Validation 5 FFPE samples analogue to FF samples, Description: A) Analogue samples FFPE-Cryo: The selected progression-associated genes are significantly differential expressed between DCIS and IBC of the same tumour (P < 0.05; n.s. = not significant). B) Remaining FFPE samples: Except for COL10A1, all genes are significantly differential expressed and confirm the results of the technical validation set (P < 0.05; n.s. = not significant). PCR values are normalized to GAPDH, ACTB and YWHAZ (PDF 45 kb
Table S2. Samples sequenced. Sample type, processing and sequencing. (XLSX 51Â kb
Background: The transition from ductal carcinoma in situ (DCIS) to invasive breast carcinoma (IBC) i...
Figure S1. Gating strategy for CDCP1 flow cytometric analysis. Flow cytometric analysis of MDA-MB-23...
WG-DASL analysis resulted in 1784 transcripts that were differentially expressed between DCIS and IB...
Overlapping genes, Description: Comparison of WG-DASL results with the data from the FF investigatio...
Table S3. Differential gene expression. Differentially expressed genes between 21 paired FF- and FFP...
Figure S2. Comparison of read alignment for FF- and FFPE-derived RNA samples sequenced on MiSeq and ...
Differentially expressed genes in DCIS.COM and SUM225 mouse intraductal xenograft model (MIND) xenog...
Top 1 % of differentially expressed genes between tumours and cell lines after filtering out genes c...
Comparison of the frequency of select mutational events in breast cancer tumours versus cell lines. ...
Figure S3. Specimen age correlation. Tumor specimen age decreases transcript correlation of sequence...
Gene expression of invasive and mesenchymal markers in cell isolates. Mammary epithelial cell (MEC),...
Supplementary methods. Detailed description of tissue preparation including microtomy, de-waxing and...
Figure S1. Gene expression in breast cancer. a Volcano plot of gene expression changes in the transc...
MTS, migration and invasion assays in ductal carcinoma in situ (DCIS) BCL9-KD cells with shRNA 2. A ...
Table S2. Samples sequenced. Sample type, processing and sequencing. (XLSX 51Â kb
Background: The transition from ductal carcinoma in situ (DCIS) to invasive breast carcinoma (IBC) i...
Figure S1. Gating strategy for CDCP1 flow cytometric analysis. Flow cytometric analysis of MDA-MB-23...
WG-DASL analysis resulted in 1784 transcripts that were differentially expressed between DCIS and IB...
Overlapping genes, Description: Comparison of WG-DASL results with the data from the FF investigatio...
Table S3. Differential gene expression. Differentially expressed genes between 21 paired FF- and FFP...
Figure S2. Comparison of read alignment for FF- and FFPE-derived RNA samples sequenced on MiSeq and ...
Differentially expressed genes in DCIS.COM and SUM225 mouse intraductal xenograft model (MIND) xenog...
Top 1 % of differentially expressed genes between tumours and cell lines after filtering out genes c...
Comparison of the frequency of select mutational events in breast cancer tumours versus cell lines. ...
Figure S3. Specimen age correlation. Tumor specimen age decreases transcript correlation of sequence...
Gene expression of invasive and mesenchymal markers in cell isolates. Mammary epithelial cell (MEC),...
Supplementary methods. Detailed description of tissue preparation including microtomy, de-waxing and...
Figure S1. Gene expression in breast cancer. a Volcano plot of gene expression changes in the transc...
MTS, migration and invasion assays in ductal carcinoma in situ (DCIS) BCL9-KD cells with shRNA 2. A ...
Table S2. Samples sequenced. Sample type, processing and sequencing. (XLSX 51Â kb
Background: The transition from ductal carcinoma in situ (DCIS) to invasive breast carcinoma (IBC) i...
Figure S1. Gating strategy for CDCP1 flow cytometric analysis. Flow cytometric analysis of MDA-MB-23...