Supplementary Table 1 from Dietary Energy Balance Modulates Epithelial-to-Mesenchymal Transition and Tumor Progression in Murine Claudin-Low and Basal-like Mammary Tumor Models

PDF file - 1.1MB, Diet Macro- and Micro-Nutrient Composition</p

Supplementary Figure S2 from Intratumoral Heterogeneity in a <i>Trp53</i>-Null Mouse Model of Human Breast Cancer

Supplementary Figure S2. FACS profile comparison and immunostaining on the p53 null parental tumor and the subsequent TIC- and CD29HCD24L niche subpopulation-derived tumor.</p

Supplementary Figure S4 from Intratumoral Heterogeneity in a <i>Trp53</i>-Null Mouse Model of Human Breast Cancer

Supplementary Figure S4. Levels of CXCL12 under different co-culture conditions.</p

Supplementary Table S2 from Intratumoral Heterogeneity in a <i>Trp53</i>-Null Mouse Model of Human Breast Cancer

Supplementary Table S2. A detailed explanation for mice used in Table 1.</p

Supplementary Figure 1 from Prognostic B-cell Signatures Using mRNA-Seq in Patients with Subtype-Specific Breast and Ovarian Cancer

PDF file - 30K, Signatures of lymphocyte infiltration in breast tumors are highly correlated in A an mRNA-seq expression data set of 728 breast tumors and 91 normal breast samples B an mRNA-seq expression data set of 266 ovarian tumors.</p

Supplementary Figure S6 from Intratumoral Heterogeneity in a <i>Trp53</i>-Null Mouse Model of Human Breast Cancer

Supplementary Figure S6. Co-transplantation of the fluorescence labeled cells showed that a majority of the cells were generated from the TIC subpopulation.</p

Supplementary Methods, Figure Legends, Tables S1, S3 - S6 from Intratumoral Heterogeneity in a <i>Trp53</i>-Null Mouse Model of Human Breast Cancer

Supplementary Table S1. Partial list of probes preferentially expressed in the Lin-CD29HCD24L cells. Supplementary Table S3. Co-transplantation of increasing numbers of niche cells resulted in increasing numbers of tumors. Supplementary Table S4. a. Pairwise comparisons using fixed number of niche cells displayed a reduced tumor latency with increasing numbers of TICs. b. Pairwise comparisons using 10 TICs demonstrated that tumor formation was more rapid with 10 niche cells as compared to 0. c. Pairwise comparisons using 20 TICs demonstrated that tumor formation was faster with 10 niche cells as compared to 0. Supplementary Table S5. Different types of niche cells were associated with different tumor forming frequencies. Supplementary Table S6. a. No difference observed between shRNA groups for 0 niche cell relative to the control shRNA. b. No difference observed between shRNA groups for 2 niche cells relative to the control shRNA. c. A marginal difference for 10 niche cells relative to the control shRNA. d. A significant difference for 20 niche cells as relative to the control shRNA.</p

Supplementary Data 3 from Prognostic B-cell Signatures Using mRNA-Seq in Patients with Subtype-Specific Breast and Ovarian Cancer

XLSX file - 298K, Unique sample IDs allowing TCGA breast and ovarian data sets to be downloaded from CGHub.</p

Supplementary Figure 5 from Prognostic B-cell Signatures Using mRNA-Seq in Patients with Subtype-Specific Breast and Ovarian Cancer

PDF file - 28K, Percent of assembled contigs significantly enriched for mutation patterns consistent with evidence of SHM in breast (A, B) and ovarian (C, D) tumors.</p

Supplementary Figure 4 from Prognostic B-cell Signatures Using mRNA-Seq in Patients with Subtype-Specific Breast and Ovarian Cancer

PDF file - 37K, Method of calculating likelihood of enrichment for somatic hypermutation from mRNA-seq reads mapping to BCR segment loci.</p