Journal: Molecules

Article Title: AutoEpiCollect 2.0: A Web-Based Machine Learning Tool for Personalized Peptide Cancer Vaccine Design

doi: 10.3390/molecules30244702

Figure Lengend Snippet: The “Personalized” Page from the AutoEpiCollect 2.0 Website. The personalized cancer vaccine process is carried out in 2 distinct steps. The first step uses the gene and mutation data from Partek Flow to output Excel files containing collected epitopes. Along with the Excel files are FASTA-formatted files with a unique set of peptides for user antigenicity collection through VaxiJen. In the second step, the user must input the antigenicity data along with the Excel data to obtain the final personalized cancer vaccine composition. Detailed information about using AutoEpiCollect 2.0 is located in the “Documentation” tab, as seen in the figure.

Article Snippet: After finishing the Partek Flow data processing, AutoEpiCollect 2.0 now follows two distinct processes that further reduce the number of prospective target genes.

Techniques: Mutagenesis

Journal: eLife

Article Title: Profiling sensory neuron microenvironment after peripheral and central axon injury reveals key pathways for neural repair

doi: 10.7554/eLife.68457

Figure Lengend Snippet: ( A ) t-SNE plot of cells from all injury conditions overlay for expression of Cd68 (red) and Fabp7 (green). ( B ) Plotting cells in the macrophage (orange) and SGC (green) clusters for expression of Cd68 (y-axis) and Fabp7 (x-axis). ( C ) Dot plot of macrophage, glial and progenitor marker genes expression in the macrophage, SGC and Imoonglia clusters. The percentage of cell expressing the gene is calculated as the number of cells in each cluster express the gene ( > 0 counts) divided by the total number of cells in the respective cluster. Expression in each cluster is calculated as mean expression of the gene relative to the highest mean expression of that gene across all clusters. ( D ) Trajectory analysis of macrophage, SGC and Imoonglia cell clusters. ( E ) Flow cytometry analysis of DRG cells from Fabp7 creER : Sun1 GFP mice, stained with the macrophage marker genes CD45, CD11b and F4/80 n = 2 (F4/80) n = 1 (CD45,CD11b,F4/80) biologically independent animals. ( F ) Representative confocal images of immunofluorescence staining of DRG sections labeled with CD68 (green) and FABP7 (magenta). Fluorescence intensity for CD68 and FABP7 was measured along the arrow line. Scale bar: 50 µm ( G ) Fraction of cells in the Imoonglia cluster by injury condition. n = 2 biologically independent experiments. ( H ) Venn diagram of differentially expressed genes in the Imoonglia cluster (1,097 genes) was compared to top differentially expressed genes in the macrophage cluster (2,469 genes) and the SGC (2,331 genes) (FDR ≤ 0.05, fold-change ≥ 2). ( I ) Pathway analysis (KEGG 2019) of differentially expressed genes in Macrophages, Imoonglia and SGC. Figure 4—source data 1. Source files for scRNAseq analysis, flow cytometry additional experiments.

Article Snippet: The data was subsequently analyzed for enrichment of GO terms and the KEGG pathways using Partek flow pathway analysis.

Techniques: Expressing, Marker, Flow Cytometry, Staining, Immunofluorescence, Labeling, Fluorescence

Journal: eLife

Article Title: Profiling sensory neuron microenvironment after peripheral and central axon injury reveals key pathways for neural repair

doi: 10.7554/eLife.68457

Figure Lengend Snippet:

Article Snippet: The data was subsequently analyzed for enrichment of GO terms and the KEGG pathways using Partek flow pathway analysis.

Techniques: Binding Assay, Recombinant, Sequencing, Reverse Transcription, Plasmid Preparation, SYBR Green Assay, Software