Nature Communications

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ncomms7351-s1.pdf (14275 kB)
Supplementary Figures 1-22

ncomms7351-s2.xlsx (32 kB)
Summary of molecular libraries and accessions

ncomms7351-s3.xlsx (48 kB)
Cell-type specific genes. Genes that are UP (DOWN) regulated in luminal epithelilal vs myo epithelilal commonly in three comparisons for RM080, RM035 and RM084. Gene lists are based on an FDR = 0.015 threshold with a minimal RPKM > 0.005 and minimal read count per gene > 25.

ncomms7351-s4.xlsx (1306 kB)
List of cell type-specific isoforms identified by RNA-seq analysis. Tab 1 is the summary of No. of isoforms identified and validated with junctions. Tab 2 is the summary of No. of isoforms between luminal and myoepithelial across three individuals. Tabs 3-8 list gene isoforms identified between pairwise comparisons between different cell types.

ncomms7351-s5.xlsx (143 kB)
Myoepithelial and luminal epithelial gene intronic retention events.

ncomms7351-s6.xlsx (113 kB)
RPM (reads per million) for breast cells miRNAs.

ncomms7351-s7.xlsx (697 kB)
lincRNAs expressed in breast cell populations. RPKM values are reported for lincRNA using Ensembl v73 annotations. Values for the fibroblast RM070 and RM071 were averaged.

ncomms7351-s8.xlsx (9 kB)
List of lincRNAs for every cluster in Figure 2e.

ncomms7351-s9.xlsx (3182 kB)
Unmethylated regions (UMRs) in myoepithelial and luminal cell types called from whole genome bisulfite datasets.

ncomms7351-s10.xlsx (12 kB)
List of GWAS SNPs associated breast cancer risk loci that overlap with luminal and myoepithelial UMRs.

ncomms7351-s11.xlsx (39 kB)
Transcription factors for which ENCODE ChIP-seq binding locations overlap significantly with UMR regions.

ncomms7351-s12.xlsx (19 kB)
Summary quality controls metrics for RNA-seq libraries included in this study.

ncomms7351-s13.xlsx (2788 kB)
Ensembl v65 protein coding RPKM expression matrix

ncomms7351-s14.xlsx (3253 kB)
Ensembl v65 non-coding RPKM expression matrix

ncomms7351-s16.xlsx (33 kB)
Annotation priorities used to resolve multiple database matches for a single alignment location and multiple alignment locations for a read. (11203 kB)