Additional file 5: of Food perception without ingestion leads to metabolic changes and irreversible developmental arrest in C. elegans

Table S1. Feeding and food perception affect metabolism-related GO terms. Top fifteen GO terms ranked by FDR are listed for genes significant in IvF vs. IvS at 1 h and F vs. S at 1 h from four biological replicates of mRNA-seq. A quadruple mutant transgenic strain was used for mRNA-seq. Full list available in Additional file 3: Dataset S1. Table S2. Feeding but not food perception affects development-related GO terms. Top fifteen GO terms ranked by FDR are listed for genes significant in F vs. S at 1 h but not IvF vs. IvS at 1 h from four biological replicates of mRNA-seq. A quadruple mutant transgenic strain was used for mRNA-seq. Full list available in Additional file 3: Dataset S1. (DOCX 23 kb

Additional file 6: of Food perception without ingestion leads to metabolic changes and irreversible developmental arrest in C. elegans

Figure S4. Perception and physiological effects of potential food cues. (A) The proportion of larvae that recovered to at least the L4 stage after 3 days of recovery is plotted for three biological replicates. (B-C) GFP::DAF-16 localization is plotted for three to six biological replicates. (D) L1 starvation survival is plotted over time. A logistic regression of mean survival from three biological replicates is shown. (E) Worm length following 48 h of recovery is plotted relative to L1 starvation survival. (F) Worm length following 48 h of recovery is plotted as a density plot, showing altered population composition. (A-E) ***p < 0.001, **p < 0.01, *p < 0.05; unpaired t test. Error bars are SEM, except for in E where they are standard deviation. (A) Quadruple mutant transgenic background. (B-F) Wild-type background. (PDF 93 kb

Additional file 2: of Food perception without ingestion leads to metabolic changes and irreversible developmental arrest in C. elegans

Figure S2. Ivermectin affects transcription in larvae. PCA of four biological replicates is plotted. Ellipses represent 80% confidence interval. Quadruple mutant transgenic background. (PDF 31 kb

Additional file 1: of Food perception without ingestion leads to metabolic changes and irreversible developmental arrest in C. elegans

Figure S1. Further characterization of ivermectin system and starvation recovery. (A) The proportion of larvae that displayed the stated localization of fluorescent beads three to four hours after bead addition is plotted for three biological replicates. (B-C) The proportion of larvae that recovered to at least the L4 stage after 3 days of recovery is plotted for three to four biological replicates. Ivermectin Resistant = JD369. Ivermectin Sensitive = LRB269. ***p < 0.001, *p < 0.05; unpaired t test. (A-C) Error bars are SEM. Quadruple mutant transgenic background. (PDF 32 kb

Additional file 3: of Food perception without ingestion leads to metabolic changes and irreversible developmental arrest in C. elegans

Dataset S1. mRNA-seq analysis of food perception. Results of mRNA-seq analysis, including counts per gene, logFC, FDR, GOrilla analysis, and GO term gene lists used are included. (XLSX 18186 kb

Additional file 4: of Food perception without ingestion leads to metabolic changes and irreversible developmental arrest in C. elegans

Figure S3. GFP::DAF-16 localization responds to perception of many bacterial foods and requires daf-2. (A-B) GFP::DAF-16 localization is plotted for three to four biological replicates. ***p < 0.001; unpaired t test. Error bars are SEM. Wild-type background. (PDF 50 kb

Additional file 4: of Increased DNA methylation variability in rheumatoid arthritis-discordant monozygotic twins

Table S3. Pathways enriched in differentially variable positions identified in RA-discordant twins, restricted to sites which were hypervariable in healthy co-twins. Pathway analysis was performed using the gometh function in the MissMethyl package. Pathways are ranked by p value (p < 0.05). (PDF 87 KB) (PDF 84 kb

Additional file 3: of Increased DNA methylation variability in rheumatoid arthritis-discordant monozygotic twins

Table S2. Pathways enriched in differentially variable positions identified in RA-discordant twins. Pathway analysis was performed using the gometh function in the MissMethyl package. Pathways are ranked by p value (p < 0.05). (PDF 112 KB) (PDF 109 kb

Additional file 2: of Increased DNA methylation variability in rheumatoid arthritis-discordant monozygotic twins

Table S1. Full list of differentially variable positions (n = 1171) between RA-affected and non-RA twins. Probe names are shown, along with t-statistic p value, Bartlett’s test for differential variability, which group was hypervariable, and probe annotation. (PDF 340 KB) (PDF 334 kb

Additional file 1: of Increased DNA methylation variability in rheumatoid arthritis-discordant monozygotic twins

Figure S1. Multidimensional scaling plot of DMARD use in RA-discordant twins. Figure S2. Cell composition estimates for RA-discordant twins. Figure S3. Feature enrichment for differentially variable positions. Figure S4. Feature enrichment for DVPs identified in both RA and type 1 diabetes disease-discordant twins. Figure S5. Variance and range for DVPs which were hypervariable in healthy co-twins. (PDF 423 KB) (PDF 410 kb