Ovation solo rna seq system

Manufactured by Tecan

Sourced in United States

The Ovation SoLo RNA-Seq System is a library preparation kit designed for low-input RNA samples. It is a fully automated solution for generating high-quality sequencing-ready libraries from small amounts of RNA.

Automatically generated - may contain errors

Lab products found in correlation

2100 bioanalyzer, by Agilent Technologies (9 mentions) Bioanalyzer, by Agilent Technologies (5 mentions) Nextseq 500, by Illumina (5 mentions) Rneasy micro kit, by Qiagen (4 mentions) Novaseq 6000 system, by Illumina (4 mentions) Qubit 2.0 fluorometer, by Thermo Fisher Scientific (4 mentions) Hiseq 1500, by Illumina (3 mentions) Hiseq pe cluster kit v4, by Illumina (3 mentions) Truseq sbs kit v3 hs, by Illumina (3 mentions) Hiseq 2500, by Illumina (3 mentions) Novaseq 6000, by Illumina (3 mentions) Novaseq 6000 s2 reagent kit, by Illumina (3 mentions) Hiseq 4000, by Illumina (3 mentions) Rneasy plus micro kit, by Qiagen (2 mentions) Dna 1000 kit, by Agilent Technologies (2 mentions) Qubit fluorometer, by Thermo Fisher Scientific (2 mentions) Nebnext poly a mrna magnetic isolation module, by Illumina (1 mentions) Nebnext ultra 2 rna library prep kit, by Illumina (1 mentions) Superscript 3 first strand synthesis kit, by Thermo Fisher Scientific (1 mentions) Nebnext ultra rna library prep kit, by Illumina (1 mentions)

Spelling variants of this product

Ovation RNA-Seq System (52 citations) Ovation SoLo (6 citations) Ovation SoLo RNA-seq System for Drosophila (4 citations) Ovation SoLo Human RNA‐Seq system (2 citations) Ovation SoLo RNA-Sequencing (RNA-seq) System (2 citations) Ovation SoLo RNA-seq System Mouse (2 citations) Ovation SoLo RNA-seq system Human kit (2 citations) Ovation SoLo RNA-Seq System Core Kit (2 citations)

31 protocols using ovation solo rna seq system

Cardiac Transcriptome Analysis Protocols

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cDNA prepared using a SuperScript III First-Strand Synthesis Kit (Invitrogen) was used for qPCR analysis. Advanced qPCR Master Mix with Supergreen Dye Low ROX (Wisent) was used for qPCR analysis on a CFX384 Touch Real-Time PCR Detection System (Bio-Rad). All samples were run in triplicate. Data were analyzed using CFX Manager Software (Bio-Rad).
For 32-week-old adult hearts, RNA-seq libraries were prepared using a NEBNext Ultra RNA Library Prep Kit for Illumina with the NEBNext Poly(A) mRNA Magnetic Isolation Module and 1 ug of starting material. Single-end sequencing (50 bp) was performed on an Illumina HiSeq 2500 platform.
For 2-month-old mice treated with isoproterenol and human fetal hearts, a NEBNext Ultra II RNA Library Prep Kit for Illumina was used with the NEBNext Poly(A) mRNA Magnetic Isolation Module and 1 ug of starting material. Single-end sequencing (50 bp) was performed on an Illumina Hi-Seq 2500 platform.
For the CPs, Ovation SoLo RNA-Seq Systems (NuGEN) for mice was used with 9 ng of total RNA as a starting material.

Ahmed A., Liang M., Chi L., Zhou Y.Q., Sled J.G., Wilson M.D, & Delgado-Olguín P. (2020). Maternal obesity persistently alters cardiac progenitor gene expression and programs adult-onset heart disease susceptibility. Molecular Metabolism, 43, 101116.

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RNA-seq Analysis of Mouse Tissue

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RNA quality was checked by Bioanalyzer (Agilent). For RNA extracted
from TECs or TMCs, indexed cDNA libraries were obtained using the Ovation
Solo RNA-Seq Systems (NuGen) following manufacturer recommendations. The
multiplexed libraries (11 pM) were loaded and sequences were produced using
a HiSeq PE Cluster Kit v4 and TruSeq SBS Kit v3-HS (250 cycles) on a HiSeq
1500 (Illumina). Approximately 8 million of paired-end reads per sample were
mapped against the mouse reference genome (GRCm38.p4/mm10) using STAR
software to generate read alignments for each sample. Annotations
Mus_musculus.GRCm38.84.gtf were obtained from ftp.Ensembl.org. After
transcripts assembling, gene level counts were obtained using HTSeq and
normalized to 20 millions of aligned reads. Fold of changes (FC) were
computed on these values between the conditions.

Latil M., Nassar D., Beck B., Boumahdi S., Wang L., Brisebarre A., Dubois C., Nkusi E., Lenglez S., Checinska A., Drubbel A.V., Devos M., Declercq W., Yi R, & Blanpain C. (2016). Cell-Type-Specific Chromatin States Differentially Prime Squamous Cell Carcinoma Tumor-Initiating Cells for Epithelial to Mesenchymal Transition. Cell stem cell, 20(2), 191-204.e5.

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RNA Extraction and Sequencing Protocol

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RNA extraction was performed by using Qiagen RNeasy Micro Kit according to the manufacturer’s instructions. Before sequencing, quality of the RNA was evaluated using a Bioanalyzer 2100 (Agilent). Indexed cDNA libraries were obtained using Ovation Solo RNA-seq Systems (NuGen) following the manufacturer’s recommendations. The multiplexed libraries were loaded onto flow cells and sequences were produced using a HiSeq PE Cluster Kit v4 and TruSeq SBS Kit v3-HS (250 cycles) on a HiSeq 1500 (Illumina).

Lin X., Swedlund B., Ton M.L., Ghazanfar S., Guibentif C., Paulissen C., Baudelet E., Plaindoux E., Achouri Y., Calonne E., Dubois C., Mansfield W., Zaffran S., Marioni J.C., Fuks F., Göttgens B., Lescroart F, & Blanpain C. (2022). Mesp1 controls the chromatin and enhancer landscapes essential for spatiotemporal patterning of early cardiovascular progenitors. Nature cell biology, 24(7), 1114-1128.

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Magnetic Bead-Based RNA Isolation and RNA-Seq Library Preparation

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Total RNA was isolated from samples with a magnetic beads-based RNA isolation method (Direct-zol-96 MagBead RNA, Zymo Research). A total of 200 µL of sample was used and then RNA was eluted in 25 µL. Libraries were prepared using the Ovation SoLo RNA-Seq Systems (NuGEN) with approximately10 ng of RNA. Libraries were subjected to a depletion of human and yeast rRNA using AnyDeplete Probe Mix (NuGEN) and (NuGEN). A total 1.3 mL of the final library at 1.8 pM, with 1% PhIX spike in was used for sequencing. Sequencing was performed on Illumina NextSeq 500 using the NextSeq 500/550 75 cycle High Output Kit v2.5 (20,024,906).

Rouchka E.C., Chariker J.H., Alejandro B., Adcock R.S., Singhal R., Ramirez J., Palmer K.E., Lasnik A.B., Carrico R., Arnold F.W., Furmanek S., Zhang M., Wolf L.A., Waigel S., Zacharias W., Bordon J, & Chung D. (2021). Induction of interferon response by high viral loads at early stage infection may protect against severe outcomes in COVID-19 patients. Scientific Reports, 11, 15715.

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RNA Extraction and Sequencing Protocol

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Transcriptomic Profiling of Macrophage Subsets

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Aortic macrophages, peritoneal macrophages, and pooled monocytes from blood and spleen were sorted directly into Buffer RLT (QIAGEN, Stockach, Germany) plus 1% β-mercaptoethanol (AppliChem, Darmstadt, Germany). After further homogenizing the cell lysates with QIAshredder (QIAGEN, Stockach, Germany), we extracted the RNA from the lysates with RNeasy Micro kit (QIAGEN, Stockach, Germany) . We prepared RNA library with the Ovation SoLo RNA-seq systems (NuGEN, Crailsheim, Germany) . The library was sequenced on a NextSeq instrument with 75 bp paired-end reads using NextSeq 500 High Output v2 kit (Illumina, San Diego, CA, USA). At least 2.5 million reads were acquired from each bulk sample.

Härdtner C., Kumar A., Ehlert C.A., Vico T.A., Starz C., von Ehr A., Krebs K., Dufner B., Hoppe N., Stachon P., Heidt T., Wolf D., von Zur Mühlen C., Grüning B., Robbins C.S., Maegdefessel L., Westermann D., Dederichs T.S, & Hilgendorf I. (2023). A comparative gene expression matrix in Apoe-deficient mice identifies unique and atherosclerotic disease stage-specific gene regulation patterns in monocytes and macrophages. Atherosclerosis, 371.

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RNA Extraction and Sequencing from Neuro-2a Cells

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Total RNA was extracted from siNEG and siA1 transfected Neuro-2a cells using the RNeasy Midi kit (catalog #75144; QIAGEN) according to manufacturer’s protocol. RNA-seq libraries were generated from 10 ng of input RNA using the Ovation SoLo RNA-Seq Systems (catalog #0407-32; Tecan Genomics) following manufacturer’s directions.

Anees A., Salapa H.E., Thibault P.A., Hutchinson C., Hammond S.A, & Levin M.C. (2021). Knock-Down of Heterogeneous Nuclear Ribonucleoprotein A1 Results in Neurite Damage, Altered Stress Granule Biology, and Cellular Toxicity in Differentiated Neuronal Cells. eNeuro, 8(6), ENEURO.0350-21.2021.

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Eosinophil RNA-Seq Analysis from Lung

Cited 1 time

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Eosinophils were sort-purified as Sytox blue^- CD45⁺ Lineage (CD3, CD5, CD19, Ly6G)^-CD11b⁺Siglec F⁺ from the lung of Nmur1^Cre-T2A-GFPId2^flox/flox and control mice on day 7 after papain administration. Cells were sorted into RLT Plus Lysis Buffer supplemented with 40 mM DTT and RNA was isolated using the RNeasy Plus Micro kit (Qiagen) according to the protocol provided by the manufacturer. RNA-seq libraries were prepared by the MDC BIMSB Core Bioinformatic Facility using the Ovation® SoLo RNA-Seq Systems (Tecan Genomics) or theSMARTer Stranded Total RNA-Seq Kit – Pico (Takara). Sequencing was performed on a NovaSeq 6000 (Illumina), yielding 100 bp single-end reads. RNA-Seq reads were mapped to the mouse genome (GRCm38.p5) with STAR^{35 (link)} version 2.7.3a using default parameters. Reads were assigned to genes with FeatureCounts^{36 (link)} with the following parameters: -t exon -g gene_id, gene annotation - Gencode GRCm38/M12. The differential expression was carried out with DESeq2 version 1.22.1^{37 (link)} using default parameters. We kept genes that have at least 5 reads in at least 3 samples.

Jarick K.J., Topczewska P.M., Jakob M.O., Yano H., Arifuzzaman M., Gao X., Boulekou S., Stokic-Trtica V., Leclere P., Preusser A., Rompe Z.A., Stamm A., Tsou A.M., Chu C., Heinrich F.R., Guerra G.M., Durek P., Ivanov A., Beule D., Helfrich S., Duerr C.U., Kühl A.A., Stehle C., Romagnani C., Mashreghi M.F., Diefenbach A., Artis D, & Klose C.S. (2022). Non-redundant functions of group 2 innate lymphoid cells. Nature, 611(7937), 794-800.

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Comprehensive RNA Sequencing Using Illumina and NuGEN

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Total RNA, including microbial and human RNA, was subjected to cDNA synthesis and NGS library construction using the two library kits, the TruSeq Stranded Total RNA (Illumina, San Diego, California, USA) and the Ovation SoLo RNA-Seq System (NuGEN Technologies, San Carlos, California, USA). The TruSeq Stranded Total RNA kit requires an input of 100 ng – 1 µg and includes rRNA depletion using a set of human-specific probes prior to the first strand cDNA synthesis. The Ovation SoLo RNA-Seq System allows lower input RNA, 10 pg – 10 ng, for initial cDNA synthesis, followed by cleavage of insertdependent adaptors specific for human rRNA transcripts. We used 500 ng total RNA as the starting material for Illumina TruSeq Stranded Total RNA. Illumina libraries were sequenced on an Illumina HiSeq 2500 in rapid mode with 2×250 base paired end reads on one lane. NuGEN Ovation SoLo RNA-Seq System cDNA libraries were prepared from 10 ng input RNA along with a blank negative control and were run on a HiSeq 4000 sequencer with 2×100 base reads, multiplexed with five other samples (unrelated to this study) in one lane.

Masters T.L., Hilker C.A., Jeraldo P.R., Bhagwate A.V., Greenwood-Quaintance K.E., Eckloff B.W., Chia N., Hanssen A.D., Abdel M.P., Yao J.Z., Jen J, & Patel R. (2018). Comparative Evaluation of cDNA Library Construction Approaches for RNA-Seq Analysis from Low RNA-Content Human Specimens. Journal of microbiological methods, 154, 55-62.

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Robust Single-Cell RNA-Seq Analysis Pipeline

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40000 LCs and 5000 BCs were isolated by FACS as described above and collected into kit lysis buffer. RNA was extracted using absolutely RNA nanoprep kit (Stratagene). RNA quality was checked using a Bioanalyzer 2100 (Agilent technologies). Indexed cDNA libraries were obtained using the Ovation Solo RNA-Seq System (NuGen) following manufacturer recommendation. The multiplexed libraries (18 pM) were loaded on flow cells and sequences were produced using a NovaSeq 6000 S2 Reagent Kit (200 cycles) from a NovaSeq 6000 System (Illumina). Approximately 19 million of paired-end reads per sample were mapped against the mouse reference genome (GRCm38/mm10) using STAR software to generate read alignments for each sample. Annotations Mus_musculus.GRCm38.87.gtf were obtained from ftp.Ensembl.org. After transcripts assembling, gene level counts were obtained using HTSeq. Fold change of mean gene expression for the duplicates were used to calculate the level of differential gene expression. Heatmap of the 500 most variable genes across the 8 samples and corresponding clustering dendrogram were drawn with heatmap.2 function of the R package gplots. Euclidian distance with complete linkage agglomeration method was used for clustering.

Wuidart A., Sifrim A., Fioramonti M., Matsumura S., Brisebarre A., Brown D., Centonze A., Dannau A., Dubois C., Van Keymeulen A., Voet T, & Blanpain C. (2018). Early lineage segregation of multipotent embryonic mammary gland progenitors. Nature cell biology, 20(6), 666-676.

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