8 research outputs found
Additional file 9: of High fidelity hypothermic preservation of primary tissues in organ transplant preservative for single cell transcriptome analysis
Table S8. Detailed annotation on assembled full-length transcripts for antibody heavy and light chains in all identified B cells. (CSV 8 kb
Additional file 6: of High fidelity hypothermic preservation of primary tissues in organ transplant preservative for single cell transcriptome analysis
Table S5. Output (top 20 hit) from GSEA on genes with negative log2(fold change) between cells from fresh and preserved tissues. (XLSX 104 kb
Additional file 1: of High fidelity hypothermic preservation of primary tissues in organ transplant preservative for single cell transcriptome analysis
Figure S1. Overall viability and abundance of Cd45+ cells across different durations of preservation time. At the bottom of each panel, the percentage in white was calculated as: counts of PI- events / counts of all events for the top panels, and counts of Cd45+ events / counts of all events for the bottom panels. Raw counts were shown in the fractions. Figure S2. cDNA concentration and smearing assessed via fragment analysis for single Cd45+ cells from mouse kidneys after different durations of preservation presented as (A) electrophoresis traces and (B) gel image. Figure S3. Genebody coverage of Cd45+ single cells from mouse kidneys after different durations of time. (A) 5′-3′ read coverage on exons. (B) Distribution of skewness of 5′-3′ read coverage on exons. Figure S4. Identification of cell types in Cd45+ single cells from mouse kidneys. (A) Number of genes detected cast on 2d tSNE. (B) Uniquely expressing genes identified for each putative cell clusters. (Coloring of cluster ID follows that in Fig. 3A.) Figure S5. genes rejected by null hypothesis (DE genes) at FDR = 0.05 between fresh and preserved tissue in cluster 2, 4, 6, 7. (A) Number of DE genes identified between each of the eight identified cell types and its nearest neighbor (defined in Fig. 3A) with incrementing FDR. (B) Volcano plots for DE gene at FDR = 0.05 between fresh and preserved tissue identified in the given cluster (blue) and DE genes identified in (A) for the same cluster (black). (C)(D) DE genes at FDR = 0.05 in cluster 4 between fresh and day 3 tissues. (Cluster ID and color for time followed that in Fig. 3A.) Figure S6. Number of gene sets enriched with FDR q value≤0.05 for genes that are (A) upregulated or (B) downregulated in cells from fresh tissues compared to those from preserved tissues. Figure S7. Number of genes with rejected null hypothesis by the Breusch-Pagan test at incrementing FDR for each identified cell cluster. Figure S8. Evaluation of gene expression variation between cells from fresh and preserved tissues via (A) dimension reduction on incrementing number of overdispersed genes (B) hierarchical clustering on top 500 over-dispersed genes (cluster ID follows that in Fig. 3A, cell clustering follows Fig. 2D). (PDF 6690 kb
Additional file 4: of High fidelity hypothermic preservation of primary tissues in organ transplant preservative for single cell transcriptome analysis
Table S3. Gene sets enriched with FDR q value ≤0.05 from GSEA. (CSV 732 bytes
Additional file 2: of High fidelity hypothermic preservation of primary tissues in organ transplant preservative for single cell transcriptome analysis
Table S1. Differentially expressed genes in the putative cluster (cluster 8). (CSV 1 kb
Additional file 8: of High fidelity hypothermic preservation of primary tissues in organ transplant preservative for single cell transcriptome analysis
Table S7. Gene ontology enrichment of genes from cluster3 with null hypothesis rejected at FDR = 0.05 by Breusch-Pagan test. (CSV 668 bytes
Additional file 7: of High fidelity hypothermic preservation of primary tissues in organ transplant preservative for single cell transcriptome analysis
Table S6. Genes with null hypothesis rejected at FDR = 0.05 by Breusch-Pagan test. (XLSX 15 kb
Fused 3‑Hydroxy-3-trifluoromethylpyrazoles Inhibit Mutant Huntingtin Toxicity
Here, we describe the selection and
optimization of a chemical
series active in both a full-length and a fragment-based Huntington’s
disease (HD) assay. Twenty-four thousand small molecules were screened
in a phenotypic HD assay, identifying a series of compounds bearing
a 3-hydroxy-3-trifluoromethylpyrazole moiety as able to revert the
toxicity induced by full-length mutant Htt by up to 50%. A chemical
exploration around the series led to the identification of compound <b>4f</b>, which demonstrated to be active in a Htt171–82Q
rat primary striatal neuron assay and a PC12-Exon-1 based assay. This
compound was selected for testing in R6/2 mice, in which it was well-tolerated
and showed a positive effect on body weight and a positive trend in
preventing ventricular volume enlargment. These studies provide strong
rationale for further testing the potential benefits of 3-hydroxy-3-trifluoromethylpyrazoles
in treating HD