Time qPCR DNA was isolated using the TIANGEN Genomic DNA Extraction Kit (catalog no. DP304; TIANGEN Biotech, Beijing, China). RNA was isolated with TRIzol reagent (Invitrogen), and 5 mg of total RNA per reaction was used to synthesize the cDNA with the SuperScripts II First-Strand cDNA Synthesis Kit (Invitrogen). Real-time qPCR was performed with the QuantiTect SYBR Green PCR Kit (QIAGEN, Dusseldorf, Germany) by the CFX Connect Real-Time PCR Detection System (Bio-Rad, Hercules, CA). Samples were tested in a 96-well format in triplicate. For experiments in the SGBS cells, GAPDH was used as an endogenous control.
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