Total RNA was assayed for quantity and quality with an Agilent 2100 Bioanalyzer instrument using the RNA 6000 Nano Kit (Agilent Technologies, Part number 5067-1512). Average RIN values were 9.786 ± 0.3. Libraries were prepared using TruSeq Stranded mRNA HT Sample Prep Kit (Illumina, Part number 20020595) as per standard protocol in the kit’s sample prep guide. Libraries were assayed for overall quality using HS D5000 ScreenTape assay (Agilent Technologies, Part numbers 5067-5592 and 5067-5593) of Agilent 2200 TapeStation System. Average library molarity was 13.9 ± 4.2 nM. Samples were multiplexed for sequencing. A MiSeq micro test lane was run to check pool balance followed by 100 bp single-read sequencing on an Illumina HiSeq 4000 sequencer. Illumina’s bcl2fastq version v2.17.1.14 software was used to convert bcl to fastq files.
Truseq stranded mrna ht sample prep kit
Manufactured by Illumina
Sourced in United States
The TruSeq Stranded mRNA HT Sample Prep Kit is a laboratory equipment product designed for sample preparation. The kit enables the generation of stranded mRNA libraries from total RNA samples for high-throughput sequencing applications.
Automatically generated - may contain errors
Lab products found in correlation
Sciclone ngs, by Illumina (6 mentions)
Next generation sequencing library qpcr kit, by Roche (5 mentions)
2100 bioanalyzer, by Agilent Technologies (4 mentions)
Hiseq 2500, by Illumina (4 mentions)
Rna 6000 nano kit, by Agilent Technologies (3 mentions)
Agilent 2100 bioanalyzer, by Agilent Technologies (3 mentions)
Lightcycler 480, by Roche (3 mentions)
Novaseq sequencer, by Illumina (3 mentions)
Hiseq 2500 platform, by Illumina (3 mentions)
Hiseq 2000 sequencer, by Illumina (3 mentions)
Nanodrop, by Thermo Fisher Scientific (3 mentions)
Hiseq truseq sbs sequencing kit, by Illumina (3 mentions)
Rneasy plant mini kit, by Qiagen (2 mentions)
Hiseq sequencing platform, by Illumina (2 mentions)
Truseq sbs sequencing kit, by Illumina (2 mentions)
Cbot instrument, by Illumina (2 mentions)
Rneasy mini kit, by Qiagen (2 mentions)
Lightcycler 480 real time pcr instrument, by Roche (2 mentions)
Qubit fluorometer, by Thermo Fisher Scientific (2 mentions)
Ribo zero rrna removal kit, by Illumina (2 mentions)
27 protocols using truseq stranded mrna ht sample prep kit
1
Total RNA Quantification and Sequencing
2
Transcriptomic Analysis of NHDF Cells
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Three NHDF lines were plated in triplicate, incubated with control or PTP4A1 ASOs and serum-starved for 24 h prior the experiment. RNA was extracted using micro RNeasy kits from Qiagen and 500 ng of total RNA for each condition were used to generate mRNA-focused libraries on a Biomek FXP automation platform from Beckman Coulter (Carlsbad, CA) with the TruSeq-Stranded mRNA HT Sample Prep Kit from Illumina (San Diego, CA). NGS was performed at the La Jolla Institute sequencing facility with a Hiseq 2500 from Illumina.
3
Profiling miR-181 and miR-324 in HPAECs
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Next-generation RNA sequencing of HPAECs transfected with miR-181 or miR-324 with two biological replicates was performed at the Imperial BRC Genomics Facility (Imperial College London, UK). RNA quality and quantity were assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies) and a Qubit 4 Fluorometer (Thermo Fisher Scientific). RNA libraries were prepared using TruSeq® Stranded mRNA HT Sample Prep Kit (Illumina Inc.) according to the manufacturer’s protocol. Briefly, 1 µg of high-quality total RNA (RNA Integrity Number Score ≥8.0) was used for polyadenylated RNA selection using poly-T oligo attached magnetic beads, followed by the fragmentation of poly-A containing mRNA. Cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase with random primers. The cDNA was further converted into double-stranded DNA that was end-repaired to incorporate the specific index adapters for multiplexing, followed by purification and amplification. The amplified libraries were examined using an Agilent 2100 Bioanalyzer and a Qubit. The samples were then pooled and run over four lanes (2 × 100 bp) on a HiSeq 2500 using TruSeq SBS V3-HS kit (Illumina Inc.) in high output run mode. Average sequencing depth across samples was 34.4 million reads.
4
Transcriptome Profiling of Ceratopteris richardii
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Total RNA was isolated from ten tissues and developmental stages of Ceratopteris richardii genotype Hn-n (Fig. 1a ) using the RNeasy Plant Mini kit (Qiagen). Plate-based RNA sample preparation was performed on the PerkinElmer Sciclone NGS robotic liquid handling system using Illumina’s TruSeq Stranded mRNA HT sample prep kit utilizing poly-A selection of mRNA following the protocol outlined by Illumina in their user guide (https://support.illumina.com/sequencing/sequencing_kits/truseq-stranded-mrna.html ) with the following conditions: total RNA starting material was 1 µg per sample and eight cycles of PCR were used for library amplification. There are four biological replicates for each tissue and developmental stage of the RNA-seq experiment.
5
Transcriptome Analysis of dscaml1 Mutants
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Progenies from heterozygous dscaml1 mutant parents were anesthetized and harvested at 3.5-4 dpf. The anterior half of the animal was used for RNA preparation using the RNA Miniprep Kit (Zymo). The posterior half was used for genotyping. Three biological replicates for each group were analyzed, each containing RNA from 6–11 animals. All samples had RIN ≥8.0 and were converted into a strand-specific library using Illumina’s TruSeq Stranded mRNA HT Sample Prep Kit (RS-122–2,103; Illumina) for subsequent cluster generation and sequencing on Illumina’s NextSeq 75 sequencer. Sequence data processing, alignment, read count, mapping, and quality control were performed as previously described (Ates et al., 2020 (link)). Differential expression was tested for significance using the false discovery rate (FDR) (Benjamini–Hochberg) corrected Likelihood Ratio Test (LRT) in the R-package DESeq2 (Love et al., 2014 (link)). 238 and 116 genes showed a significant difference in read counts at FDR < 0.01 and 0.001, respectively. Original sequence data have been deposited in NCBI’s Gene Expression Omnibus (Edgar et al., 2002 (link)) and accessible through GEO Series accession number GSE213858.
6
Integrative Epigenomic Profiling of Pre-B Cells
7
Illumina RNA-Seq with PolyA Selection
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Total RNA was extracted from 100 mg of tissue with CTAB lysis buffer and the Spectrum Plant Total RNA Kit. Illumina RNASeq w/PolyA Selection, Plates—Plate-based RNA sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system using Illumina TruSeq Stranded mRNA HT sample prep kit using poly(A) selection of messenger RNA following the protocol outlined by Illumina in their user guide (https://support.illumina.com/sequencing/sequencing_kits/truseq-stranded-mrna.html ) and with the following conditions: total RNA starting material was 1 μg per sample and eight cycles of PCR were used for library amplification.
The prepared libraries were quantified using the KAPA Biosystem next-generation sequencing library qPCR kit and run on a Roche LightCycler 480 real-time PCR instrument. Sequencing of the flowcell was performed on the Illumina NovaSeq sequencer using NovaSeq Xp v.1 reagent kits, S4 flowcell, following a 2 × 150 indexed run recipe.
The prepared libraries were quantified using the KAPA Biosystem next-generation sequencing library qPCR kit and run on a Roche LightCycler 480 real-time PCR instrument. Sequencing of the flowcell was performed on the Illumina NovaSeq sequencer using NovaSeq Xp v.1 reagent kits, S4 flowcell, following a 2 × 150 indexed run recipe.
8
Illumina-based RNA Sequencing Protocol
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RNA sequencing libraries were prepared using the “TruSeq Stranded mRNA HT Sample Prep” kit (Illumina, San Diego, CA, EUA), mRNA enrichment was performed using magnetic beads coupled with oligo (dT). Sequencing was carried out in the HiSeq 2500 system (Illumina, San Diego, CA, EUA) at the NGS facility located at the Brazilian Bioethanol Science and Technology Laboratory (CTBE), Campinas, SP, Brazil.
9
Illumina RNA-Seq with Automated Poly(A) Selection
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Illumina RNA-Seq with poly(A) selection plate-based RNA sample preparation was performed on the PerkinElmer Sciclone NGS robotic liquid handling system using Illumina’s TruSeq Stranded mRNA HT sample prep kit using poly(A) selection of mRNA following the protocol outlined by Illumina in their user guide: https://support.illumina.com/sequencing/sequencing_kits/truseq-stranded-mrna.html , and with the following conditions: total RNA starting material was 1 ug per sample and eight cycles of PCR were used for library amplification. The prepared libraries were quantified using KAPA Biosystems’ next-generation sequencing library qPCR kit and run on a Roche LightCycler 480 real-time PCR instrument. Sequencing of the flowcell was performed on the Illumina NovaSeq sequencer using NovaSeq XP v.1 reagent kits and an S4 flowcell, following a 2 × 150 bp indexed run recipe.
10
Lacrimal Gland RNA Sequencing
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For each lacrimal gland sample, 500 ng of RNA were used to construct sequencing libraries using Illumina’s TruSeq Stranded mRNA HT Sample prep kit (Cat # RS-122-2103). The products were purified and enriched with PCR for 12 cycles to create the final cDNA library. Automated library preparations were carried out according to manufacturer’s recommendations using an Arrayplex automated liquid handler (Biomek FXP Arrayplex, Beckman Coulter). TruSeq adapter sequences available in the Illumina Customer Sequence Letter on Illumina support were used in the experiment. Libraries were quantified using Illumina Library Quantification Kit (KK4824). Multiplexed samples were equimolarly pooled, diluted to 2nM pool for final analysis on Agilent High Sensitivity DNA Kit to run on three rapid flowcells per lane and sequenced using 2 x 50 ntd paired-end runs of Illumina HiSeq 2500 platform.
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