Total RNA was extracted from FFPE slices using the RNeasy FFPE kit (Qiagen) and the manufacture’s protocol. Synthesis of cDNA and library preparation were performed using the SMARTer Universal Low Input RNA Kit for Sequencing (Clontech) and the Ion Plus Fragment Library Kit (ThermoFisher) as previously described [10 (link), 31 (link), 32 (link)]. Sequencing was performed using the Ion Proton S5/XL systems (ThermoFisher) in the Analytical and Translational Genomics Shared Resource at the UNM Comprehensive Cancer Center. RNA sequencing data is available for download from the NCBI BioProject database using study accession number PRJNA940178.
Smarter universal low input rna kit for sequencing
Manufactured by Takara Bio
Sourced in United States
The SMARTer Universal Low Input RNA Kit for Sequencing is a tool designed to enable the preparation of high-quality cDNA libraries from low input RNA samples for next-generation sequencing. The kit utilizes proprietary SMART (Switching Mechanism at 5' end of RNA Template) technology to generate full-length cDNA from as little as 10 pg of total RNA.
Automatically generated - may contain errors
Lab products found in correlation
Ion plus fragment library kit, by Thermo Fisher Scientific (14 mentions)
Rneasy ffpe kit, by Qiagen (9 mentions)
Ion proton s5 xl systems, by Thermo Fisher Scientific (5 mentions)
Ercc rna spike in control mix 1, by Thermo Fisher Scientific (3 mentions)
Ion proton s5 xl platform, by Thermo Fisher Scientific (2 mentions)
Micro rna isolation kit, by Qiagen (1 mentions)
2200 tapestation system, by Agilent Technologies (1 mentions)
High sensitivity d1000 screentape, by Agilent Technologies (1 mentions)
High sensitivity d1000 reagents, by Agilent Technologies (1 mentions)
Rna 6000 pico labchip, by Agilent Technologies (1 mentions)
Nucleospin totalrna ffpe xs kit, by Macherey-Nagel (1 mentions)
Ribo zero magnetic gold kit, by Illumina (1 mentions)
Low input library prep kit, by Takara Bio (1 mentions)
2100 bioanalyzer, by Agilent Technologies (1 mentions)
Mirna isolation kit, by Qiagen (1 mentions)
Trizol reagent, by Thermo Fisher Scientific (1 mentions)
Fastqc software, by Babraham Bioinformatics (1 mentions)
Ion proton, by Thermo Fisher Scientific (1 mentions)
Ion s5 xl, by Thermo Fisher Scientific (1 mentions)
Low input library prep kit v2, by Takara Bio (1 mentions)
21 protocols using smarter universal low input rna kit for sequencing
1
FFPE RNA Extraction and Sequencing
2
Transcriptome Analysis of Lin- and Lin+ Fractions
3
RNA Sequencing of FFPE Samples
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Total RNA was extracted from FFPE slices using the RNeasy FFPE kit (Qiagen) and the manufacture’s protocol. Synthesis of cDNA and library preparation were performed using the SMARTer Universal Low Input RNA Kit for Sequencing (Clontech) and the Ion Plus Fragment Library Kit (ThermoFisher) as previously described (29 (link), 10 (link), 30 (link)). Sequencing was performed using the Ion Proton S5/XL systems (ThermoFisher) in the Analytical and Translational Genomics Shared Resource at the University of New Mexico Comprehensive Cancer Center. RNA sequencing data is available for download from the NCBI BioProject database using study accession number PRJNA940178.
4
Single-cell RNA-seq of FFPE samples
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Total RNA was extracted from the pooled LCM-captured cells with the NucleoSpin totalRNA FFPE XS kit (Macherey-Nagel, REF740969) with minor modifications. In short, cells in the cap were covered with lysis buffer, incubated at 56°C for 15 min and then spun down. Extracted RNA was bound onto the column with binding buffer and genomic DNA was digested for 15 min in rDNase incubation solution. After two washes, RNA was eluted with 10 μl of RNase-free water. rRNA was removed from the purified RNA with the Ribo-Zero Magnetic Gold Kit (Epicentre, MRZG126). The purified RNA was amplified with the SMARTer Universal Low Input RNA Kit for Sequencing (Clontech, 634938) and libraries were generated with the Low Input Library Prep Kit (Clontech, 634947). Libraries were sequenced on an Illumina HiSeq2000 (100 PE bp) at the Welgene Biotech Company, which generated 6 Gb of data per sample. RNA was quantified and qualitated with the Bioanalyzer 2100 (Agilent Technologies) using a RNA 6000 Pico LabChip (Agilent, 5065–4401). DNA was quantified and qualitated with an Agilent 2200 TapeStation system using High Sensitivity D1000 ScreenTape (Agilent, 5067–5584) and High Sensitivity D1000 Reagents (Agilent, 5067–5585).
5
Profiling FFPE Transcripts with ERCC Spike-Ins
6
RNA-Seq of Lin+ and Lin- Fractions
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RNA was isolated from Lin− and Lin+ fractions (25–50 × 103 cells, respectively) after FACS. RNA extraction was performed using a miRNA Isolation kit (Qiagen Inc., catalog no. 74004). RNA from matching Lin− and Lin+ fractions were compared with RNA from PBMCs of healthy donors (negative controls). RNA analysis, cDNA amplification, and library preparation were performed using the human microarray platform (SMARTer Universal Low Input RNA kit for sequencing (Clontech, catalog no. 634946). The Ion Plus Fragment Library kit (Thermo Fisher Scientific, catalog no. 4471252) was used for fragmented RNA, as reported previously (30–32 (link)). The Ion Proton S5/XL platform (Thermo Fisher Scientific) was used for sequencing at the Analytical and Translational Genomics Shared Resource Core at the University of New Mexico Comprehensive Cancer Center (UNM-CCC).
7
RNA Extraction and Sequencing of Differentiated MSCs
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Total RNAs was extracted using TRIzol reagent (Invitrogen; Thermo Fisher Scientific, Inc.) and the quality of RNAs were evaluated by modified formaldehyde agarose gel electrophoresis and OD260/OD280 absorbance ratio detection using a Genova Nano spectrophotometer (Bibby Scientific; Cole-Palmer, Stone, UK). RNA-seq data from the osteoblastic or adipocytic differentiation induced MSCs were obtained at 7, 14 or 21 days using SMARTer Universal Low Input RNA kit for sequencing (Clontech Laboratories, Inc., Mountainview, CA, USA), according to the manufacturer's protocol. The Fast-QC software (Babraham Bioinformatics, Cambridge, UK; http://www.bioinformatics.babraham.ac.uk/projects/fastqc ) was used to assess the data, including the quality value distribution of bases. RNA sequences were subsequently mapped to human genome sequences using TopHat software 1.3 release (Center for Computational Biology, John Hopkins University, Baltimore, MD, USA; https://ccb.jhu.edu/software/tophat/index.shtml ) (16 (link)). Expression values of mRNAs were calculated based on the fragments per kilobase of exon, per million of fragments mapped and fragment length.
8
FFPE RNA Sequencing Protocol
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Total RNA was isolated from one or two 5-micron slide-mounted FFPE sections using the RNeasy FFPE kit (Qiagen). cDNA synthesis and library preparation were performed using the SMARTer Universal Low Input RNA Kit for Sequencing (Clontech) and the Ion Plus Fragment Library Kit (Life Technologies) as previously described [17 (link)]. Sequencing was performed using the Ion Proton and Ion S5/XL systems (Life Technologies) in the Analytical and Translational Genomics Shared Resource at the University of New Mexico Comprehensive Cancer Center. RNA sequencing data is available for download from the NCBI BioProject database using study accession number PRJNA287156.
9
FFPE RNA Extraction and Sequencing
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Total RNA was extracted from FFPE slices using the RNeasy FFPE kit (Qiagen) and the manufacture’s protocol. Synthesis of cDNA and library preparation were performed using the SMARTer Universal Low Input RNA Kit for Sequencing (Clontech) and the Ion Plus Fragment Library Kit (ThermoFisher) as previously described [10 (link), 31 (link), 32 (link)]. Sequencing was performed using the Ion Proton S5/XL systems (ThermoFisher) in the Analytical and Translational Genomics Shared Resource at the UNM Comprehensive Cancer Center. RNA sequencing data is available for download from the NCBI BioProject database using study accession number PRJNA940178.
10
Profiling RNA Expression in Hematopoietic Cells
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RNA was isolated from 25–50 × 103 cells from the Lin− and Lin+ fractions after FACS using a MicroRNA kit (Qiagen, Cat# 74004, Germantown, MD, USA). RNAs from matching Lin− and Lin+ patient samples were also compared with RNA from PBMC samples of normal healthy donors (negative controls). Synthesis of cDNA and library preparation were performed using the SMARTer Universal Low Input RNA kit for sequencing (Clontech, Cat# 634946, San Jose, CA, USA), and the Ion Plus Fragment Library kit (Thermo Fisher, Waltham, MA, USA, Cat# 4471252), as previously described [25 (link),26 (link),27 (link)]. Sequencing was performed using the Ion Proton S5/XL system (Thermo Fisher, Waltham, MA, USA) in the Analytical and Translational Genomics Shared Resource at the University of New Mexico Comprehensive Cancer Center.
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