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Vahts rna adapters

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VAHTS RNA Adapters are a set of oligonucleotide sequences designed for the preparation of libraries for RNA sequencing. These adapters are used to ligate to the ends of RNA fragments, enabling the fragments to be amplified and sequenced on next-generation sequencing platforms.

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Lab products found in correlation

Vahts stranded mrna seq library prep kit, by Vazyme (8 mentions) Smartspec plus, by Bio-Rad (7 mentions) Hiseq x ten system, by Illumina (7 mentions) Rq1 dnase, by Promega (4 mentions) Trizol, by Thermo Fisher Scientific (3 mentions) Hiseq 4000 system, by Illumina (2 mentions) Oligo dt conjugated magnetic beads, by Thermo Fisher Scientific (1 mentions) Rneasy mini kit, by Qiagen (1 mentions) Rneasy kit, by Qiagen (1 mentions)

8 protocols using vahts rna adapters

1

RNA Extraction and RNA-seq Library Preparation

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Total RNA was extracted by the TRIZOL (Ambion). The RNA was further purified with two phenol–chloroform treatments and then treated with RQ1 DNase (Promega) to remove DNA. The quality and quantity of the purified RNA were redetermined by measuring the absorbance at 260 nm/280 nm (A260/A280) using Smartspec Plus (Bio-Rad). The integrity of RNA was further verified by 1.5% agarose gel electrophoresis. For each sample, 1 μg of total RNA was used for RNA-seq library preparation by VAHTS Stranded mRNA-seq Library Prep Kit (Vazyme). Polyadenylated mRNAs were purified and fragmented, and then converted into double strand cDNA. After the step of end repair and a tailing, the DNAs were ligated to VAHTS RNA Adapters (Vazyme). Purified ligation products corresponding to 200–500 bp were digested with heat-labile UDG, and the single strand cDNA was amplified, purified, quantified, and stored at -80℃.
For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions and applied to Illumina HiSeq X Ten system for 150 NT paired-end sequencing.
Liao M., Cao J., Chen W., Wang M., Jin Z., Ye J., Ren Y., Wei Y., Xue Y., Chen D., Zhang Y, & Chen S. (2024). HMGB1 prefers to interact with structural RNAs and regulates rRNA methylation modification and translation in HeLa cells. BMC Genomics, 25, 345.
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2

RNA Extraction and RNA-seq Library Preparation

Cited 1 time
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Total RNA was extracted with TRIZOL (Life Technology, Carlsbad, CA, USA) as previous study descripted [16 (link)]. The RNA was further purified with two phenol–chloroform treatments and then treated with RQ1 DNase (Promega, Madison, WI, USA) to remove DNA. The quality and quantity of the purified RNA were redetermined by measuring the absorbance at 260 nm/280 nm (A260/A280) using Smartspec Plus (BioRad, Hercules, CA, USA). The integrity of RNA was further verified by 1.5% agarose gel electrophoresis. For each sample, 1 μg of the total RNA was used for RNA-seq library preparation by VAHTS Stranded mRNA-seq Library Prep Kit (Vazyme, Nanjing, China). Polyadenylated mRNAs were purified and fragmented, and then converted into double strand cDNA. After the end repair and A tailing step, the DNAs were ligated to VAHTS RNA Adapters (Vazyme, Nanjing, China). Purified ligation products corresponding to 200‒500 bps were digested with heat-labile UDG, and the single strand cDNA was amplified, purified, quantified, and stored at − 80ºC before sequencing. For high-throughput sequencing, the libraries were prepared following the manufacturer’s instructions and applied to an Illumina HiSeq X Ten system for 150 nt paired-end sequencing.
Liu Y., Peng L., Chen J., Chen L., Wu Y., Cheng M., Chen M., Ye X, & Jin Y. (2023). EIF5A2 specifically regulates the transcription of aging-related genes in human neuroblastoma cells. BMC Geriatrics, 23, 83.
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3

RNA-Seq Library Preparation Protocol

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Total RNA for RNA-seq experiments was isolated from colon cancer cells using a RNeasy mini kit (QIAGEN, Hilden, Germany). The quality and quantity of RNA samples were assessed by measuring the absorbance at 260 nm/280 nm (A260/A280) using Smartspec plus (Bio-Rad, USA). The integrity of RNA was further verified by 1.5% agarose gel electrophoresis. For each sample, 2 μg of the total RNA was used for RNA-seq library preparation by VAHTS stranded mRNA-seq library prep kit (Vazyme). The polyadenylated mRNAs were purified and concentrated with oligo (dT)-conjugated magnetic beads (Invitrogen, Carlsbad, CA, USA). After fragmentation, polyadenylated mRNAs were converted into double-strand cDNA followed by ligation into VAHTS RNA adapters (Vazyme). Purified ligation products corresponding to 200–500 bps were digested, amplified, purified, and quantified for sequencing. For high-throughput sequencing, the libraries were prepared following the manufacturer’s instructions and applied to the Illumina HiSeq X Ten system for 150-nt paired-end sequencing. The Illumina HiSeq4000 system was used to collect sequencing data (Illumina, San Diego, CA, USA).
Zhang X.L., Li K.J., Feng J.X., Liu G.J, & Feng Y.L. (2021). Blocking the IGF2BP1-promoted glucose metabolism of colon cancer cells via direct de-stabilizing mRNA of the LDHA enhances anticancer effects. Molecular Therapy. Nucleic Acids, 23, 835-846.
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4

RNA-Seq Library Preparation from Total RNA

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Total RNA was extracted using TRIzol (Ambion). The RNA was further purified with two phenol-chloroform treatments and RQ1 DNase (Promega) was administered to remove the DNA. The quality and quantity of the purified RNA was assessed by measuring the absorbance at 260 nm/280 nm (A260/A280) using a Smartspec Plus (BioRad). The integrity of the RNA was further verified by 1.5% agarose gel electrophoresis.
For each sample, 1 μg of the total RNA was used for RNA-seq library preparation via VAHTS Stranded mRNA-seq Library Prep Kit (Vazyme). Polyadenylated mRNA was purified and fragmented, and then converted into double stranded cDNA. After the step of end repair and A tailing, the DNAs were ligated to VAHTS RNA Adapters (Vazyme). The purified ligation products corresponding to 200–500 bps were digested with heat-labile UDG, and the single stranded cDNA was amplified, purified, quantified, and stored at − 80 °C before sequencing.
For high-throughput sequencing, the libraries were prepared following the manufacturer’s instructions and applied to the Illumina HiSeq X Ten system for 150 nt paired-end sequencing.
Tu Y., Wu X., Yu F., Dang J., Wang J., Wei Y., Cai Z., Zhou Z., Liao W., Li L, & Zhang Y. (2019). Tristetraprolin specifically regulates the expression and alternative splicing of immune response genes in HeLa cells. BMC Immunology, 20, 13.
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5

RNA-seq Library Preparation Protocol

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The quality and quantity of the purified RNA samples were redetermined by measuring the absorbance at 260 nm/280nm (A260/A280) using Smartspec Plus (BioRad, USA). The integrity of RNA was further verified by 1.5% agarose gel electrophoresis. For each sample, 1μg of the total RNA was used for RNA-seq library preparation by VAHTS Stranded mRNA-seq Library Prep Kit (Vazyme Biotech Co., Ltd, Nanjing, China). Polyadenylated mRNAs were purified and fragmented and then converted into double-strand cDNA. After the step of end repair and A tailing, the DNAs were ligated to VAHTS RNA Adapters (Vazyme Biotech Co., Ltd, Nanjing, China). Purified ligation products corresponding to 200–500 bps were digested with heat-labile UDG, and the single-strand cDNA was amplified, purified, quantified and stored at −80°C before sequencing. For high-throughput sequencing, the libraries were prepared following the manufacturer’s instructions and applied to Illumina HiSeq X Ten system for 150 nt paired-end sequencing.
Ding Y., Gao S., Zheng J, & Chen X. (2022). Blocking lncRNA-SNHG16 sensitizes gastric cancer cells to 5-Fu through targeting the miR-506-3p-PTBP1-mediated glucose metabolism. Cancer & Metabolism, 10, 20.
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6

RNA-seq Library Preparation Protocol

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Total RNA extraction was performed using an RNeasy kit (#74134, QIAGEN, Hilden, Germany) according to the manufacturer’s instructions. The quantity of RNA samples was assessed by NanoDrop. The integrity of RNA was verified by running on 1.5% agarose gel electrophoresis. 2 μg of total RNA of each sample was used for RNA-seq library preparation by a VAHTS stranded mRNA-seq library prep kit (Vazyme). Polyadenylated mRNAs were fragmented and then converted into double-strand cDNA followed by ligation into VAHTS RNA adapters (Vazyme). Purified ligation products were used for sequencing. The Illumina HiSeq 4000 system was used to collect sequencing data (Illumina, San Diego, CA, USA).
Chen P., Liu X.Q., Lin X., Gao L.Y., Zhang S, & Huang X. (2021). Targeting YTHDF1 effectively re-sensitizes cisplatin-resistant colon cancer cells by modulating GLS-mediated glutamine metabolism. Molecular Therapy Oncolytics, 20, 228-239.
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7

RNA-seq Library Preparation from BHT101 Cells

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Total RNA extracted from BHT101 cells was purified using 2 phenol-chloroform treatments and then treated using RQ1 DNase (Promega, Madison, USA) to remove DNA. The Smartspec Plus (Bio-Rad) was employed to evaluate the quality and quantity of the purified RNA by measuring the absorbance at 260 nm/280 nm (A260/A280), and 1.5% agarose gel electrophoresis was used to verify the integrity of the RNA.
The VAHTS Stranded mRNA-seq Library Prep Kit (Vazyme Biotech) was used to perform RNA-seq library preparation with 1 µg of the total RNA. Polyadenylated mRNAs were converted into double-stranded cDNAs after purification and fragmentation. The DNAs were then ligated to VAHTS RNA Adapters (Vazyme Biotech) following end repair and A tailing. Purified ligation products ranging from 200 bps to 500 bps were digested using heat-labile uracil-DNA glycosylase (UDG), and the single-stranded cDNA was amplified, purified, quantified, and stored at -80°C before high-throughput sequencing.
For high-throughput sequencing, the libraries were prepared according to the instructions of the manufacturer and applied to Illumina HiSeq X Ten system (Illumina, Inc., San Diego, USA) for 150 nt paired-end sequencing.
Wan J., Lv J., Wang C, & Zhang L. (2022). RPS27 selectively regulates the expression and alternative splicing of inflammatory and immune response genes in thyroid cancer cells. Advances in clinical and experimental medicine : official organ Wroclaw Medical University, 31(8).
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8

RNA-seq Library Preparation Protocol

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The quality and quantity of the puri ed RNA samples were redetermined by measuring the absorbance at 260 nm/280nm (A260/A280) using Smartspec Plus (BioRad, USA). The integrity of RNA was further veri ed by 1.5% agarose gel electrophoresis. For each sample, 1μg of the total RNA was used for RNA-seq library preparation by VAHTS Stranded mRNA-seq Library Prep Kit (Vazyme Biotech Co., Ltd, Nanjing, China). Polyadenylated mRNAs were puri ed and fragmented, and then converted into double strand cDNA. After the step of end repair and A tailing, the DNAs were ligated to VAHTS RNA Adapters (Vazyme Biotech Co., Ltd, Nanjing, China). Puri ed ligation products corresponding to 200-500 bps were digested with heat-labile UDG, and the single strand cDNA was ampli ed, puri ed, quanti ed and stored at -80℃ before sequencing. For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions and applied to Illumina HiSeq X Ten system for 150 nt paired-end sequencing.
Ding Y., Gao S., Zheng J., & Chen X. (2021). Blocking lncRNA-SNHG16 Sensitizes Gastric Cancer Cells to 5-Fu Through Targeting the miR-506-3p-PTBP1-Mediated Glucose Metabolism.
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