Processing and Analysis of RNA-seq Data from Public Resources

Advances in next generation sequencing (NGS) technologies resulted in a broad array of large-scale gene expression studies and an unprecedented volume of whole messenger RNA (mRNA) sequencing data, or the transcriptome (also known as RNA sequencing, or RNA-seq). These include the Genotype Tissue Expression project (GTEx) and The Cancer Genome Atlas (TCGA), among others. Here we cover some of the commonly used datasets, provide an overview on how to begin the analysis pipeline, and how to explore and interpret the data provided by these publicly available resources.

Modular and Processable Fluoropolymers Prepared via a Safe, Mild, Iodo-Ene Polymerization

Fluoropolymers have infiltrated society as coatings and insulators. However, low processability, few opportunities for polymer functionalization, and explosive monomers hampering academic investigation of these materials have precluded the extension of the unique properties of perfluorocarbons to the cutting edge of material science. Here, we present semifluorinated iodo-ene polymers as a scaffold to overcome fluoropolymer limitations. A sodium dithionate initiated polymerization of perfluorodiiodides and dienes allows for high-molecular-weight polymers (>100 kDa) to be prepared in the presence of oxygen and water with up to 59 wt % fluorine content. These conditions are sufficiently mild to enable the polymerization of functional dienes, leading to biodegradable fluoropolymers. The iodo-ene polymerization results in the addition of polarizable iodine atoms, which improve polymer processability; yet, these atoms can be removed after processing for enhanced stability. Displacement of the iodine atoms with thiols or azides facilitates covalent surface modification and cross-linking. Finally, the low bond dissociation energy of the C-I bond allows allyl group addition as well as photo-cross-linking. Collectively, the simple synthesis and modular nature of the semifluorinated iodo-ene polymers will enable the convergence of perfluorocarbons and advanced materials.

Reversible DNA micro-patterning using the fluorous effect

We describe a new method for the immobilisation of DNA into defined patterns with sub-micron resolution, using the fluorous effect. The method is fully reversible via a simple solvent wash, allowing the patterning, regeneration and re-patterning of surfaces with no degradation in binding efficiency following multiple removal/attachment cycles of different DNA sequences.

Controlling Ligand Spacing on Surface: Polyproline-Based Fluorous Microarray as a Tool in Spatial Specificity Analysis and Inhibitor Development for Carbohydrate-Protein Interactions

Multivalent carbohydrate-protein interactions are essential for many biological processes. Convenient characterization for multivalent binding property of proteins will aid the development of molecules to manipulate these processes. We exploited the polyproline helix II (PPII) structure as molecular scaffolds to adjust the distances between glycan ligand attachment sites at 9, 18, and 27 Å on a peptide scaffold. Optimized fluorous groups were also introduced to the peptide scaffold for immobilization to the microarray surface through fluorous interaction to control the orientation of the helical scaffolds. Using lectin LecA and antibody 2G12 as model proteins, the binding preference to the 27 Å glycopeptide scaffold, matched the distance of 26 Å between its two galactose binding sites on LecA and 31 Å spacing between oligomannose binding sites on 2G12, respectively. We further demonstrate this microarray system can aid the development of inhibitors by transforming the selected surface-bound scaffold into multivalent ligands in solution. This strategy can be extended to analyze proteins that lacking structural information to speed up the design of potent and selective multivalent ligands.

Fluorous photosensitizers enhance photodynamic therapy with perfluorocarbon nanoemulsions

Photodynamic therapy (PDT) requires a photosensitizer, light and oxygen to induce cell death. Here, we simultaneously deliver oxygen and photosensitizer using perfluorocarbon nanoemulsions.

Automated fluorous-assisted solution-phase synthesis of β-1,2-, 1,3-, and 1,6-mannan oligomers

Automated solution-phase syntheses of β-1,2-, 1,3-, and 1,6-mannan oligomers have been accomplished by applying a β-directing C-5 carboxylate strategy. Fluorous-tag-assisted purification after each reaction cycle allowed the synthesis of short β-mannan oligomers with limited loading of glycosyl donor-as low as 3.0 equivalents for each glycosylation cycle. This study showed the capability of the automated solution-phase synthesis protocol for synthesizing various challenging glycosides, including use of a C-5 ester as a protecting group that could be converted under reductive conditions to a hydroxymethyl group for chain extension.

Automated Solution-Phase Synthesis of Insect Glycans to Probe the Binding Affinity of Pea Enation Mosaic Virus

Pea enation mosaic virus (PEMV)--a plant RNA virus transmitted exclusively by aphids--causes disease in multiple food crops. However, the aphid-virus interactions required for disease transmission are poorly understood. For virus transmission, PEMV binds to a heavily glycosylated receptor aminopeptidase N in the pea aphid gut and is transcytosed across the gut epithelium into the aphid body cavity prior to release in saliva as the aphid feeds. To investigate the role of glycans in PEMV-aphid interactions and explore the possibility of viral control through blocking a glycan interaction, we synthesized insect N-glycan terminal trimannosides by automated solution-phase synthesis. The route features a mannose building block with C-5 ester enforcing a β-linkage, which also provides a site for subsequent chain extension. The resulting insect N-glycan terminal trimannosides with fluorous tags were used in a fluorous microarray to analyze binding with fluorescein isothiocyanate-labeled PEMV; however, no specific binding between the insect glycan and PEMV was detected. To confirm these microarray results, we removed the fluorous tag from the trimannosides for isothermal titration calorimetry studies with unlabeled PEMV. The ITC studies confirmed the microarray results and suggested that this particular glycan-PEMV interaction is not involved in virus uptake and transport through the aphid.

Fluorous enzymatic synthesis of phosphatidylinositides

A fluorous tagging strategy coupled with enzymatic synthesis is introduced to efficiently synthesize multiple phosphatidylinositides, which are then directly immobilized on a fluorous polytetrafluoroethylene (PTFE) membrane to probe protein-lipid interactions.

Chemistry of natural glycan microarrays

Glycan microarrays have become indispensable tools for studying protein-glycan interactions. Along with chemo-enzymatic synthesis, glycans isolated from natural sources have played important roles in array development and will continue to be a major source of glycans. N-glycans and O-glycans from glycoproteins, and glycans from glycosphingolipids (GSLs) can be released from corresponding glycoconjugates with relatively mature methods, although isolation of large numbers and quantities of glycans is still very challenging. Glycosylphosphatidylinositol (GPI) anchors and glycosaminoglycans (GAGs) are less represented on current glycan microarrays. Glycan microarray development has been greatly facilitated by bifunctional fluorescent linkers, which can be applied in a 'Shotgun Glycomics' approach to incorporate isolated natural glycans. Glycan presentation on microarrays may affect glycan binding by GBPs, often through multivalent recognition by the GBP.

Highly efficient one-pot multienzyme (OPME) synthesis of glycans with fluorous-tag assisted purification

Oligo(ethylene glycol)-linked light fluorous tags have been found to be optimal for conjugating to glycans for both high-yield enzymatic glycosylation reactions using one-pot multienzyme (OPME) systems and quick product purification using fluorous solid-phase extraction (FSPE) cartridges. The combination of OPME glycosylation systems and the FSPE cartridge purification scheme provides a highly effective strategy for facile synthesis and purification of glycans.

Analysis of microarrays by MALDI-TOF MS

Ligand libraries can be printed onto a sandwich composed of activated lipids embedded in a hydrophobic layer conjugated to an indium-tin oxide (ITO) surface. Arrays produced this way can be analyzed by fluorescence spectroscopy and mass spectrometry. Applications include the assignment of enzyme specificity, the profiling of glycoforms and the identification of lectins.