EMBO/sd-character-level-ner huggingface dataset:
Figure 3GPRC5A depletion markedly increases caspase-3 activation/PARP cleavage during hypoxia. Three independent siRNA sequences targeting GPRC5A induce caspase-3 activation/PARP cleavage during hypoxia. GPRC5A depletion reduces hypoxic cell growth/survival. Crystal violet cell assays show reduced cell growth/survival in GPRC5A depleted cells during hypoxia [n=3]. Expression of an siRNA-resistant GPRC5A cDNA rescues hypoxic GPRC5A-depleted cells from apoptosis. Upper: doxycycline-induced expression GPRC5Asi1R rescues increases caspase-3/PARP cleavage induced by GPRC5A depletion in hypoxia. Lower: generation of an siRNA1 resistant GPRC5A cDNA by synonymous mutations. Caspase inhibitor QVD prevents caspase-3 activation/PARP cleavage by GPRC5A depletion in hypoxia. GPRC5A depletion in hypoxia induces apoptosis as determined by the violet ratiometric membrane asymmetry probe/dead cell apoptosis assay and flow cytometry
Figure 3(A) Schematic representation of the eukaryotic elongation cycle with ribosome footprint sizes to illustrate the functional states isolated by CHX+TIG. PreAcc, pre-accommodation; PrePT, pre-peptide bond formation; PreTrans, pre-translocation. (B) Size distributions of ribosome footprints for WT (black and grey) and eEF3d (purple and blue) cells from libraries prepared with CHX+TIG. Two biological replicates are shown. (C) Similar to (A), with footprint sizes isolated by CHX+ANS. (D) Similar to (B), from libraries prepared with CHX+ANS. (E) Scatter plot of codon-specific ribosome occupancies for 21 nt RPFs comparing eEF3d to WT cells from libraries prepared with CHX+TIG. Trend line (blue) and its slope are shown. The diagonal line indicates the distribution expected for no change. (F) Codon-specific ribosome occupancies for 21 nt RPFs from WT and eEF3d cells (two biological replicates). CGA and AGG codons are shown in red and purple, respectively. Variance for each dataset is indicated. (G) Scatter plot of codon-specific occupancies for 28 nt RPFs comparing eEF3d to WT cells from libraries prepared with CHX+ANS. Trend line (blue) and its slope are shown. Codons that encode proline and glycine are colored in purple and green, respectively. (H) 28 nt RPF-ribosome occupancies of 5,771 tripeptide motifs are plotted for WT and eEF3d cells, for motifs more than 100 occurrences in yeast transcriptome. Motif sequences enriched upon eIF5A depletion are labeled.
The CARD8 inflammasome is functional in human T cells (A) Gene expression profile of 15 inflammasome-related genes in human T cell and monocyte subsets.Figure 3(A) Gene expression profile of 15 inflammasome-related genes in human T cell and monocyte subsets. TPM values were retrieved from a public RNASeq dataset and log2 transformed. Both, rows and columns are clustered using euclidean distance and complete linkage. (Tfh, T follicular helper cells; Tregs, T regulatory cells; Th, T helper cells; CM, central memory T cells; EM, effector memory T cells; TE, terminal effector T cells; CD14+ C16-, classical monocytes; CD14+ CD16+, intermediate monocytes; CD14- CD16+, non-classical monocytes). (B) Immunoblotting of CD4 T cells and MDMs treated with Pam3CSK4 for 6 hours. * indicates an unspecific band. One representative experiment out of three is shown. (C) Immunoblotting of polyclonal CD4 T cells targeted with two gRNAs for each indicated target gene. One representative experiment out of three is shown. (D) CD4 T cells from the indicated polyclonal gene targeting approach were treated with the indicated stimuli for 18 hours. Individual data points ± SEM from three independent donors are shown. Statistics indicate significance by two-way ANOVA: ***p ≤ 0.001; ns, not significant. P-values were corrected for multiple comparisons (Dunnett).