Documents for Equipment & Protocols

• ABI QuantStudio·6 – qPCR

• ABI Veriti PCR – 96-well: 6 thermal gradient blocks

• ABI 3130xl – DNA Sequencing & FA

• Diagenode Bioruptor NGS

• Ion Torrent S5 – NGS

• SmartCheck

• Agilent Bioanalyzer

• E-gel – DNA Size-selection

• BluePippin – DNA Size-selection

• SpeedVac SPD1010

• Victor·3 Multilabel Counter

• Eppendorf Centrifuge 5810R

• Typhoon 8600 Variable Mode Imager

• Nanodrop – Nucleic Acid & Protein quantitation

• Qubit 4.0 – DNA/RNA/Protein quantitation; RNA Integrity

Note: The pdf documents below are original vendor documents and were not designed for use with screen reader applications.

ABI QuantStudio·6 (qPCR)

Science Aid Center
Real-time PCR Handbook 2.0 (2024; periodically updated)
TaqMan Gene Expression, User Guide (vendor pdf)
MIQE: towards reproducible qPCR (journal pdf, 2017)
Case study using MIQE guidelines (vendor pdf, 2011)
qPCR Tutorial Videos (YouTube: BioRad, 2019)
Primer Express v3.0, User Guide (vendor pdf)
Protein Thermal Shift (PTS) (vendor pdf, 2022)
Protein Thermal Shift (PTS) (online user guide)
Manual for QuantStudio·6 (vendor pdf)
QuantStudio-6 qPCR, freeware, v1.3 only (PC)
– Warning: v1.7 is not compatible with our platforms.

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ABI Veriti PCR (96-well: 6 thermal gradient blocks)

ABI Veriti PCR Manual (vendor pdf)

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ABI 3130xl (DNA Sequencing/Fragment Analysis)

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Diagenode Bioruptor NGS

Bioruptor-NGS User-Manual-v1.5 (vendor pdf)
Bioruptor NGS DNA-Shearing protocol (vendor pdf)
Bioruptor NGS DNA-Shearing (Small-vol) (vendor pdf)
Bioruptor Chromatin Shearing Guide (vendor pdf)
Bioruptor NGS RNA-Shearing protocol (vendor pdf)

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Ion Torrent S5 (NGS)

Ion Express Barcodes(96).xlsx
Links to ThermoFisher Ion resources
Targeted RNA-Seq on Ion PGM (vendor pdf)

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SmartCheck

in progress

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Agilent Bioanalyzer

The RIN: an RNA integrity number for assigning integrity values to RNA measurements (BMC article [pdf] which explains the RIN concept and shows a graphic of the different regions that make up the RIN estimate for the Bioanalyzer assay.)
Interpreting mRNA electropherograms (vendor pdf)
Mastering the Bioanalyzer DNA-HS assay.docx
Agilent Bioanalyzer Troubleshooting Guide (vendor pdf)

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E-gel (DNA Size-selection)

E-gel Technical Guide (vendor pdf)
Tips for E-gels.docx

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BluePippin (DNA Size Selection for NGS)

BluePippin User Manual (vendor pdf)

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SpeedVac SPD1010

SpeedVac SPD1010 User Manual (vendor pdf)
SpeedVac Rotor-&-Tube Selection Guide (vendor pdf)

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Victor·3 Multilabel Counter

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Eppendorf Centrifuge 5810R

5810R Quick Guide.docx
5810R User Manual (vendor pdf)

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Typhoon 8600 Variable Mode Imager

Typhoon Quick Guide.docx
Typhoon User Manual (vendor pdf)
Typhoon Application Note 1 (vendor pdf)
Typhoon Application Note 2 (vendor pdf)
Principles-Methods: Fluorescence Imaging (vendor pdf)

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Nanodrop (Nucleic Acid & Protein quantitation)

The Genomics Core does not have a Nanodrop; however, next door to this Core (in A624), there is a Thermo NanoDrop 2000 (micro-volume spectrophotometer) for use by members of the Department of Biological Sciences. Visit Common Room for a partial listing of additional equipment and restrictions upon its use.

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Documents for Equipment & Protocols