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Additional file 3: Table S2. Hub protein analysis.

Showing the size and colony appearance of Sca-1 subpopulations. A Size differences in freshly isolated Sca-1 subpopulations from cBM. B Size differences in cultured Sca-1 subpopulations. Bright-field images of C Sca-1− and D Sca-1+ expanded colonies after 10 days of culture. First column = 4× magnification (bar = 200 μm) and second column = 10× magnification (bar = 100 μm). Data are the mean ± SD of at least three independent experiments. *p <0.05, Student’s t test. (TIFF 1643 kb)

Additional file 2: Fig. S2. Scatter plot of percentage imputation accuracy against genomic length of CNVs. A CNV was deemed to be correctly imputed when the called copy number matched the imputed copy number. The red circles represent double deletions (n = 9 in Charolais, 15 in Limousin and Holstein-Friesian), green triangles represent single deletions (n = 34 in Charolais, n = 38 in Limousin, and 22 in Holstein-Friesian), blue squares represent normal state (n = 36 in Charolais, 40 in Limousin, and 24 in Holstein-Friesian), double duplications are represented by a purple cross (n = 2 in Charolais, n = 1 in Limousin and Holstein-Friesian).

Additional file 16: Figure S8. Differential Expression of Genes in Presence of Indirect Contact of MSCs. Pathway Enrichment Analysis of Differentially Expressed Genes (DEGs) performed based on KEGG database by pairwise analysis. Here, X axis represents number of DEGs. Y axis represents second KEGG pathway terms. All second pathway terms were grouped in top pathway terms indicated in different colour.

Additional file 4: Figure S2. Combined effect of high glucose and albumin on RPTEC/TERT1 inflammatory responses. A. Schematic diagram of the experimental protocol. In brief, RPTEC-TERT-1 cells cultured at 27500/cm2, medium was replaced every second day. From day 12, cells were grown in high-glucose or control conditions (CTRL/HG/MAN) with or without 100 μg/ml human serum albumin. Mediium was replaced at day 15 for a further two days. B. Mean ± SD levels of inflammatory mediators including IL-8 (top left), IL-6 (top right), MCP-1 (bottom left) and NGAL (bottom right) in the supernatants are represented in grey (CTRL), blue (HG) and green (MAN) bars. Bright colours represent the levels in samples when treated without albumin. * denoted unpaired t-tests for CTRL vs HG, HG vs MAN, MAN vs CTRL. ¥ denoted ANOVA to analyse differences between CTRL, HG and MAN. ****/¥¥¥¥ p <0.0001, ***/¥¥¥ p <0.001, **/¥¥ p <0.01, */¥ p <0.05.

CAZy comparison of the species. (XLSX 30 kb)

JAM-A overexpression is insufficient to improve cell viability following short-term treatment with HER2-targeted drugs. MDA-MB-231 cells overexpressing full-length human JAM-A (JAM+) or a pcDNA3 empty vector control (EV) were treated for 3 days in serum-free medium with the indicated concentrations of trastuzumab (A) or lapatinib (B) and subjected to MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) viability assays. In parallel, the same cell lines were treated for 6 days in complete medium with the indicated concentrations of trastuzumab (C) or lapatinib (D) and subjected to MTT viability assays. JAM-A overexpression did not alter the drug sensitivity of cells under any of the short-term conditions tested. (E) Representative protein overexpression of JAM-A in transfected MDA-MB-231 cells. (TIF 145 kb)

Additional file 7: Table S6. Pathway enrichment analysis using PANTHER.

Figure S2. False positives detected using each species classifier with the total number of reads from each sequencer. (PNG 128Â kb)

List of differentially expressed genes (including new CDS) in four experimental conditions: hypoxia, exposure to erythromycin, exposure to kanamycin and growth in artificial sputum medium. (XLSX 99 kb)