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RNA-seq data Mapping with Tophat/Bowtie Assembling by Cufflinks without -G option Detect differentially expressed bins Putative differentially expressed.

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Presentation on theme: "RNA-seq data Mapping with Tophat/Bowtie Assembling by Cufflinks without -G option Detect differentially expressed bins Putative differentially expressed."— Presentation transcript:

1 RNA-seq data Mapping with Tophat/Bowtie Assembling by Cufflinks without -G option Detect differentially expressed bins Putative differentially expressed lincRNA UCSC database (affyU133Plus2, knownGene) Count reads on 200bp bins Select putative transcripts sharing genomic position Get intergenic transcripts (Exclusive) RNA-seq data Mapping with Tophat/Bowtie Get lincRNA probe list (Exclusive) Detect differentially expressed lincRNA Query lincRNA expression value UCSC database (affyU133Plus2, knownGene) Affymetrix microarray data (GENT database) Run Cufflinks with -G option (affyU133Plus.gtf from UCSC) Detect differentially expressed lincRNA Intersection by probe ID Putative differentially expressed lincRNA BA Supplementary Fig 1.

2 Supplementary Fig 2.

3 236118_at chr7:138357000-138360000chr18:18000500-18003000 ch7_138 Supplementary Fig 3. NT_1 NT_2 Tumor_1 Tumor_2 Tumor_3 SNU484 SNU601 SNU668 NT_1 NT_2 Tumor_1 Tumor_2 Tumor_3 SNU484 SNU601 SNU668

4 Supplementary Fig 4. 236118_at -actin BM742401 SNU-620SNU-216SNU-484AGSKATOIIIMKN-1SNU-668 AK123079

5 AK098156_F + AK098156_RUP_AK098156_F + AK098156_RUP2_AK098156_F + AK098156_R ZC3HAViL_F + AK098156_R chr7:138357000-138360000 ch7_138 RAK UP UP2 ZC Supplementary Fig 5.

6 p = 0.326 rfs GSE6532 Breast rfs p = 0.045 GSE9195 mfs p = 0.009 GSE20711 ovs p = 0.257 Supplementary Fig 6. GSE2658 Multiple Myeloma p = 0.428 mfs GSE19234 Melanoma p = 0.383 ovs GSE31210 Lung adenocarcinoma p = 0. 196 ovs

7 -actin AK098156 siControl siRNA #1siRNA #2 MKN-1 A B C Relative intensity # of colonies colony size Supplementary Fig 7.

8 -actin BM742401 controlBM742401 control BM742401 Supplementary Fig 8. Cell viability Colony forming intensity C AB

9 Supplementary Fig 9. Migration assay Control BM742401 AGS

10 Invasion assay Control BM742401 Supplementary Fig 10. MKN-1

11 -actin 236118_at MMP9 controlBM742401 controlBM742401 C t p= 0.864 -actin MMP9 controlBM742401 p = 0.631 conc. (pg/ml) Supplementary Fig 11. RT-PCR qRT-PCR Immunoblot assay ELISA


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