Supplementary MaterialsFigure S1: Comparison of DNA and RNA variant allele frequency (VAF) in 4T1 cells. genes AMG 487 S-enantiomer of 4T1. Matters per million (cmp) had been computed by edgeR. Picture_5.TIFF (1.3M) GUID:?1A2BB113-9B88-43CC-97E7-62C76E25E561 Body S6: Scatterplot of the primary component analysis of TCGA BRCA gene expression of genes ERBB2, ESR1, and PGR. Proven are the initial two principal elements (Computer1 and Computer2). Ellipses suggest normal-probability contours. Picture_6.PNG (75K) GUID:?A64C029E-C8AF-4650-9287-E3A27F4B865F Body S7: Boxplot of TCGA BRCA gene expression of genes ERBB2, ESR1, and PGR, separated by TNBC position. Appearance on y-axis is certainly provided as log2 (FPKM+1) models. Image_7.PNG (44K) GUID:?F4FA8DD5-129E-4619-B187-F2632852899A Physique S8: Gene expression of users AMG 487 S-enantiomer of the MHC class I and II antigen presenting pathway in 4T1 and BALB/c mammary gland. Image_8.TIFF (650K) GUID:?DA81B645-5E20-401F-B795-A42685EA0AA3 Table S1: Natural Control-FREEC output (sheet 1) and predicted complete gene copy numbers of 4T1 genes (sheet 2). Table_1.XLSX (9.4M) GUID:?A3EB28AD-8772-4FF2-95CF-F4EDC2377C1B Table S2: Somatic SNVs in 4T1, including annotation on amino acid substitutions, affected genes/transcripts, expression of these, and protection/VAF in the DNA/RNA NGS libraries. Table_2.XLSX (427K) GUID:?C4C4947F-44F8-4BD2-BC18-E7EA0E6694D3 Table S3: Somatic INDELs in 4T1, including annotation on frameshift, affected genes/transcripts and coverage/VAF in the DNA/RNA NGS libraries. A VAF of ?1 means not covered, while a VAF of 0 indicates protection but absence of the variant allele. Table_3.XLSX (17K) GUID:?72BAEC27-EEC3-462C-8991-65E712B13A0C Table S4: Fusion genes in 4T1, including predicted positions of breakpoints, quantity of junction reads, and spanning read pairs and the program that detected a fusion. Table_4.XLSX (9.9K) GUID:?AE0C0C3B-21DE-4FE8-8A17-FC849A58A5FE Table S5: Gene expression in 4T1 and BALB/c mammary gland in TPM. Table_5.XLSX (1.3M) GUID:?B2165757-4EB8-4C2C-BF1C-36941DB0F97B Table S6: Differential gene expression in 4T1 vs. BALB/c mammary gland, showing log fold switch, FDR, and baseline expression values. Table_6.XLSX (2.4M) GUID:?3E94A3B3-050B-4F60-8385-433D9D033230 Table S7: Gene set and pathway enrichment in differentially expressed genes of 4T1 cells for upregulated and downregulated genes in GO gene sets and KEGG pathways, respectively (sheets are labeled up GO, up KEGG, down GO, and down KEGG, respectively). Table_7.XLSX (976K) GUID:?035E73C8-41D8-49FA-AD94-5A600BE3FBA0 Table S8: Differential gene expression in human TNBC vs. breast tissue, showing log fold switch, FDR and baseline expression values. Table_8.XLSX (3.3M) GUID:?3EEE4108-1A26-426E-9807-E43211677FB4 Table S9: Expression in RPKM of MMTV genes for two replicates of 4T1 RNA-Seq libraries. Table_9.XLSX (8.3K) GUID:?62F2A5B0-5A63-4C44-BCCA-F40F9B1C0F94 Table AMG 487 S-enantiomer S10: Expression values in TPM of MHC genes in 4T1 MMP2 and BALB/c tissues. The used research sequences from your UCSC known genes or Genbank are also outlined. Table_10.XLSX (9.4K) GUID:?EC4C9950-1DD2-4442-9C9C-9D521C78C5B2 Table S11: Results of immunogenicity screening, including details on mutation, amino acid substitution, the result of the ELISpot assay, the subtype of the T-cell response, and the specificity when compared to a WT control. Table_11.XLSX (14K) GUID:?355B8952-0042-4586-90C4-2E97A1D34B2F Data Availability StatementThe datasets generated for this study can be found in the European Nucleotide Archive (https://www.ebi.ac.uk/ena/browser/home) with the study accession number PRJEB36287. Abstract Background: Tumor models are critical for our understanding of cancer and the development of malignancy therapeutics. The 4T1 murine AMG 487 S-enantiomer mammary malignancy cell line is one of the most widely used breast cancer models. Here, we present an integrated map of the genome, transcriptome, and immunome AMG 487 S-enantiomer of 4T1. Results: We found Trp53 (Tp53) and Pik3g to be mutated. Other frequently mutated genes in breast malignancy, including Brca1 and Brca2, are not mutated. For malignancy related genes, Nav3, Cenpf, Muc5Ac, Mpp7, Gas1, MageD2, Dusp1, Ros, Polr2a, Rragd, Ros1, and Hoxa9 are mutated. Markers.