RNA-seq from archival FFPE breast cancer samples: molecular pathway fidelity and novel discovery

Pennock, Nathan D.; Jindal, Sonali; Horton, Wesley; Sun, Duanchen; Narasimhan, Jayasri; Carbone, Lucia; Fei, Suzanne S.; Searles, Robert; Harrington, Christina A.; Burchard, Julja; Weinmann, Sheila; Schedin, Pepper; Xia, Zheng

doi:10.1186/s12920-019-0643-z

BMC Medical Genomics

Table 1 RNA-seq Sample Characteristics

From: RNA-seq from archival FFPE breast cancer samples: molecular pathway fidelity and novel discovery

Figure: Sample	Year of Diagnosis	ER Status - IHC	Sample Type	GEO- Accession #
Figure 2: S1	2009	Positive	FFPE	GSM3737461, GSM3737462, GSM3737463,GSM3737467, GSM3737468, GSM3737469
Figure 2: S2	2010	Positive	FFPE	GSM3737464, GSM3737465, GSM3737466, GSM3737470, GSM3737471, GSM3737472
Figure 3-6: S1	2002	Positive	FFPE	GSM3737473, GSM3737474
Figure 3-6: S2	2005	Positive	FFPE	GSM3737475, GSM3737476
Figure 3-6: S3	2010	Positive	FFPE	GSM3737477
Figure 3-6: S4	1997	Negative	FFPE	GSM3737478
Figure 3-6: S5	2011	Negative	FFPE	GSM3737479
Figure 3-6: S6	2009	Negative	FFPE	GSM3737480, GSM3737481
Figure 3-6: P1	2000	Positive	Fresh-Frozen	GSM1401676
Figure 3-6: P2	2001	Positive	Fresh-Frozen	GSM1401677
Figure 3-6: P3	2001	Positive	Fresh-Frozen	GSM1401678
Figure 3-6: P4	2001	Positive	Fresh-Frozen	GSM1401679
Figure 3-6: P5	2001	Positive	Fresh-Frozen	GSM1401680
Figure 3-6: P6	2001	Positive	Fresh-Frozen	GSM1401684
Figure 3-6: P7	2009	Positive	Fresh-Frozen	GSM1401713
Figure 3-6: P8	2010	Positive	Fresh-Frozen	GSM1401715
Figure 3-6: P9	2002	Positive	Fresh-Frozen	GSM1401716
Figure 3-6: P10	2006	Positive	Fresh-Frozen	GSM1401717
Figure 3-6: P11	2005	Negative	Fresh-Frozen	GSM1401719
Figure 3-6: P12	2006	Negative	Fresh-Frozen	GSM1401720
Figure 3-6: P13	2003	Negative	Fresh-Frozen	GSM1401721
Figure 3-6: P14	2002	Negative	Fresh-Frozen	GSM1401722
Figure 3-6: P15	2004	Negative	Fresh-Frozen	GSM1401724
Figure 3-6: P16	2001	Negative	Fresh-Frozen	GSM1401726
Figure 3-6: P17	2009	Negative	Fresh-Frozen	GSM1401727
Figure 3-6: P18	2010	Negative	Fresh-Frozen	GSM1401729
Figure 3-6: P19	2001	Negative	Fresh-Frozen	GSM1401733
Figure 3-6: P20	2004	Negative	Fresh-Frozen	GSM1401757

Each sample designation is identified with relevant figures. Year of diagnosis indicates the year the specimen was collected. ER status in all cases was performed by clinical diagnostic IHC. Sample type for retrieval of RNA is indicated as either Formalin Fixed Paraffin Embedded (FFPE) or fresh tissue processed and stored frozen (Fresh-frozen). GEO Accession number for ascribed samples is indicated

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ISSN: 1755-8794

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