Novel genes are expressed in olfactory organs.

<p>(A) Chromosome 2 is schematized on the top and the locus where two previously unidentified genes were found is amplified below. In black are <i>Lcn16</i> and <i>Lcn17</i> gene models, where boxes correspond to the exons. The mapped RNAseq reads are below: each read is drawn in grey and blue lines join read fragments that span exon junctions. Black segments within the reads indicate indels. (B) <i>In situ</i> hybridization reveals <i>Lcn16</i> is expressed in glandular tissue of the VNO and (C) <i>Lcn17</i> is expressed in cells within the main olfactory epithelium. Scale bars: (B) 100 µm, (C) 50 µm.</p

RNAseq provides comprehensive gene models for ORs and VRs.

<p>(A–B) An example of new gene models generated for <i>Olfr168</i> (A) and <i>Vmn1r34</i> (B) are shown in black. Boxes correspond to exons and arrowheads indicate the direction of the gene. The existing Ensembl annotations for the genes are shown in red with their UTRs in grey. New 5′ exons and extended 3′UTRs were identified for both. The mapped RNAseq reads that support the models are below. Each read is drawn in grey and blue lines join read fragments that span exon junctions. Black segments within the reads indicate indels. (C) Boxplots of the transcript length as annotated in Ensembl (pink) or as obtained from the reconstructed models from our RNAseq data (blue) for the V1R, V2R and OR genes. The increase in transcript length is highly significant (*** P<0.0001, two-tailed Mann-Whitney test). (D) As above, but quantifying the proportion of unique sequence for probe design (*** P<0.0001 and *P<0.01, two-tailed Mann-Whitney test). The <i>uniqueness</i> corresponds to the proportion of all 100 nucleotide long windows within the transcript that map uniquely to the genome. In all boxplots, outliers are defined as data points that fall outside 1.5 of the inter-quartile range, and are plotted as open circles.</p

Limited sexual dimorphism in the olfactory system.

<p>The mean gene expression is plotted against their log₂ fold change between male and female samples for the VNO (A) and OM (B). Genes with ±infinite fold changes were assigned to ±13 to ease visualization. Triangles depict genes located on the sex chromosomes. Genes significantly differentially expressed in one tissue (FDR 5%) are red while the 11 genes that are significantly differentially expressed in both tissues are blue. The genes in the VNO plotted in green are eight lipocalins that are highly variable between replicates. Dotted lines indicate a log₂ fold change of ±2.</p

Expression of the complete OR repertoire in the OM.

<p>The mean FPKM expression values for all OR and trace amine-associated receptors (TAAR) genes in the OM. Genes are ordered by their chromosomal location and chromosomes are annotated in the boxes at the bottom. Class I OR genes are blue, class II OR genes are red and TAAR genes are green. Black shading below each bar indicates the gene is annotated as a functional receptor, and grey indicates an annotated pseudogene. Error bars represent the standard error of the mean from the six biological replicates. <i>Olfr1507</i> is the highest expressed OR gene and is indicated with an asterisk.</p

Putative novel genes.

<p>Putative novel genes.</p

Comparison of methods measuring OR gene expression.

<p>A comparison of the expression levels obtained from the RNAseq data to those previously reported using (A) NanoString nCounter and (B) nanoCAGE <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004593#pgen.1004593-Khan2" target="_blank">[23]</a>, <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004593#pgen.1004593-Plessy1" target="_blank">[29]</a>. The Spearman correlation values are indicated. (C) Comparison of the 5′ of OR transcripts obtained with Cufflinks here, with data estimated by nanoCAGE <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004593#pgen.1004593-Plessy1" target="_blank">[29]</a>. The difference in nucleotides between the two ends was calculated; a negative value indicates the 5′ end reported by nanoCAGE is upstream of the one reported by Cufflinks. (D) The receptor genes with most dissimilar 5′ end coordinates can be explained by one of four scenarios; the proportions of each are shown in the pie chart, for the 25 genes with the biggest differences.</p

Expression of the complete VR repertoire in the VNO.

<p>The mean FPKM expression values are shown for all the VR and formyl peptide receptor (FPR) genes in the VNO. Genes are ordered by their chromosomal location and chromosomes are annotated in the boxes at the bottom. V1R genes are blue, V2R genes are red and FPR genes are green. Black shading below each bar indicates the gene is annotated as a functional receptor, and grey indicates an annotated pseudogene. Error bars represent the standard error of the mean from the six biological replicates. <i>Vmn2r89</i> is the highest VR gene expressed and is indicated with an asterisk.</p

Additional file 5: of CTCF maintains regulatory homeostasis of cancer pathways

Mouse and human tumor metadata and differential expression results of RNA-seq data. Sample information regarding all mouse and human tumor samples included in analyses. Results from the differential expression analysis of mouse liver tumors and human uterine and breast cancer dataset (performed using DESeq2). Gene set enrichment analysis for mouse concordant genes. Intersection results of MEF and tumor DE analyses. Format: xls. File size: 20.7 MB. (XLS 20148 kb

Additional file 4: of CTCF maintains regulatory homeostasis of cancer pathways

Proteome quantification. Normalized protein abundances from the TMT proteomics dataset along with the results from the differential abundance analysis. Format: xls. File size: 2.9 MB. (XLS 2840 kb

Additional file 3: of CTCF maintains regulatory homeostasis of cancer pathways

Differential expression results of RNA-seq data. Results from the differential expression analysis of the RNA-seq dataset using DESeq2. Also, results from the gene set enrichment analyses for both Gene Ontology sets and KEGG pathways. Format: xls. File size: 13.5 MB. (XLS 13174 kb