|Instrument||Recommended Number of Samples||Read Length|
|NextSeq 550 System||RNA Profiling: 13–40 samples per run (based on 10 million reads per sample)
Transcriptome Analysis: 5–16 samples per run (based on 25 million reads per sample)
|2 x 75 bp
2 x 75 bp
|HiSeq 2500 System||RNA Profiling: 60–400 samples per run (dual flow cell; based on 10 million reads per sample)
Transcriptome Analysis: 24–160 samples per run (dual flow cell; based on 25 million reads per sample)
|2 x 75 bp
2 x 75 bp
|NovaSeq 6000 System||RNA Profiling (samples per run, dual flow cell): S1: 320, S2:384, S4:768. Limited by index combinations (dual). Based on 10 million reads.
Transcriptome Analysis (samples per run, dual flow cell): S1: 128, S2: 256, S4: 768. Limited by index combinations (dual). Based on 25 million reads.
|≤ 2 × 100 bp
≤ 2 × 100 bp
|TruSeq Stranded mRNA||Illumina Stranded mRNA Prep||Illumina RNA Prep with Enrichment|
|Assay Time||~10.5 hours||6.5 hours||< 9 hours|
|Automation Capability||Liquid Handling Robots||Liquid Handling Robots||Liquid Handling Robots|
|Content Specifications||Captures the coding transcriptome with strand information||Captures the coding transcriptome with strand information||Captures the coding transcriptome when used with Illumina Exome Panel|
|Description||Gives researchers a clear, comprehensive view of the coding transcriptome with precise strand information.||A simple, cost-effective solution for analysis of the coding transcriptome with precise strand information||A reproducible, economical solution enabling targeted transcript detection and discovery from a broad range of sample types and inputs including formalin-fixed, paraffin- embedded (FFPE) tissues and other low-quality samples|
|Hands-On Time||~4.5 hours||< 3 hours||< 2 hours|
|Input Quantity||0.1 – 1 ug total RNA or 10 - 100 ng previously isolated mRNA (from species with polyA tails)||25-1000 ng standard-quality total RNA||10ng total RNA from fresh/frozen samples, or 20ng total RNA from FFPE samples|
|Mechanism of Action||Oligo-dT beads capture polyA tails||PolyA capture, ligation-based addition of adapters and indexes||Bead-linked transposome|
|Method||mRNA Sequencing||mRNA Sequencing||mRNA Sequencing, Target Enrichment, Targeted RNA Sequencing|
|Multiplexing||1–96||Up to 384 Unique Dual Indexes (UDIs)||Up to 384 Unique Dual Indexes (UDIs)|
|Specialized Sample Types||Not FFPE-Compatible||Low-Input Samples, Not FFPE-Compatible||Blood, FFPE Tissue, Low-Input Samples|
|Species Category||Bovine, Human, Mammalian, Mouse, Rat||Bovine, Human, Mammalian, Mouse, Rat||Human, Virus|
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Figure 2 from TruSeq Stranded mRNA and Total RNA Library Prep Kits Data Sheet, December 2015
Technical replicates of FFPE tissue show high concordance, indicating robust library prep performance. Axes are log2(FPKM). R2 value is shown.
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