Truseq small rna kit adapter

Manufactured by Illumina

The TruSeq small RNA kit adapter is a laboratory equipment product designed for use in small RNA sequencing workflows. It serves the core function of ligating adapters to small RNA molecules, enabling their subsequent amplification and sequencing.

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Lab products found in correlation

Truseq small rna primers, by Illumina (5 mentions) Nextseq platform, by Illumina (3 mentions) Nextseq, by Illumina (1 mentions) Mineral oil, by Merck Group (1 mentions) Hoechst 34580, by Merck Group (1 mentions) Nextseq 500, by Illumina (1 mentions)

5 protocols using truseq small rna kit adapter

Single-cell Transcriptomics of Zebrafish Cells

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Single-cell sequencing libraries were prepared using SORT-seq (Muraro et al., 2016 (link)). Live cells were sorted into 384-well plates with Vapor-Lock oil containing a droplet with barcoded primers, spike-in RNA and dNTPs, followed by heat-induced cell lysis and cDNA syntheses using a robotic liquid handler. Primers consisted of a 24 bp polyT stretch, a 4 bp random molecular barcode (UMI), a cell-specific 8 bp barcode, the 5′ Illumina TruSeq small RNA kit adapter and a T7 promoter. After cell lysis for 5 min at 65°C, RT and second strand mixes were distributed with the Nanodrop II liquid handling platform (Inovadyne). After pooling all cells in one library, the aqueous phase was separated from the oil phase, followed by IVT transcription. The CEL-Seq2 protocol was used for library prep (Hashimshony et al., 2016 (link)). Illumina sequencing libraries were prepared with the TruSeq small RNA primers (Illumina) and paired-end sequenced at 75 bp read length on the Illumina NextSeq platform. Mapping was performed against the zebrafish reference assembly version 9 (Zv9).

de Bakker D.E., Bouwman M., Dronkers E., Simões F.C., Riley P.R., Goumans M.J., Smits A.M, & Bakkers J. (2021). Prrx1b restricts fibrosis and promotes Nrg1-dependent cardiomyocyte proliferation during zebrafish heart regeneration. Development (Cambridge, England), 148(19), dev198937.

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Single-cell RNA-seq of Zebrafish Using SORT-seq

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Single-cell sequencing libraries were prepared using SORT-seq (Muraro et al., 2016 (link)). Live cells were sorted into 384-well plates with Vapor-Lock oil containing a droplet with barcoded primers, spike-in RNA and dNTPs, followed by heat-induced cell lysis and cDNA syntheses using a robotic liquid handler. Primers consisted of a 24 bp polyT stretch, a 4 bp random molecular barcode (UMI), a cell-specific 8 bp barcode, the 5’ Illumina TruSeq small RNA kit adapter and a T7 promoter. After cell-lysis for 5 min at 65 °C, RT and second strand mixes were distributed with the Nanodrop II liquid handling platform (Inovadyne). After pooling all cells in one library, the aqueous phase was separated from the oil phase, followed by IVT transcription. The CEL-Seq2 protocol was used for library prep (Hashimshony et al., 2016 (link)). Illumina sequencing libraries were prepared with the TruSeq small RNA primers (Illumina) and paired-end sequenced at 75 bp read length on the Illumina NextSeq platform. Mapping was performed against the zebrafish reference assembly version 9 (Zv9).

Honkoop H., de Bakker D.E., Aharonov A., Kruse F., Shakked A., Nguyen P.D., de Heus C., Garric L., Muraro M.J., Shoffner A., Tessadori F., Peterson J.C., Noort W., Bertozzi A., Weidinger G., Posthuma G., Grün D., van der Laarse W.J., Klumperman J., Jaspers R.T., Poss K.D., van Oudenaarden A., Tzahor E, & Bakkers J. (2019). Single-cell analysis uncovers that metabolic reprogramming by ErbB2 signaling is essential for cardiomyocyte proliferation in the regenerating heart. eLife, 8, e50163.

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Single-Cell RNA-Seq Using SORT-Seq Protocol

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Single-cell RNA-sequencing was performed using the SORT-seq protocol (Muraro et al., 2016 (link)). Briefly, after sorting cells were lysed at 65°C for 5 minutes. RT and second strand mixes were dispensed by the Nanodrop II liquid handling platform for cDNA library preparation (GC Biotech). The aqueous phase was separated from the oil phase after pooling all cells from one plate into one library, followed by IVT transcription. For each 384 well plate, 384 primers (1 library of 384 cells) was used for mRNA reverse transcription, conversion to double-stranded cDNA, and in vitro transcription. Each primer consists of a 24 bp polyT stretch, a 4 bp random molecular barcode (UMI), a cell-specific 8 bp barcode, the 5’ Illumina TruSeq small RNA kit adapter, and a T7 promoter. Single-cell double-stranded cDNAs were pooled and in-vitro transcribed for linear amplification following the CEL-Seq 2 protocol. Illumina sequencing libraries were prepared using TruSeq small RNA primers (Illumina) and sequenced paired-end at a read length of 75 bp using the Illumina NextSeq.

Mok K.W., Saxena N., Heitman N., Grisanti L., Srivastava D., Muraro M., Jacob T., Sennett R., Wang Z., Su Y., Yang L.M., Ma’ayan A., Ornitz D.M., Kasper M, & Rendl M. (2018). Dermal Condensate Niche Fate Specification Occurs Prior to Formation and Is Placode Progenitor Dependent. Developmental cell, 48(1), 32-48.e5.

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Single-cell RNA-seq of Frozen Adenoma Tissue

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Snap-frozen adenoma tissue was stained with 10 μg ml⁻¹ Hoechst 34580 (Sigma-Aldrich) and minced in a petri dish, on ice, using a cross-hatching motion with two scalpels. The minced tissue was kept on ice for 1 h after which it was filtered through 70 μm and 35 μm strainer. Nuclei were sorted in a 384-well plate containing 5 μl of mineral oil (Sigma) in each well and stored at −20 °C until further processing for library preparation and sequencing. For library preparation primers consisted of a 24 bp polyT stretch, a 4 bp random molecular barcode (UMI), a cell-specific 8 bp barcode, the 5′ Illumina TruSeq small RNA kit adapter and a T7 promoter. mRNA of each cell was then reverse transcribed, converted to double-stranded cDNA, pooled and in vitro transcribed. Illumina sequencing libraries were prepared with the TruSeq small RNA primers (Illumina). Libraries were sequenced on an Illumina Nextseq 500 with 1 × 75 bp single-end sequencing^{44 (link),77 (link)}. The fastq files were mapped to GRCH38 using the Burrows-Wheeler Aligner. The mapped data was further analyzed using custom scripts in Python, which parsed for library barcodes, removed reads without a NlaIII sequence and removed PCR-duplicated reads. Copy number analysis was performed performed with the AneuFinder1.6.0 pipeline^{78 (link)}.

Hoevenaar W.H., Janssen A., Quirindongo A.I., Ma H., Klaasen S.J., Teixeira A., van Gerwen B., Lansu N., Morsink F.H., Offerhaus G.J., Medema R.H., Kops G.J, & Jelluma N. (2020). Degree and site of chromosomal instability define its oncogenic potential. Nature Communications, 11, 1501.

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Single-cell Sequencing of Zebrafish Samples

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Single-cell sequencing libraries were prepared using SORT-seq (Muraro et al. 2016 ). Live cells were sorted into 384-well plates with Vapor-Lock oil containing a droplet with barcoded primers, spike-in RNA and dNTPs, followed by heat-induced cell lysis and cDNA syntheses using a robotic liquid handler. Primers consisted of a 24 bp polyT stretch, a 4 bp random molecular barcode (UMI), a cell-specific 8 bp barcode, the 5' Illumina TruSeq small RNA kit adapter and a T7 promoter. After cell-lysis for 5 min at 65°C, RT and second strand mixes were distributed with the Nanodrop II liquid handling platform (Inovadyne). After pooling all cells in one library, the aqueous phase was separated from the oil phase, followed by IVT transcription. The CEL-Seq2 protocol was used for library prep (Hashimshony et al. 2016) .
Illumina sequencing libraries were prepared with the TruSeq small RNA primers (Illumina) and paired-end sequenced at 75 bp read length on the Illumina NextSeq platform. Mapping was performed against the zebrafish reference assembly version 9 (Zv9).

Bakker D.E.M.d., Dronkers E., Bouwman M., Vink A., Goumans M., Smits A.M., & Bakkers J. (2020). Prrx1b directs pro-regenerative fibroblasts during zebrafish heart regeneration.

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