Decoding the fine-scale structure of a breast cancer genome and transcriptome

The results of whole-genome ESP performed on MCF-7 may be accessed here. Full mapping results for whole-genome ESP on MCF-7 can be accessed here (WARNING! 8.6 MB text file). The results of targeted ESP can be accessed here, and mapping data for targeted ESP can be accessed here.

All MCF-7 BAC clones are available from Amplicon Express. The library name is HTA. The plate/row/column name are the same (e.g. MCF7_1-100G11 clone is the clone located in HTA library, plate 100, column G, row 11).

Supplemental Table 1: The results of PCR confirmation of genome breakpoints.

tESP results can be accessed here, cDNA mapping data can be found here (WARNING! 2 MB text file). All MCF7 cDNA clones are available from collins{at}cc.ucsf.edu

Supplemental Table 2. The structure of putative fusion transcripts in MCF-7 cDNA library. The validated transcripts are shown in bold.

The primers used for the validation are shown in red. The breakpoint location is shown as a small purple box.

Confirmed with conventional RT-PCR:
MCF7_RNA_L_18_D17  and full sequence


Confirmed using nested PCR:
MCF7_RNA_L_13_D07  and full sequence
MCF7_RNA_L_18_F09 and full sequence 
MCF7_RNA_L_23_L23 and full sequence
In these cases in order to better portray the structure of the fusion transcript, the sequence, corresponding to the original gene sequence was split into 50 bp fragments. The breakpoint is localized at the point of the break of continuity of numbering/orientation of these 50 bp fragments.


Detailed description of BFB model of evolution of MCF7 genome.