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Truseq stranded total rna sequencing kit

Manufactured by Illumina
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The TruSeq Stranded Total RNA sequencing kit is a laboratory equipment product designed for high-throughput sequencing of total RNA samples. It provides a method for library preparation, enabling the analysis of gene expression and transcript abundance from a variety of sample types.

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Lab products found in correlation

Ribozero rrna depletion, by Illumina (3 mentions) Ercc spike in mix, by Thermo Fisher Scientific (3 mentions) Ampure xp bead, by Beckman Coulter (3 mentions) Hiseq 4000, by Illumina (2 mentions) Tapestation, by Agilent Technologies (2 mentions) Ribo zero yeast kit, by Illumina (1 mentions) Hiseq 2500, by Illumina (1 mentions)

5 protocols using truseq stranded total rna sequencing kit

1

Bulk RNA-seq of Isolated Cell Types

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Isolated SG, SC, and RS cells were counted, and 1 × 10 ^ 6 cells were resuspended in 1 mL of Trizol and spiked with 1 uL of 1:10 diluted ERCC Spike-in Mix (Invitrogen). RNA was purified according to manufacturer protocol and RNA integrity was confirmed using a TapeStation (Agilent). 210 ng of RNA from each sample was diluted in 10 uL of water as input RNA for library generation using the TruSeq Stranded Total RNA sequencing kit with RiboZero rRNA depletion (Illumina). Manufacturer instructions were followed except for substitution of SuperScriptIII for SuperScriptII. The final libraries were amplified to 10–12 cycles and purified using AMPure XP beads (Beckman Coulter). Pooled libraries (10 nM) were sequenced (paired-end 150 cycles) on an Illumina HiSeq 4000 at Novogene.
Kaye E.G., Basavaraju K., Nelson G.M., Zomer H.D., Roy D., Joseph I.I., Rajabi-Toustani R., Qiao H., Adelman K, & Reddi P.P. (2024). RNA polymerase II pausing is essential during spermatogenesis for appropriate gene expression and completion of meiosis. Nature Communications, 15, 848.
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2

Yeast rRNA Depletion and Stranded RNA-Seq

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Samples were rRNA depleted using the Ribo Zero yeast kit (Epicenter) and sequencing libraries were prepared using the Truseq Stranded Total RNA sequencing kit (Illumina), as recommended by the manufacturers. The RiboZero (yeast) kit was substituted in the protocol for the Ribozero kit supplied with the Truseq Stranded Total RNA sequencing kit. Sequencing of the libraries was carried out on an Illumina HiSeq 2500 in Rapid output mode using the Illumina Truseq Rapid v1 chemistry.
Bresson S., Tuck A., Staneva D, & Tollervey D. (2017). Nuclear RNA Decay Pathways Aid Rapid Remodeling of Gene Expression in Yeast. Molecular Cell, 65(5), 787-800.e5.
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3

RNA-seq Analysis of Drosophila Mettl3 Mutants

Cited 3 times
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Flies of the specified genotypes(w;;Mettl3[null]/+, w;;Mettl3[null]/Mettl3[cat], w;;Df(3 R)BSC461/ + , w;;Ythdf[NP3]/Df(3 R)BSC461, were aged to 1 or 3 weeks at 25 °C. Female heads were dissected and collected for total RNA extraction using TRIzol reagent. Sequencing libraries were prepared using the TruSeq Stranded Total RNA Sequencing Kit (Illumina) following the manufacturer’s protocol. Sequencing was performed on a HiSeq 2500 System in paired end read mode, with 100 bases per read at the Integrated Genomics Operation (IGO) at Memorial Sloan Kettering Cancer Center.
RNA sequencing libraries were mapped to the Drosophila reference genome sequence (BDGP Release 6/dm6) using HISAT2105 (link) under the default settings. Gene counts were obtained by assigning and counting reads to the Ensembl transcript models for BDGP6.94 using Rsubread106 (link). Differential gene expression analysis was performed with comparisons as listed in Supplementary Dataset 5 using the R package DESeq2107 (link) and applying a strict adjusted p-value cutoff of 0.05.
Kan L., Ott S., Joseph B., Park E.S., Dai W., Kleiner R.E., Claridge-Chang A, & Lai E.C. (2021). A neural m6A/Ythdf pathway is required for learning and memory in Drosophila. Nature Communications, 12, 1458.
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4

RNA-seq of Isolated Cell Types

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Isolated SG, RC, and RS cells were counted, and 1 × 10^6 cells were resuspended in 1mL of Trizol and spiked with 1 uL of 1:10 diluted ERCC Spike-in Mix (Invitrogen). RNA was purified according to manufacturer protocol and RNA integrity was confirmed using a TapeStation (Agilent). 210 ng of RNA from each sample was diluted in 10uL of water as input RNA for library generation using the TruSeq Stranded Total RNA sequencing kit with RiboZero rRNA depletion (Illumina). Manufacturer instructions were followed except for substitution of SuperScriptIII for SuperScriptII. The final libraries were amplified to 10–12 cycles and purified using AMPure XP beads (Beckman Coulter). Pooled libraries (10nM) were sequenced (paired-end 150 cycles) on an Illumina HiSeq 4000 at Novogene.
Kaye E.G., Nelson G.M., Zomer H.D., Roy D., Joseph I.I., Adelman K, & Reddi P.P. (2023). RNA polymerase II pausing is essential during spermatogenesis for appropriate gene expression and completion of meiosis. bioRxiv.
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5

RNA-seq analysis of INTS8 knockdown

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293T cells were treated for 48 hours with either control or INTS8 targeting siRNAs as described above. Cells were harvested and washed with PBS. Cells were counted, and 1 × 106 cells were resuspended in 1mL of Trizol and spiked with 1 μL of 1:10 diluted ERCC Spike-in Mix (Invitrogen) and RNA was purified. 1 μg of RNA from each sample was diluted in 10uL of water. The input RNA was subjected to RNA-seq library generation using the TruSeq Stranded Total RNA sequencing kit with RiboZero rRNA depletion (Illumina). The final libraries were amplified to 10 cycles and purified using AMPure XP beads (Beckman Coulter). Pooled libraries (10nM) were sequenced (PE150) on the HiSeq platform at Novogene.
Reads were filtered to require a mean quality score ≥ 20, trimmed to 100 nt, and mapped to the hg38 human genome assembly using STAR. Default parameters were used, except that multimappers were randomly assigned (outMultimapperOrder Random), spurious junctions were filtered (outFilterType BySJout), minimum overhang for non-annotated junctions was set to 8 nt (alignSJoverhangMin 8), and non-canonical alignments were removed (outFilterIntronMotifs RemoveNoncanonicalUnannotated).
The total number of RNA-seq reads aligned in the control or INTS8-dep. samples is described below:
Huang K.L., Jee D., Stein C.B., Elrod N.D., Henriques T., Mascibroda L.G., Baillat D., Russell W.K., Adelman K, & Wagner E.J. (2020). Integrator Recruits Protein Phosphatase 2A to Prevent Pause Release and Facilitate Transcription Termination. Molecular cell, 80(2), 345-358.e9.
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