Table 1

Summary of RNA-Seq samples

Sample name

Sample description

BRCA1 mutation

Sequencing strategy


HCC1937

Cell line

5266dupC

SE

SUM149PT

Cell line

2769delT

PE

SUM1315O2

Cell line

30_31delAG

PE

HCC3153

Cell line

815_824dup

PE

T92

Primary tumor

5266dupC

PE

T50

Primary tumor

4327C>T

PE

T160

Primary tumor

5521A>C*

PE

HCC2337

Lymphocyte cell line

5266dupC

PE

MCF10A

Non-tumorigenic breast epithelial cell line

-

PE

SEC1

Primary tumor

-

PE

SEC2

Primary tumor

-

PE


* See Lee et al. [58] for more details

Ten breast cancer samples (eight with known germline BRCA1 mutations and two secretory breast cancers) and one non-tumorigenic breast epithelial control was sequenced using the Illumina Genome Analyzer IIx. Only HCC1937 was sequenced using a single-end (SE) strategy, while the rest was sequenced using paired-end (PE). The cell line HCC2337 is a lymphocytic cell line derived from the same patient as HCC1937. Known BRCA1 mutations are based on RefSeq accession NM_008294.3.

Ha et al. BMC Medical Genomics 2011 4:75   doi:10.1186/1755-8794-4-75

Open Data