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Truseq rna libraries

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The TruSeq RNA libraries are a set of lab equipment products from Illumina designed for the preparation of RNA sequencing libraries. The core function of the TruSeq RNA libraries is to enable the conversion of RNA samples into sequencing-ready libraries, which can then be used for various RNA analysis applications.

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Lab products found in correlation

Hiseq 2000, by Illumina (3 mentions) Nanodrop, by Thermo Fisher Scientific (2 mentions) Purelink rna mini kit, by Thermo Fisher Scientific (2 mentions) Spectrum plant total rna kit, by Merck Group (1 mentions) Agilent bioanalyzer, by Agilent Technologies (1 mentions) 2100 bioanalyzer, by Illumina (1 mentions) Qubit instrument, by Thermo Fisher Scientific (1 mentions) Direct zol rna miniprep, by Zymo Research (1 mentions) Rna seq, by Macrogen (1 mentions) Hiseq 2000 v3, by Illumina (1 mentions) Trizol, by Thermo Fisher Scientific (1 mentions) Rnalater, by Thermo Fisher Scientific (1 mentions) Genejet rna purification kit, by Thermo Fisher Scientific (1 mentions) Hiseq 4000 sequencer, by Illumina (1 mentions) Agilent 2100 bioanalyzer, by Agilent Technologies (1 mentions) 2100 bioanalyzer, by Agilent Technologies (1 mentions) Hiseq 1500, by Illumina (1 mentions) Mirvana rna extraction kit, by Thermo Fisher Scientific (1 mentions)

Close spelling variants of this product

TruSeq libraries (17 citations) TruSeq strand-specific RNA libraries (4 citations) TruSeq RNA-seq libraries (3 citations) TruSeq RNA sequencing libraries (3 citations) TruSeq Stranded Total RNA libraries that include rRNA depletion (2 citations)

9 protocols using truseq rna libraries

1

RNA-Seq Workflow for Plant Tissues

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For each sample, liquid nitrogen frozen tissue sample (100 mg) was ground using a mortar and pestle cooled in presence of liquid nitrogen. A SpectrumTM Plant Total RNA kit (Sigma-Aldrich, St. Louis, MO, United States) was employed according to the manufacturer’s instructions. Quality control was performed on a Thermo Scientific NanoDrop with all 260/280 nm and 260/230 nm readings above 1.8. Illumina TruSeq RNA libraries were constructed per the manufacturer’s protocol, with quality evaluated using the Agilent Bioanalyzer. Samples were sequenced on a HiSeq 2000 instrument (Illumina, San Diego, CA, United States). Six lanes were multiplexed with five samples per lane in the single ended, 50 bp configuration. A mean of 41 M reads passing quality filters was obtained for each sample (min. 31 M, max. 50 M). Cluster generation used the cBot SR Cluster Gen Kit (V3) and the flow cell used was SR FC Information (V3).
Hixson K.K., Marques J.V., Wendler J.P., McDermott J.E., Weitz K.K., Clauss T.R., Monroe M.E., Moore R.J., Brown J., Lipton M.S., Bell C.J., Paša-Tolić L., Davin L.B, & Lewis N.G. (2021). New Insights Into Lignification via Network and Multi-Omics Analyses of Arogenate Dehydratase Knock-Out Mutants in Arabidopsis thaliana. Frontiers in Plant Science, 12, 664250.
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2

Comprehensive RNA-seq Data Generation

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The full-length cDNA molecules were fragmentized and used for preparation of Illumina TruSeq RNA libraries with an insert size of 300–400 bp. Each library was verified for the size with Bioanalyzer 2100 and quantified according to Illumina qPCR Quantification Protocol Guide (Illumina, USA). Illumina HiSeq 2000 250PE (250-bp read length, paired-end) platform was used for human peripheral blood, and HiSeq 4000 250PE was used for tumor and paired non-malignant samples. After the adapters and low-quality reads were filtered, the Bowtie-TopHat-Cufflinks pipeline was applied to map the filtered reads to human reference genome and quantify the expression of genes or isoforms37 (link). The NCBI build 38 (GRCh38) of hg38 and GENECODE version 31 were used38 (link). To align the reads against long transcript sequences, bowtie was used, and SAM files were generated for further analysis.
Hu Y., Shu X.S., Yu J., Sun M.A., Chen Z., Liu X., Fang Q., Zhang W., Hui X., Ying Y., Fu L., Lu D., Kumar R, & Wang Y. (2020). Improving the diversity of captured full-length isoforms using a normalized single-molecule RNA-sequencing method. Communications Biology, 3, 403.
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3

Total RNA Extraction and Sequencing

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Total RNA was extracted from a total of 72 larvae, six per time point, per treatment. RNA was purified with the Direct-zol RNA MiniPrep (Zymo, Irvine, CA, United States) as per manufacturer’s instructions. Quality and quantity of the total RNA purified were determined using Experion equipment (Bio-Rad, Hercules, CA, United States) and a Qubit instrument (Thermo Fisher Scientific, Waltham, MA, United States) Due to technical error one individual of the PBS treatment failed, therefore this sampling point only has five replicates, which resulted in the final total of 71 individuals sequenced. Library preparation, sequencing and data processing of the RNA was performed at the National Genomics Infrastructure Sweden (NGI Stockholm) using strand specific Illumina TruSeq RNA libraries with poly-A selection (Illumina HiSeq HO mode v4, paired-end 2 × 125 bp).
Keehnen N.L., Kučerová L., Nylin S., Theopold U, & Wheat C.W. (2021). Physiological Tradeoffs of Immune Response Differs by Infection Type in Pieris napi. Frontiers in Physiology, 11, 576797.
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4

Transcriptome Profiling of Hypoxia Adaptation

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Transcriptome profiling using Next Generation Sequencing (NGS) was performed for individuals exposed to normoxia and hypoxia for one week. Three replicate pools of males (n = 10) for each treatment were fast frozen in liquid nitrogen, and immediately stored at −80 °C. Total RNA was isolated using a PureLink RNA Mini Kit (ThermoFisher Scientific, UK). TruSeq RNA libraries (Illumina, USA) were synthesised and sequenced using 100 base paired-end sequencing (HiSeq 2000, Illumina, USA). Details of assembly, annotation and data availability are provided in55 (link). Alignment of the assembled transcriptome to the original reads was performed using Bowtie v.1.1.156 (link). Gene counts were generated by RSEM v.1.2.29 and imported into R v.3.3.1 using Tximport v.1.0.3. Differential gene expression analysis was performed at the level of Trinity “genes” using DESeq2.v.1.12.457 (link) to identify haemocyanin genes that displayed significantly different expression (P < 0.05) between the hypoxic and normoxic treatment.
Truebano M., Tills O., Collins M., Clarke C., Shipsides E., Wheatley C, & Spicer J.I. (2018). Short-term acclimation in adults does not predict offspring acclimation potential to hypoxia. Scientific Reports, 8, 3174.
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5

Illumina RNA-Seq transcriptome profiling

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Global messenger RNA sequencing was performed by Macrogen’s “RNA-seq” service in South Korea. In summary, Illumina TruSeq RNA libraries were prepared, and 100 bp (Paired-End) sequences were obtained from each of them on a HiSeq 4000 platform. Between 12 and 14 million reads per library were obtained. The data are deposited at the NCBI, BioProject ID: PRJNA739193.
Lazcano-Ramírez H.G., Gamboa-Becerra R., García-López I.J., Montes R.A., Díaz-Ramírez D., de la Vega O.M., Ordaz-Ortíz J.J., de Folter S., Tiessen-Favier A., Winkler R, & Marsch-Martínez N. (2021). Effects of the Developmental Regulator BOLITA on the Plant Metabolome. Genes, 12(7), 995.
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6

Transcriptome Profiling of Diverse Fireflies

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We selected 10 firefly species for RNA sequencing based on taxonomic divergence, divergence in signaling mode and emission wavelength, and the availability of specimens (Figure 1; Table S1). Males were used since females of many species are difficult to locate in the field. For each of the 10 species, RNA was isolated from 1–6 heads harvested during the active period and immediately frozen in liquid nitrogen or stored in RNAlater (LifeTechnologies). Bodies of specimens selected for RNA and genomic sequencing, and all other specimens used in PCR amplification, were preserved in 95% ethanol at −80°C until extraction. RNA was also isolated from the adult light organs of Photinus pyralis and Photinus macdermotti, and from the larval light organ of Pn. pyralis based on specimen availability.
Total RNA from all samples was extracted using Trizol (LifeTechnologies) and treated with DNase prior to library construction. TruSeq RNA libraries (Illumina) were constructed at the Georgia Genomics Facility (Athens, GA) with an average insert size of 150 bp. Samples were individually barcoded and pooled before submission to BGI (Hong Kong) for 100 bp, paired-end sequencing in one lane of Illumina HiSeq2000 v3.
Sander S.E, & Hall D.W. (2015). Variation in opsin genes correlates with signaling ecology in North American fireflies. Molecular ecology, 24(18), 4679-4696.
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7

Transcriptomic Analysis of Individuals

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Total RNA was isolated from individuals using the GeneJET RNA Purification Kit (Thermo Scientific, USA) (N = 5 per treatment). RNA integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies, USA). Library preparation and RNA sequencing were performed at the Beijing Genomics Institute, Hong Kong. A total of 20 TruSeq RNA libraries (Illumina, San Diego, USA) were prepared and sequenced on two lanes of an Illumina HiSeq 4000 sequencer using 100‐bp paired‐end sequencing (Illumina, San Diego, USA).
Collins M., Clark M.S., Spicer J.I, & Truebano M. (2020). Transcriptional frontloading contributes to cross‐tolerance between stressors. Evolutionary Applications, 14(2), 577-587.
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8

ASFV Infection in Xenopus Transcriptome Analysis

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PAMs were infected with ASFV CN/GS/2018 or ASFV-ΔQP509L/383R for 24 h. Total RNA was extracted as previously described (42 (link)). The quality of total RNA with an RNA integrity number of 7 or higher was assessed using an Agilent 2100 Bioanalyzer. Illumina TruSeq RNA libraries were constructed from two total RNA samples (each sample was a mixture of three biological repeats). The libraries were sequenced using 100-bp paired-end reads on an Illumina HiSeq 2000. Sequenced reads were checked for base qualities, trimmed wherein 20% of bases were below a quality score of 20, and filtered to exclude sequences that were shorter than 20 bp using Fastx (Version 0.0.13). Sequences were aligned to the Xenopus tropicalis genome JGI 4.2/xenTro3 using gsnap (43 (link)) with the following parameters: -B 4-E 100 -N 1. The aligned reads were counted using HTSeq (version 0.5.4p2) with the following parameters: -m intersection-strict -s no -a 20, and further differential gene expression analysis was carried out using DESeq2 (version 1.0.19) (44 (link)) with default settings.
Li D., Wu P., Liu H., Feng T., Yang W., Ru Y., Li P., Qi X., Shi Z, & Zheng H. (2022). A QP509L/QP383R-Deleted African Swine Fever Virus Is Highly Attenuated in Swine but Does Not Confer Protection against Parental Virus Challenge. Journal of Virology, 96(1), e01500-21.
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9

Total RNA Extraction and Sequencing

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Total RNA from the nucleated cells was extracted using either the MirVana RNA extraction kit (Invitrogen). The concentration and quality of total RNA for each sample were quantified and evaluated by spectrophotometry (Epoch; Thermo Scientific) and automated chip electrophoresis analyses (Experion, BioRad) respectively. Each sample met the quality standards of a 260/280 ratio > 2.0 and a RNA integrity number (RIN) > 9. Illumina TruSeq RNA libraries (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.
The copyright holder for this preprint this version posted August 13, 2021. ; https://doi.org/10.1101/2021.08.13.454953 doi: bioRxiv preprint were prepared from 1 μg total RNA and sequenced to generate 50 base pair single-end reads using the the HiSeq 1500 (Illumina, USA) at the Children's Mercy OMICs Research Core Lab (Kansas City, MO).
Hsieh L., Tu L.N., Paquette A.G., Kibiryeva N., Marshall J., Bittel D.C., O’Brien J.E., Vickers K.C., Pastuszko P., & Nigam V. (2021). microRNA Expression Levels Change in Neonatal Patients During and After Exposure to Cardiopulmonary Bypass.
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