tRNA sequencing methods - T-psi-C database

• Using CHARGE-seq to survey the pools of charged tRNAs in amino-acid-deprived cells and investigate how amino acid deficit-associated patterns of tRNA charging affect protein synthesis.
  
• Ordered Two-Template Relay Sequencing
  using retroelement RT for serial template jumping to add distinct 5′ and 3′ adaptors during cDNA library synthesis. Streamlined, automation-friendly, single-tube cDNA library production for next-generation sequencing (NGS)
• Ligation-independent detection of all types of RNA
  Quasi-random priming with template switching to construct sequencing libraries from RNA molecules of any length and with any type of 3′ modifications.
• Quantitative Mature tRNA sequencing
  A simple high-throughput tRNA sequencing protocol utilizing commercially available reagents
• Long hairpin oligonucleotide based tRNA high-throughput sequencing
  CCA-specific 3ʹ-adapter is ligated to mature tRNAs without previous purification. The second adapter is ligated to the resulting cDNA 3ʹ-ends. As a result, both full-length and shorter cDNA fragments are included in the data analysis. Further, with the use of a selective adapter for mature tRNA 3ʹ-ends, no purification of a tRNA fraction is required, and a crude total RNA preparation can be used.
• Dimethyl-sulfate chemical probing and mutational profiling coupled with demethylase treatment in transcriptome-wide tRNA sequencing
  
• Adapter-ligated libraries of tRNA-derived sequences
  Specifically designed for the detection of full-length tRNA molecules and tRNA-derived products in clinical tissue samples. Utiliing highly processive group II intron maturase MarathonRT. Adapter ligation strategy facilitated by molecular crowding, to capture both full-length species and RNA fragments already present in the assessed samples. Optimized strategy for mature tRNA quantification in samples with lower RNA qulity.
• Induro-tRNAseq
  Using Induro a group-II intron-encoded RT to map and quantify genome-wide tRNA modifications 5 human cell lines and 3 mouse tissues
• The extension of DM-tRNA-seq method determining fraction of charged isodecoders using periodate treatment followed by β-elimination.
  
• Y-shaped Adapter-ligated MAture TRNA sequencing
  Employing the efficient and specific ligation of Y-shaped adapter to mature tRNAs using T4 RNA Ligase 2
• Misincorporation tRNA sequencing
  Uniform sequence coverage of tRNA pools, while retaining modification signatures, by identifying conditions that enable efficient RT readthrough together with a comprehensive and user-friendly computational toolkit.
• tRNA sequencing using engineered demethylases to remove base methylations and a highly processive thermostable group II intron reverse transcriptase
  
• Absolute Quantification RNA-Seq
  AQRNA-Seq enables absolute quantification of all small RNA species in a sample by providing a direct, linear correlation between sequencing read count and RNA abundance
• AlkB-facilitated RNA Methylation sequencing
  ARM-Seq uses pre-treatment with Escherichia coli AlkB to demethylate 1-methyladenosine, 3-methylcytidine, and 1-methylguanosine foloowed by tRNA sequencing
• An integrated method that uses chemical ligation to sandwich the amino acid of a charged tRNA in between the body of the tRNA and an adaptor oligonucleotide, followed by high throughput nanopore sequencing.
  
• Hydrolysis-Based tRNA Sequencing
  hydro-tRNAseq is based on partial alkaline RNA hydrolysis that generates fragments amenable for sequencing
• Demethylation-assisted multiple methylation sequencing
  Method allows us to monitor the modification level based on the mutation rate for m1A, m3C, m1G and m22G sites using engineered AlkB
• DNA Oligo for RNA Quantification sequencing
  Combination of cDNA hybridization technique with next generation sequencing. A tRNA-cDNA hybridization step transfers quantitative information to the cDNA template, thus omitting reverse transcription and any enzymatic step except for a low-cycle index PCR which takes place on the cDNA template.
• Nanopore-based approach to sequence native tRNA
  

Methods