Truseq rna sample prep kit v2

Manufactured by Illumina

Sourced in United States, China, United Kingdom, Canada

The TruSeq RNA Sample Prep Kit v2 is a laboratory equipment product designed for RNA sample preparation. It provides a standardized workflow for converting RNA into a library of template molecules suitable for subsequent sequencing analysis.

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Lab products found in correlation

Hiseq 2000, by Illumina (111 mentions) 2100 bioanalyzer, by Agilent Technologies (61 mentions) Hiseq 2500, by Illumina (57 mentions) Agilent 2100 bioanalyzer, by Agilent Technologies (53 mentions) Trizol reagent, by Thermo Fisher Scientific (51 mentions) Rneasy mini kit, by Qiagen (46 mentions) Hiseq 4000, by Illumina (29 mentions) Trizol, by Thermo Fisher Scientific (24 mentions) Rneasy plant mini kit, by Qiagen (23 mentions) Hiseq 2000 platform, by Illumina (21 mentions) Qubit 1.0 fluorometer, by Thermo Fisher Scientific (17 mentions) Bioanalyzer, by Agilent Technologies (15 mentions) Hiseq 2500 platform, by Illumina (15 mentions) Qubit 2.0 fluorometer, by Thermo Fisher Scientific (14 mentions) Truseq sbs kit v3, by Illumina (14 mentions) Hiseq 2500 system, by Illumina (14 mentions) Hiseq 4000 platform, by Illumina (13 mentions) Nanodrop spectrophotometer, by Thermo Fisher Scientific (12 mentions) Ribo zero rrna removal kit, by Illumina (12 mentions) Novaseq 6000, by Illumina (11 mentions)

Close spelling variants of this product

TruSeq kits (44 citations) TruSeq v2 kit (38 citations) Illumina sample prep kit (8 citations) V2 kits (4 citations) Prep Kit V2 (2 citations) Kit v2 (2 citations)

555 protocols using truseq rna sample prep kit v2

RNA-seq Library Preparation Protocol

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RNA libraries were constructed using the TruSeq RNA Sample Prep Kit v2 (Illumina, Inc., San Diego, CA, USA). mRNA was purified using oligo(dT) magnetic beads and fragmented at 95 ℃ for 8 min using the fragment buffer in the TruSeq RNA Sample Prep Kit v2 (Illumina, Inc., San Diego, CA, USA). The first cDNA strand was synthesized using random oligonucleotides and SuperScript III reverse transcriptase (Invitrogen; Thermo Fisher Scientific Inc., Waltham, MA, USA) under the following conditions: 65 ℃ for 5 min, 4 ℃ for 2 min, 42 ℃ for 1 h, and 70 ℃ for 10 min. The second cDNA strand was synthesized by adding buffer, dNTP, RNase H (Invitrogen; Thermo Fisher Scientific Inc.), and DNA polymerase I (Invitrogen; Thermo Fisher Scientific Inc.) under the following conditions: 16 ℃ for 2.5 h and 70 ℃ for 10 min. The sequencing adapters were repaired and ligated using the NEB Next End Repair Module (New England Biolabs, Ipswich, MA, USA) after purification with the QIAQuick PCR Purification Kit (Qiagen, Inc., Valencia, CA, USA).

Feng X., Zhu S., Qiao J., Ji Z., Zhou B, & Xu W. (2023). CX3CL1 promotes M1 macrophage polarization and osteoclast differentiation through NF-κB signaling pathway in ankylosing spondylitis in vitro. Journal of Translational Medicine, 21, 573.

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Primary human lung fibroblast RNA-seq

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A total of 2 × 10⁵ primary human lung fibroblasts obtained from fresh and cryopreserved explants from 3 donors in 2–5 technical replicates were harvested at passage 3. Total RNA was isolated using the RNeasy Plus Micro Kit (Qiagen) following the manufacturer’s instructions (for details of reagents please see Supplemental Table 8). DNA was removed by passing the lysate through the genomic DNA eliminator column provided with the kit and by on-column DNase treatment before elution (Qiagen). RNA was eluted using nuclease-free water (Thermo Fisher Scientific) and the concentration measured with Qubit RNA Assay Kit in Qubit 3.0 Fluorometer (Thermo Fisher Scientific). RNA integrity was assessed using the RNA Pico 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies), and only samples with RIN higher than 8 were processed further. Stranded mRNA-Seq libraries were prepared at the EMBL GeneCore from 200 ng of total RNA using the Illumina TruSeq RNA Sample Prep v2 Kit implemented on the liquid handling robot Beckman FXP2. The libraries were pooled in equimolar amounts, and 1.8 pM solution of each pool was loaded on the Illumina sequencer NextSeq 500 high output and sequenced unidirectionally, generating approximately 450 million reads per run, each 75 bases long.

Llamazares-Prada M., Espinet E., Mijošek V., Schwartz U., Lutsik P., Tamas R., Richter M., Behrendt A., Pohl S.T., Benz N.P., Muley T., Warth A., Heußel C.P., Winter H., Landry J.J., Herth F.J., Mertens T.C., Karmouty-Quintana H., Koch I., Benes V., Korbel J.O., Waszak S.M., Trumpp A., Wyatt D.M., Stahl H.F., Plass C, & Jurkowska R.Z. (2021). Versatile workflow for cell type–resolved transcriptional and epigenetic profiles from cryopreserved human lung. JCI Insight, 6(6), e140443.

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Transcriptome Analysis of Fungal Conditions

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Total RNA from aliquots was extracted using the RNeasy Plant Mini kit (Qiagen) according to manufacturer’s instructions. RNA concentration was determined in a Nanodrop 2100c (Thermo Fisher Scientific, Waltham, MA, USA) and the integrity was evaluated in a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) using the Agilent RNA 6000 Nano kit (Agilent Technologies, Santa Clara, CA, USA). Total RNA from two biological replicates per condition (SEB or fructose) from both fungi was used as input for the TruSeq RNA Sample Prep v2 kit (Illumina, San Diego, CA, USA) and the libraries were sequenced at the USC Epigenome Center (CA, USA) using the Illumina® HiSeq2000 system, producing single-end reads of 50 bp.

Borin G.P., Sanchez C.C., de Santana E.S., Zanini G.K., dos Santos R.A., de Oliveira Pontes A., de Souza A.T., Dal’Mas R.M., Riaño-Pachón D.M., Goldman G.H, & Oliveira J.V. (2017). Comparative transcriptome analysis reveals different strategies for degradation of steam-exploded sugarcane bagasse by Aspergillus niger and Trichoderma reesei. BMC Genomics, 18, 501.

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RNA-Seq Analysis of Peripheral Neuropathy

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RNA extraction and Illumina RNA sequencing was done as described previously.⁴² RNA-Seq libraries were constructed from 1 μg total RNA after rRNA depletion using Ribo-Zero GOLD (Illumina). The Illumina TruSeq RNA Sample Prep V2 Kit was used according to manufacturer’s instructions except where noted. The data were processed using RTA v. 1.18.64 and CASAVA v. 1.8.2. The data for 23 PN and two normal adult Schwann cells samples were further processed using standard Tuxedo pipeline.^{43 (link)} The resulting gene expression from transcriptome datasets were then log2 transformed and standardized (z-scored). Genes with the median log2 FPKM score below 0.5 in both groups (PN and normal Schwann cells) were considered unexpressed and removed from the analysis. The resulting expression set of 11 293 genes was analyzed with GSEA as described.^{44 (link)} We used 5000 permutations and shuffled the expression dataset by gene-sets rather than by sample labels. Gene-sets with FDR < 0.01 were considered statistically significant and with 0.01 ≤ FDR < 0.02 as trending.

Pemov A., Li H., Patidar R., Hansen N., Sindiri S., Hartley S., Wei J., Elkahloun A., Chandrasekharappa S., Boland J., Bass S., Mullikin J., Khan J., Widemann B., Wallace M, & Stewart D. (2017). The primacy of NF1 loss as the driver of tumorigenesis in neurofibromatosis type 1-associated plexiform neurofibromas. Oncogene, 36(22), 3168-3177.

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RNA Extraction and Sequencing

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Total RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, CA, USA), treated with TURBO DNase I (Ambion, Austin, TX, USA) for 30 min and purified using RNeasy^® Plant Mini Kit (QIAGEN, Hilden, Germany). RNA sequence libraries were prepared with TruSeq RNA sample Prep V2 kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. The quality and size of cDNA libraries were checked using Agilent 2200 TapeStation system (Agilent, Santa Clara, CA, USA) prior to sequencing. cDNA libraries were sequenced using the Illumina HiSeqX10 sequencing system with the 150-cycle paired-end sequencing protocol.

Yang X., Guo X., Yang Y., Ye P., Xiong X., Liu J., Dong D, & Li G. (2018). Gene Profiling in Late Blight Resistance in Potato Genotype SD20. International Journal of Molecular Sciences, 19(6), 1728.

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RNA-Seq of Myoblast and Myotube Cells

Cited 1 time

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RNA was isolated from XX primary myoblast and 24-h-differentiated myotube cells using Tripure (Roche) followed by the RNeasy Micro kit (Qiagen). Samples with RNA Integrity numbers of ≥9 were used for sequencing. RNA-Seq was performed in two batches: (A) two wild type myoblasts, three wild type myotubes and two ΔICR/ΔICR myotube samples were sequenced at the NIH Intramural Sequencing Center using Illumina HiSeq2000 sequencers; and (B) two wild type myoblasts, two wild type myotubes and two ΔICR/ΔICR myoblasts were sequenced at the NICHD Molecular Genomics Core using an ABI SOLiD 5500xl sequencer. Ribosomal RNA was depleted from 1 to 5 μg total RNA using the RiboZero Gold kit (Illumina). Library preparation for the Illumina HiSeq2000 was performed using the TruSeq RNA Sample Prep V2 kit (Illumina). Pooled barcoded libraries were sequenced to generate paired-end 101 bp reads and raw data was aligned to mouse genome version mm9 using Tophat2 (33 (link)). For the ABI SOLiD sequencing, libraries were prepared using the SOLiD Whole Transcriptome Analysis kit (Thermo Fisher Scientific). Pooled barcoded libraries were sequenced to generate paired-end 35 × 75 bp reads and colorspace XSQ data was aligned to mouse genome version mm9 using Lifescope software (Thermo Fisher Scientific).

Park K.S., Mitra A., Rahat B., Kim K, & Pfeifer K. (2017). Loss of imprinting mutations define both distinct and overlapping roles for misexpression of IGF2 and of H19 lncRNA. Nucleic Acids Research, 45(22), 12766-12779.

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Illumina RNA-Seq Library Preparation

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The majority of RNA was used to make 200-450bp fragment libraries using Illumina's TruSeq RNA Sample Prep v2 kit, with 10 cycles of PCR amplification using KAPA Hifi Polymerase rather than the kit-supplied Illumina PCR Polymerase. Two samples required 14 cycles of PCR (T1_46-4 and T1_47-4). Mosquito-transmitted P. chabaudi CB samples (MTCB) were subjected to 15 cycles of PCR.
The libraries were sequenced using an Illumina HiSeq 2000 v3 with 100bp paired-end reads (samples beginning ‘T’), an Illumina HiSeq 4000 with 75bp paired-end reads (MTCB samples) or an Illumina HiSeq 2500 with 75bp paired-end reads for the rest. RNA from cloned parasites was used to make 100-300bp fragment libraries produced using Illumina’s TruSeq Stranded mRNA Sample Prep Kit with 10 cycles of PCR amplification using KAPA Hifi Polymerase. These libraries were sequenced using an Illumina HiSeq 2500 with 75bp paired-end reads. A description of the libraries can be found in Supplementary Table 10.

Brugat T., Reid A.J., Lin J., Cunningham D., Tumwine I., Kushinga G., McLaughlin S., Spence P., Böhme U., Sanders M., Conteh S., Bushell E., Metcalf T., Billker O., Duffy P.E., Newbold C., Berriman M, & Langhorne J. (2017). Antibody-independent mechanisms regulate the establishment of chronic Plasmodium infection. Nature microbiology, 2, 16276.

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RNA-Seq Library Preparation and Sequencing

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RNA-Seq libraries were constructed from 1 µg total RNA after rRNA depletion using Ribo-Zero GOLD (Illumina). The Illumina TruSeq RNA Sample Prep V2 Kit was used according to the manufacturer’s instructions. The cDNAs were fragmented to ~275 bp using a Covaris E210. Amplification was performed using 10 cycles, which was optimized for the input amount and to minimize the chance of overamplification. Unique barcode adapters were applied to each library for cataloging. Libraries were pooled together for sequencing. The pooled libraries were sequenced on multiple lanes of a HiSeq 2500 using version 4 chemistry to achieve a minimum of 43 million 126 base read pairs. The data was processed using RTA version 1.18.64 and CASAVA 1.8.2.

Winter J.M., Gildea D.E., Andreas J.P., Gatti D.M., Williams K.A., Lee M., Hu Y., Zhang S., Mullikin J.C., Wolfsberg T.G., McDonnell S.K., Fogarty Z.C., Larson M.C., French A.J., Schaid D.J., Thibodeau S.N., Churchill G.A, & Crawford N.P. (2016). Mapping complex traits in a Diversity Outbred F1 mouse population identifies germline modifiers of metastasis in human prostate cancer. Cell systems, 4(1), 31-45.e6.

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RNA-Seq of E14.5 Mouse Testes

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RNA from a single pair of E14.5 testes (one biological replica) was extracted using the PicoPure extraction kit (Arcturus). Three or four biological replicas were used for each genotype. RNA-Seq libraries were constructed from ~0.3 μg total RNA after rRNA depletion using Ribo-Zero GOLD (Illumina). The Illumina TruSeq RNA Sample Prep V2 Kit was used according to manufacturer’s instructions except where noted. The poly-A selection step was omitted and random primers were used for first-strand synthesis. cDNAs were fragmented to ~275 bp using a Covaris E210. Amplification was performed using 16 cycles, which was optimized for the input amount and to minimize the chance of over-amplification. Unique barcode adapters were applied to each library. The pooled libraries were sequenced on multiple lanes of a HiSeq. 2500 using version 4 chemistry to achieve a minimum of 40 million 125 base read pairs. The data was processed using RTA version 1.18.61 and CASAVA 1.8.2.

Ungewitter E.K., Rotgers E., Kang H.S., Lichti-Kaiser K., Li L., Grimm S.A., Jetten A.M, & Yao H.H. (2018). Loss of Glis3 causes dysregulation of retrotransposon silencing and germ cell demise in fetal mouse testis. Scientific Reports, 8, 9662.

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Multi-Organ Transcriptome Profiling of Arundo donax

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Four different organs were collected for Illumina sequencing from mature A. donax plants: (i) fully expanded, nonsenescing leaves (4th and 5th from the top), (ii) sections of culm including 4th and 5th nodes and the corresponding lateral buds (each section about 7 cm long), (iii) roots and (iv) dormant buds originating from the pachyrhizome. In addition, 454 sequencing was carried out for culms and root samples. Plant material was ground in liquid nitrogen with precooled mortars and pestles followed by RNA isolation using the Spectrum Plant Total RNA Extraction Kit (Sigma-Aldrich, St. Louis, MO) according to the manufacturer's instructions. Integrity of the isolated RNA was visually checked on agarose gels. Quality checks were carried out using the RNA 6000 Pico kit and the Agilent Bioanalyser 2100 (Agilent, Santa Clara, CA). Four independent paired-end libraries were prepared using the TruSeq RNA Sample Prep V2 kit (Illumina, San Diego, CA), pooled in equimolar ratio and were sequenced on an Illumina HiSeq2000 sequencer (The Genome Analysis Center, Norwich, UK). Two normalized culm and root libraries were prepared by Eurofins MWG Operon (Ebersberg, Germany) using 454 adapters A and B. Sequencing was performed on a Genome Sequencer GS FLX Titanium Instrument (454 Life Sciences, a Roche company, Branford, CT).

Sablok G., Fu Y., Bobbio V., Laura M., Rotino G.L., Bagnaresi P., Allavena A., Velikova V., Viola R., Loreto F., Li M, & Varotto C. (2014). Fuelling genetic and metabolic exploration of C3 bioenergy crops through the first reference transcriptome of Arundo donax L.. Plant Biotechnology Journal, 12(5), 554-567.

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