The green, orange and red shapes represent the putative DNA-binding proteins involved in the structure. As the locus is located at a genomic distance of over 800 Kb from and promoter (Figure 3D). an asterisk.(TIF) pgen.1003549.s001.tif (757K) GUID:?FE344169-C816-4E0C-A472-A63E0C3E4089 Figure S2: A) Zoom-in plot of the region showing increased relative interaction frequency with the promoter fragment (adapted from Figure 3D). The locations of the resistance allele harboring the 14 bp deletion of the COUP-TF binding motif upregulates transcript levels, which is associated with decreased mammary carcinoma multiplicity.(TIF) pgen.1003549.s002.tif (2.0M) GUID:?9E96CF96-E164-406A-9CF2-DFA8AEBC4D45 Figure S3: Matrigel colony-forming ability for luminal RMEC subpopulations. In the upper left panel, a representative FACS MAC13243 dot plot is shown for luminal RMECs labeled with anti-CD61 and peanut lectin (PNL). Three gates were applied to sort the CD61+PNLhi (green), the CD61hiPNL+ (orange) and the entire CD61+ (purple) MAC13243 populations of luminal RMECs. An equal number of cells was plated in Matrigel to test for colony-forming ability. In the lower right panel, the results of the colony-forming ability assay are shown as the average (+/? sem) number of colonies relative to the number of colonies for the CD61+ luminal population (n?=?8 assays). The CD61+PNLhi population had a significantly increased and the CD61hiPNL+ had MAC13243 a significantly decreased colony-forming ability as compared with the CD61+ luminal population (P<0.05). For each sorted population, the range of absolute amount of colonies per 10,000 plated cells is printed in the lower left panel.(TIF) pgen.1003549.s003.tif (2.6M) GUID:?21E01C4B-D0C7-459F-B547-D2E446F3D0DE Figure S4: A) Graphed are the average (+/?sem) transcript levels relative to transcript levels of the endogenous control for siRNA-treated cell lines MCF10A and MCF7. B) Mean fluorescence intensities in artificial units (AU) of anti-CD24, -CD29, -CD49f and -CD44 labeling of MCF10A and MCF7 cells treated with siRNAs against (siNR2F1) or non-targeting control siRNAs (siCONTROL). Significantly different mean fluorescence intensity (P<0.05) is indicated by an asterisk.(TIF) pgen.1003549.s004.tif (1.2M) GUID:?23CF3C58-F66A-4F08-9477-631357DAD094 Table S1: Markers with asterisk designed for negative strand. Markers in bold used to define congenic lines in Figure 1. Markers in grey shading defining the current critical interval boundaries. gUwm, g2Uwm, bUwm are microsatelite markers. rf are SNP markers, discovered by resequencing rat-fugu (rf) conserved elements in the locus; variants are listed in Table S3.(XLSX) pgen.1003549.s005.xlsx (13K) GUID:?A2A3E740-D15C-40D9-A2DD-1FE65703A4CB Table S2: Positions are in basepairs on rat chromosome MGP 2 (UCSC version 3.4/rn4).(XLSX) pgen.1003549.s006.xlsx (48K) GUID:?A51539DD-FA08-4A17-8FFE-1EAD826148D9 Table S3: Positions are in basepairs on rat chromosome 2 (UCSC version 3.4/rn4). For all variants, the WF allele matches the genome sequence (from the Brown Norway inbred rat strain). All variants have been submitted to dbSNP (accession number pending).(XLSX) pgen.1003549.s007.xlsx (31K) GUID:?5ABA32C2-234D-4F53-AAA8-39EACDFE7760 Table S4: Listed are 1,531 genes with a unadjusted P-value of <0.05, sorted by P-value starting with the MAC13243 412 genes with 1-1-1 mouse-rat-human orthologs. LogFC?=?log of the Fold Change between the WT and MD samples. The WT.1-4 and MD.1-4 columns contain the RSEM output .nu values.(XLSX) pgen.1003549.s008.xlsx (270K) GUID:?17C9D4F8-AAEB-4B7C-8D75-3E52F9BC245E Table S5: The same groups and background list were run using 2 online GO enrichment tools, GOrilla and DAVID. The enriched terms printed in red reach best significance, as determined by an adjusted P-value<0.05 (FDR adjust in GOrilla, Benjamini-Hochsberg adjust in DAVID).(XLSX) pgen.1003549.s009.xlsx (446K) GUID:?FCF6E8A2-AE8F-48F2-B802-C5A9000BAD5D Table S6: The same groups and background list were run using 2 online GO enrichment tools, GOrilla and DAVID. The enriched terms printed in red reach best significance, as determined by an adjusted P-value<0.05 (FDR adjust in GOrilla, Benjamini-Hochsberg adjust in DAVID).(XLSX) pgen.1003549.s010.xlsx (604K) GUID:?34F1DFDC-E61E-4720-8966-4EF35A586C5D Table S7: The same groups and background list were run using 2 online GO enrichment tools, GOrilla and DAVID. The enriched terms printed in red reach best significance, as determined by an adjusted P-value<0.05 (FDR adjust in GOrilla, Benjamini-Hochsberg adjust in DAVID).(XLSX) pgen.1003549.s011.xlsx (443K) GUID:?2B0E066B-FFBE-44EA-960B-FC7FC4DB0036 Abstract Genome-wide association studies have revealed that many low-penetrance breast cancer susceptibility loci are located in non-protein coding genomic regions; however, few have been characterized. In a comparative genetics approach to model such loci in a rat breast cancer model, we MAC13243 previously identified the mammary carcinoma susceptibility locus to a critical interval (277 Kb) within a gene desert. reduces mammary carcinoma multiplicity by 50%.