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Transcriptional profiling of long non-coding RNAs and novel transcribed regions across a diverse panel of archived human cancers

Alayne L Brunner1, Andrew H Beck12, Badreddin Edris13, Robert T Sweeney1, Shirley X Zhu1, Rui Li1, Kelli Montgomery1, Sushama Varma1, Thea Gilks1, Xiangqian Guo1, Joseph W Foley3, Daniela M Witten4, Craig P Giacomini15, Ryan A Flynn6, Jonathan R Pollack1, Robert Tibshirani78, Howard Y Chang6, Matt van de Rijn1 and Robert B West1*

Author Affiliations

1 Department of Pathology, Stanford University School of Medicine, 269 Campus Drive, Stanford, CA 94305-5324, USA

2 Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, 330 Brookline Avenue, Boston, MA 02215, USA

3 Department of Genetics, Stanford University School of Medicine, 269 Campus Drive, Stanford, CA 94305-5120, USA

4 Department of Biostatistics, University of Washington, 1705 NE Pacific Street, Seattle, WA 98195-7232, USA

5 Program in Cancer Biology, Stanford University School of Medicine, 269 Campus Drive, Stanford, CA 94305-5456, USA

6 Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, 269 Campus Drive, Stanford, CA 94305, USA

7 Department of Statistics, Stanford University, 390 Serra Mall, Stanford, CA 94305-4065, USA

8 Department of Health Research and Policy, Stanford University School of Medicine, 269 Campus Drive, Stanford, CA 94305-5405, USA

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Genome Biology 2012, 13:R75  doi:10.1186/gb-2012-13-8-r75

Published: 28 August 2012

Additional files

Additional file 1:

Supplemental tables 1-7. Table S1 shows the sequencing statistics for the 3SEQ libraries. Table S2 shows the numbers of 3SEQ peaks overlapping lncRNAs and other annotation classes. Table S3 lists the 1,065 known lncRNAs. Table S4 lists the 1,071 novel intergenic peaks. Table S5 shows the number of peaks differentially expressed in each diagnostic class. Table S6 includes primer sequences used in qRT-PCR experiments. Table S7 includes primer sequences used for the northern blot probes.

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Additional file 2:

Supplemental figures 1-5. Figure S1 plots sequencing depth versus RefSeq transcripts detected by 3SEQ. Figure S2 shows differential expression for the 23 peaks examined by qRT-PCR. Figure S3 plots the mean expression in cancer versus the mean expression in normal samples. Figure S4 shows expression of peak 13741 by 3SEQ, qRT-PCR and northern blot. Figure S5 is a browser shot showing the predicted breast transcripts near peak 13741.

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