1
Preface
2
Quartzy Requests and Inventory
2.1
Quartzy Inventory
2.2
Quartzy Requests
2.3
Freezer Boxes
3
Molecular: Best Practices
3.1
Things to Consider
3.1.1
Contamination
3.1.2
Centrifugation
3.1.3
Pipetting
3.2
Preparing for an Experiment
3.2.1
Reading
3.2.2
Calculating
3.2.3
Pre-Cleaning
3.3
During the Experiment
3.3.1
Testing
3.3.2
Timing
3.3.3
Writing
3.3.4
Post-Cleaning
4
Molecular: Sample Collection
4.1
Sample Types
4.2
DNA Isolation
4.3
16S rRNA Isolation
4.4
RNA Isolation
4.4.1
Sample Conditions
4.4.2
Tissue Processing with RNAlater
4.5
Fibroblast Isolation
5
Molecular: Isolation
5.1
Leukocytes (Buffy Coat) Isolation
5.2
Isolating DNA
5.3
Isolating RNA
5.4
Relevant Protocols
6
Molecular: Genotyping
6.1
Polymerase Chain Reaction (PCR)
6.1.1
Primers
6.1.2
Restriction Fragment Length Polymorphism (RFLP)
6.1.3
Thermocycler
6.2
Electrophoresis
6.2.1
Analyzing Gels
6.3
DNA Sequencing
6.4
Relevant Protocols
7
Molecular: Phenotyping
7.1
Quantitative/Real-Time PCR
7.2
RNA Sequencing
7.3
Single-Cell RNA Sequencing
7.4
16S rRNA Gene (DNA) Sequencing
7.5
Relevant Protocols
8
Molecular: Protocols
8.1
Dilutions
8.1.1
Stock vs Psuedo-stock vs Working Solutions
8.2
Leukocytes (Buffy Coat) Isolation Protocol
8.2.1
Further Washing and Platelet Removal (Optional)
8.3
DNA Isolation Protocol
8.3.1
DNA Isolation from Blood
8.3.2
DNA Isolation from Blood Write-Up
8.3.3
DNA Isolation from Solid Tissue Write-Up
8.4
RNA Isolation Protocol
8.4.1
RNase Free
8.4.2
Kits
8.5
Designing Primers
8.5.1
Ordering Primers
8.5.2
Stock Solution
8.5.3
Working Solution
8.6
PCR Protocol
8.6.1
GoTaq Colorless Master Mix
8.6.2
Restriction Fragment Length Polymorphism Analysis (Optional)
8.6.3
Thermocycler
8.7
Capillary Electrophoresis
8.7.1
Organizing Data
8.7.2
Syncing Data
8.8
qPCR Protocol
8.8.1
Materials
8.8.2
Experiment Preparation
8.8.3
Wet Chemistry
8.8.4
LightCycler 96 Setup
9
Appendix A: Troubleshooting
9.1
PCR
9.2
qPCR
10
Appendix B: Scaling Tables
11
Appendix C: Equipment and Manuals
12
Appendix D: Kit Protocols
13
Appendix E: Experiment Templates
14
Appendix F: Safety Information
15
Appendix G: Projects
16
Appendix H: Vendors
Vallender Lab Protocol Manual
12
Appendix D: Kit Protocols
Insert unmodified kit protocols that we use…