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Truseq stranded mrna sample prep kit

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The TruSeq Stranded mRNA Sample Prep Kit is a laboratory equipment product designed for RNA-Seq library preparation. It is used to convert messenger RNA (mRNA) into a library of cDNA fragments with adaptors attached to one or both ends. The kit enables the preservation of strand orientation information during the library preparation process.

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Lab products found in correlation

Hiseq 2500, by Illumina (76 mentions) Rneasy mini kit, by Qiagen (39 mentions) Trizol reagent, by Thermo Fisher Scientific (36 mentions) Agilent 2100 bioanalyzer, by Agilent Technologies (33 mentions) Hiseq 2000, by Illumina (30 mentions) Trizol, by Thermo Fisher Scientific (27 mentions) Hiseq 2500 platform, by Illumina (25 mentions) Nextseq 500, by Illumina (25 mentions) Novaseq 6000, by Illumina (24 mentions) Bioanalyzer, by Agilent Technologies (23 mentions) 2100 bioanalyzer, by Agilent Technologies (23 mentions) Casava 1, by Illumina (21 mentions) Hiseq 3000, by Illumina (15 mentions) Rneasy plus mini kit, by Qiagen (13 mentions) Hiseq 4000, by Illumina (12 mentions) Mirneasy mini kit, by Qiagen (11 mentions) Rnalater, by Thermo Fisher Scientific (11 mentions) Nanodrop, by Thermo Fisher Scientific (11 mentions) Hiseq 1500, by Illumina (10 mentions) Direct zol rna miniprep kit, by Zymo Research (10 mentions)

Spelling variants of this product

TruSeq Stranded mRNA (115 citations) TruSeq kits (44 citations) Stranded mRNA Prep (27 citations) Illumina sample prep kit (8 citations) MRNA TruSeq kit (7 citations)

409 protocols using truseq stranded mrna sample prep kit

1

RNA-seq Analysis Pipeline for Differential Expression

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Total RNA was extracted using TRIzol (Invitrogen) and the miRNeasy Mini Kit (Qiagen) according to manufacturer instructions. After ribosomal RNA depletion using RiboMinus (Life Technologies), the resulting RNA samples were then used as input for library construction using Illumina TruSeq stranded mRNA sample prep kit (RS-122-2101), as per manufacturer's instructions. RNA libraries were then sequenced on the Illumina Genome Analyzer IIx (86 bp paired-end). For the second sequencing run, total RNA was sent to I.G.A. Applied Genomics Institute (Udine, IT) for library preparation using the Illumina TruSeq stranded mRNA sample prep kit (RS-122-2101) and subjected to sequencing on an Illumina HiSeq 2000 (100 bp paired-end). All RNA-seq data were aligned to hg19 genome using TopHat v2.0.12 with default parameters and assem-bled using Cufflinks 2.2.1 [28 (link)] and Gencode v.19 as reference file. We used Cuffdiff v2.2.1 [29 (link)] for all differential expression, with a false discovery rate (FDR) of 0.1.
Hughes J.M., Legnini I., Salvatori B., Masciarelli S., Marchioni M., Fazi F., Morlando M., Bozzoni I, & Fatica A. (2015). C/EBPα-p30 protein induces expression of the oncogenic long non-coding RNA UCA1 in acute myeloid leukemia. Oncotarget, 6(21), 18534-18544.
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2

m6A Methylation Profiling by meRIP-Seq

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meRIP-Seq and data analysis were performed as previously described with minor modifications (Dominissini et al., 2013 (link)). Briefly, mRNA was first purified from total RNA using PolyATtract® mRNA Isolation Systems (Promega). Then 5 μg mRNA was fragmented and immunoprecipated with anti-m6A antibody (Synaptic Systems, 202003), the immunoprecipated RNA was washed and eluted by competition with N6-Methyladenosine (Sigma-Aldrich, M2780). The purified RNA fragments from m6A meRIP were used for library construction using TruSeq Stranded mRNA Sample Prep Kits (Illumina RS-122-2101) and sequenced with Illumina HiSeq 2000. Reads mapping, m6A peak calling and motif search were performed as described (Dominissini et al., 2013 (link)). Analysis of the published PAR-CLIP was performed as previously described (Liu et al., 2014 (link)). For deep sequence analysis of RNA expression, 2 μg total RNA was used for the library construction using TruSeq Stranded mRNA Sample Prep Kits (Illumina RS-122-2101) according to the manufacturer’s instructions.
Lin S., Choe J., Du P., Triboulet R, & Gregory R.I. (2016). METTL3 promotes translation in human cancer cells. Molecular cell, 62(3), 335-345.
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3

TruSeq Stranded mRNA Sequencing

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mRNA-seq libraries were constructed using the TruSeq Stranded mRNA Sample Prep kit following the manufacturer’s protocol (Illumina) and sequenced on a HiSeq 2500 platform (Illumina) using 50-bp single-end SBS chemistry.
van den Hurk M., Lau S., Marchetto M.C., Mertens J., Stern S., Corti O., Brice A., Winner B., Winkler J., Gage F.H, & Bardy C. (2022). Druggable transcriptomic pathways revealed in Parkinson’s patient-derived midbrain neurons. NPJ Parkinson's Disease, 8, 134.
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4

Serotonergic Neuron RNA Sequencing Protocol

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Six to eight-week old serotonergic neurons were harvested for RNA isolation. Total cellular RNA was extracted from approximately 3 × 106 cells using TriZol (Thermo Fisher Scientific) according to the manufacturer’s instructions. RNA was isolated using phenol, chloroform and isopropanol. RIN values were calculated to ensure high quality of RNA prior to library preparation (average RIN of the samples was 8.8). RNA-Seq libraries were prepared using the TruSeq Stranded mRNA Sample Prep Kit according to the manufacturer’s instructions (Illumina) and reverse transcribed into cDNA with protoscript II reverse transcriptase (Invitrogen). Stranded cDNA libraries were generated according to manufacturer’s instructions (Illumina). Total (mRNA) RNA-Seq libraries were sequenced as 50 basepairs (single-end) using the Illumina® HiSeq 2500 platform as per the manufacturer’s specifications. Low quality ends and adapter removal/trimming were performed using cutadapt. Trimmed reads were mapped using STAR [30 (link)] and assigned to genes with featurecounts [31 (link)], and normalized counts and differential expression were calculated using the DESeq2 R package [32 (link)]. Normalized count numbers were processed using R software for visualization and for further comparisons. RNA-sequencing data can be made available to reviewers via a GEO accession code#.
Vadodaria K.C., Ji Y., Skime M., Paquola A.C., Nelson T., Hall-Flavin D., Heard K.J., Fredlender C., Deng Y., Elkins J., Dani K., Le A.T., Marchetto M.C., Weinshilboum R, & Gage F.H. (2019). Altered serotonergic circuitry in SSRI-resistant major depressive disorder patient-derived neurons. Molecular psychiatry, 24(6), 808-818.
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5

Profiling m6A Epitranscriptome Landscape

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Polyadenylated RNA was extracted from treated cells using FastTrack MAG Maxi mRNA isolation kit (Life technology, USA). RNA fragmentation Reagents (Ambion, USA) was used to randomly fragment RNA. The specific anti-m6A antibody (Synaptic Systems, 202003, 1:50) was applied for m6A pull down. The library preparation for next-generation sequencing was constructed by TruSeq Stranded mRNA Sample Prep Kit (Illumina, USA) and quantified by BioAnalyzer High Sensitivity DNA chip, and then deeply sequenced on the Illumina HiSeq 2500. For data analysis, the reads from input and m6A-IP sequencing libraries were aligned to hg19 reference genome using Tophat. Both MACS/MACS2 and exomePeak were used to call m6A peaks based on the m6A-seq bam files. To achieve high specificity, only the m6A peaks called by both MACS/MACS2 and exomePeak were retained for further analysis. Differentially methylated m6A peaks were identified according to the procedure described by Schwartz et al.51 (link). Sequence motifs enriched in m6A peak regions compared to control regions were identified using DREME.
Zeng J., Xie C., Huang Z., Cho C.H., Chan H., Li Q., Ashktorab H., Smoot D.T., Wong S.H., Yu J., Gong W., Liang C., Xu H., Chen H., Liu X., Wu J.C., Ip M., Gin T., Zhang L., Chan M.T., Hu W, & Wu W.K. (2024). LOX-1 acts as an N6-methyladenosine-regulated receptor for Helicobacter pylori by binding to the bacterial catalase. Nature Communications, 15, 669.
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6

Total RNA Extraction and RNA-Seq Library Prep

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RNA was extracted using GenElute™ Mammalian Total RNA Miniprep Kit (Sigma-Aldrich) from 30 whole female flies, 4 to 6 days old, per replicate (three replicates per strain analyzed). RNA samples were treated with DNAse I (Thermo Fisher Scientific) following manufacturer’s instructions. RNA concentration was measured using NanoDrop spectrophotometer (NanoDrop Technologies) and quality was assessed with Bioanalyzer. Library preparation for RNA sequencing was performed using the Truseq Stranded mRNA Sample Prep kit from Illumina following the manufacturer's instructions. Libraries were sequenced using Illumina 125 bp paired-end reads.
Horváth V., Guirao-Rico S., Salces-Ortiz J., Rech G.E., Green L., Aprea E., Rodeghiero M., Anfora G, & González J. (2023). Gene expression differences consistent with water loss reduction underlie desiccation tolerance of natural Drosophila populations. BMC Biology, 21, 35.
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7

Transcriptome Profiling of ND and OP Clones

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RNA was extracted from three ND and three OP clones using a NucleoSpin RNA kit (Macherey-Nagel, Düren, Germany) according to the manufacturer's instructions. DNA contamination was assessed using a PicoGreen dsDNA assay kit (Thermo Fisher Scientific), and RNA quantity and quality were examined using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) with an RNA integrity number ≥ 7. A cDNA library was generated using a TruSeq Stranded mRNA sample prep kit (Illumina, San Diego, CA), and transcriptome sequencing was performed using a TruSeq 3000/4000 SBS kit and HiSeq 4000 sequencer (Illumina) with 101 bp paired-end reads per sample (Macrogen, Seoul, Korea).
Kim Y.H., Cho K.A., Lee H.J., Park M., Kim H.S., Park J.W., Woo S.Y, & Ryu K.H. (2019). Identification of WNT16 as a Predictable Biomarker for Accelerated Osteogenic Differentiation of Tonsil-Derived Mesenchymal Stem Cells In Vitro. Stem Cells International, 2019, 8503148.
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8

RNA-seq Analysis of Pathogen Infection

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RNA extractions were performed as previously described (Gascuel et al., 2016b). RNA‐seq libraries were prepared at the GeT‐PlaGe facility (Toulouse, France) from mRNA selected using poly‐T beads, according to the Illumina TruSeq Stranded mRNA sample prep kit protocols. RNA‐seq read pairs were mapped on P. halstedii 710 genome using the glint software with parameters set as follows: matches ≥50 nucleotides, ≤4 mismatches, no gap allowed, only best‐scoring hits taken into account (Table S6). Ambiguous matches (same best score) were removed. Statistical treatment of the mapped reads was carried out with under [R] environment using the DESeq package (Love et al., 2014). Independent filtering and outlier detection methods proposed by the package were used. Genes presenting a false‐discovery rate (FDR)‐corrected P‐value ≤0.05 were considered as differentially expressed between two given conditions. The overwhelming number of sunflower reads in the samples collected at the beginning of infection by P. halstedii (24 hpi) compared with the P. halstedii ones implies to consider results on differential expression with caution (Table S6).
Pecrix Y., Buendia L., Penouilh‐Suzette C., Maréchaux M., Legrand L., Bouchez O., Rengel D., Gouzy J., Cottret L., Vear F, & Godiard L. (2019). Sunflower resistance to multiple downy mildew pathotypes revealed by recognition of conserved effectors of the oomycete Plasmopara halstedii. The Plant Journal, 97(4), 730-748.
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9

RNA-Seq Analysis of Gene Expression

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We conducted RNA sequencing as previously described.18 (link) The library was prepared using a TruSeq Stranded mRNA Sample Prep Kit (Illumina, San Diego, CA, USA). Sequencing was performed using the Illumina HiSeq 2500 platform in 75-base single-end mode. Illumina Casava 1.8.2 software was used for base calling, and the sequenced reads were mapped to human reference genome sequences (hg19) using TopHat version 2.0.13 combined with Bowtie2 version 2.2.3 and SAMtools version 0.1.19. We calculated the fragments per kilobase of exon per million mapped fragments (FPKMs) using Cuffnorm version 2.2.1. We identified a series of genes that were enhanced (>2.0-fold) or reduced (<2.0-fold) for further gene expression analysis. The raw data were deposited in the NCBI Gene Expression Omnibus database under GEO accession number GSE134442. We identified enhanced or suppressed pathways using Qiagen’s Ingenuity Pathway Analysis (IPA; Qiagen Redwood City, www.qiagen.com/ingenuity) with the default settings.
Morimoto Y., Mizushima T., Wu X., Okuzaki D., Yokoyama Y., Inoue A., Hata T., Hirose H., Qian Y., Wang J., Miyoshi N., Takahashi H., Haraguchi N., Matsuda C., Doki Y., Mori M, & Yamamoto H. (2020). miR-4711-5p regulates cancer stemness and cell cycle progression via KLF5, MDM2 and TFDP1 in colon cancer cells. British Journal of Cancer, 122(7), 1037-1049.
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10

Ant Venom Gland RNA Sequencing

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Venom glands and sacs from 20 live ant workers, anesthetized by cooling, were dissected in a PBS solution. Each tissue was immediately placed in 500 µL of TRIzol reagent (Invitrogen, Carlsbad, CA, USA) and total RNAs were extracted afterward using the RNeasy Micro Kit (Qiagen) according to manufacturer’s instructions. Contaminating genomic DNA was removed using a DNA-free kit (Applied Biosystem) according to the manufacturer’s instructions. RNA quantity was evaluated using a nanodrop and a bioanalyzer (Nanodrop 2000, ThermoFisher Scientific; Agilent 2100 Bioanalyzer System). RNAseq was performed at the GeT-PlaGe core facility, INRA Toulouse, France. RNA-seq libraries were prepared according to Illumina’s protocols using the Illumina TruSeq Stranded mRNA sample prep kit to analyze mRNA. Briefly, mRNA was selected using poly-T beads. Then, the RNA was fragmented to generate double stranded cDNA and adaptors were ligated to be sequenced. Eleven cycles of PCR were applied to amplify the libraries. Library quality was assessed using a Fragment Analyser, and the libraries were quantified through qPCR using the Kapa Library Quantification Kit. RNA-seq experiments were performed on an Illumina HiSeq3000 using a paired-end read length of 2 × 150 pb with the Illumina HiSeq3000 sequencing kits.
Barassé V., Touchard A., Téné N., Tindo M., Kenne M., Klopp C., Dejean A., Bonnafé E, & Treilhou M. (2019). The Peptide Venom Composition of the Fierce Stinging Ant Tetraponera aethiops (Formicidae: Pseudomyrmecinae). Toxins, 11(12), 732.
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