Software

• Weighted Gene Co-Expression Network Analysis Software (WGCNA) is a user-friendly systems biologic microarray analysis software tool for finding important genes, pathways and clinical outcomes. This network based gene screening method can be used to identify candidate biomarkers and to group genes into modules (clusters of highly correlated genes). WGCNA can be used for constructing a gene co-expression network, finding co-expression modules, and calculating module membership measures (related to intra-modular connectivity). It can be used to integrate gene significance measures and intra-modular connectivity to find biologically and statistically significant genes. The software has a graphical interface that allows straightforward input of microarray and clinical trait data or predefined gene information. The software can analyze networks comprised of tens of thousands of genes and implements several options for automatic and manual gene selection ("network screening").
  Visit the WGCNA site to download the software and manual, and for more information.


• MirMiner is a software package that searches for significant miRNAs (or mRNAs) based on predefined database of base pair matches between miRNAs and mRNAs. It provides hit counts for a input list of miRNAs (or mRNAs) and lists all the detailed hits between each miRNA/mRNA pair as well.
  Visit the MirMiner site to download the software and manual, and for more information.

DNA Protocols

• DNA CPT v.1
  Protocol for isolation of genomic DNA from whole blood using BD Vacutainer CPT Cell Preparation Tube with Sodium Citrate.
• DNA Purple Top v.1
  Protocol for iIsolation of DNA from whole blood using Vacutainer Purple Top Tube containing EDTA (from QIAamp DNA Blood Midi Kit Handbook).
• DNA PBLs v1
  Protocol for isolation of DNA from PBLs (from QIAamp DNA Blood Mini Kit Handbook).
• DNA Plasma v1
  Protocol for isolation of DNA from Plasma (from QIAamp DNA Blood Mini Kit Handbook) .

RNA Protocols

• RNA CPT v.1
  Protocol for isolation of RNA from whole blood using BD Vacutainer Cell Preparation Tube with Sodium Citrate.
• RNA Pax v.1
  Protocol for isolation of RNA from whole blood using Qiagen PAXgene Blood RNA Tube (from PAXgene Blood RNA Kit Handbook).
• Globin Reduction v.1
  Protocol for removal of globin mRNA from total RNA isolated from whole blood (from GLOBINclear – Human Kit instruction manual).

Protein Protocols

• Protein CPT v.1
  Protocol for isolation of Protein from whole blood using BD Vacutainer Cell Preparation Tube with Sodium Citrate.

• Purple Top Tube Experiment
• Qiagen AllPrep Extraction of DNA, RNA and Protein
• PAX Gene Column Test
• PAX Gene CPT Tube Validation
• Affy, Ambion, NuGEN Labeling Comparisons
• Tempus, PAXgene, and CPT Tubes Comparisons
• Globin Reduction Protocol