Supplement 1. Code for epidemiological model run in WinBUGS.

<h2>File List</h2><p> <a href="code.txt">code.txt</a> (md5: 6cc6cc260bf1ebb8b6818c46fedc6253) </p><h2>Description</h2><p> The code.txt file contains the code for WinBUGS used to run Bayesian epidemiological related to genotype-specific chronic wasting disease infection and mortality rates of white-tailed deer in Wisconsin, USA. </p> <p> The code was written to estimate epidemiological rates (infection rate and disease-induced mortality rate for chronic wasting disease) specific for white-tailed deer with two PRNP genotype variants. The G nucleotide in the third position of codon 96 codes for the glycine amino acid, the A nucleotide in this position causes a change in the amino acid code to serine. We considered genotypes either homozygous for the G allele (GG) or consisting of at least one copy of the A allele (A*). Data for the model were based SNP genotypes for 1,119 white-tailed deer from the core CWD infected area of Wisconsin, USA. The code is written in for WinBUGS version 1.4.3; Imperial College and Medical Research Council, UK. </p

Additional file 1 of Obesity alters the mouse endometrial transcriptome in a cell context-dependent manner

Additional file 1: Supplemental Figure 1. Increased macrophages in the high-fat diet endometrium. Supplemental Figure 2. Purification of endometrial cells. Supplemental Figure 3. Differential gene expression analysis of high-fat diet uterine macrophages. Supplemental Figure 4. Impact of estrous cycle stage on differential gene expression. Supplemental Figure 5. Negative immunohistochemistry staining

Additional file 1: of Cross-site comparison of ribosomal depletion kits for Illumina RNAseq library construction

Figure S1. BioAnalyzer traces for samples used in the study. Left: Intact UHR, Right: Heat degraded UHR RNA. (PPTX 127 kb

Additional file 4: of Cross-site comparison of ribosomal depletion kits for Illumina RNAseq library construction

Figure S3. Insert size distribution for RNAseq libraries from intact RNA. The insert size for each library passing the 50% rRNA filter was calculated for reads with convergent reads that were separated by < 1000 bp. Kit abbreviations: RZ = RiboZero Gold, LX = Lexogen RiboCop, NE = NEBNext rRNA Depletion, K=Kapa RiboErase, CR = Clontech Ribogone, CZ = SMARTer Pico total RNA. Top: length of the 90th percentile of inserts reads. Middle: length of the median insert read. Bottom: length of the 10th percentile of inserts read. (PPTX 82 kb

Additional file 2: of Cross-site comparison of ribosomal depletion kits for Illumina RNAseq library construction

Contains the following: Describes normalization of kit protocols and any individual site deviations from this normalization. Figure S1. – BioAnalyzer traces for samples used in the study. Left: Intact UHR, Right: Heat degraded UHR RNA. Figure S2. – Clustering of differentially detected genes. Top 50 most differentially detected genes, as measured by variance of log2RPKM across all samples, were clustered based on their differential expression. TOP: Hierarchical tree of clustering based on a complete linkage function using Euclidean distance. 2ND LINE: Intact/Degraded status is shown. Intact samples are indicated in white while degraded samples are indicated in grey. 3RD LINE: Kit. Dark Blue = RZ|RiboZero Gold, Yellow = LX|Lexogen RiboCop, Aqua = NE|NEBNext rRNA Depletion, Green = Q|Qiagen, Grey = K|Kapa RiboErase, Blue = CR|Clontech Ribogone, Orange = CZ|SMARTer Pico total RNA. HEAT MAP: Red indicate higher level of absolute expression. Scale shown to right. White lines indicate the highest branches within the hierarchical tree. Figure S3. – Insert size distribution for RNAseq libraries from intact RNA. The insert size for each library passing the 50% rRNA filter was calculated for reads with convergent reads that were separated by < 1000 bp. Kit abbreviations: RZ = RiboZero Gold, LX = Lexogen RiboCop, NE = NEBNext rRNA Depletion, K=Kapa RiboErase, CR = Clontech Ribogone, CZ = SMARTer Pico total RNA. Top: length of the 90th percentile of inserts reads. Middle: length of the median insert read. Bottom: length of the 10th percentile of inserts read. Figure S4. - Relative ratio of reads mapping to ERCCs. Fraction of reads mapping to each ERCC mRNA is shown for each replicate. Light horizontal lines show 2-fold changes in fraction observed (log scale). Each expected concentration is shown in a different color. Data sets ordered by intact/degraded status followed by site within each kit left to right. Table S1. Catalog numbers and manual versions for protocols used. Table S2. Comparison of RNA library preparation chemistry variables. (DOCX 21 kb

Additional file 5: of Cross-site comparison of ribosomal depletion kits for Illumina RNAseq library construction

Figure S4. Fraction of reads mapping to each ERCC mRNA is shown for each replicate. Light horizontal lines show 2-fold changes in fraction observed (log scale). Each expected concentration is shown in a different color. Data sets ordered by intact/degraded status followed by site within each kit left to right. (PPTX 165 kb