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A B Supplementary Fig 1. RNA-seq data Mapping with Tophat/Bowtie

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1 A B Supplementary Fig 1. 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) Intersection by probe ID Putative differentially expressed lincRNA RNA-seq data Mapping with Tophat/Bowtie Assembling by Cufflinks without -G option UCSC database (affyU133Plus2, knownGene) Count reads on 200bp bins Get intergenic transcripts (Exclusive) Detect differentially expressed bins Select putative transcripts sharing genomic position Putative differentially expressed lincRNA

2 Supplementary Fig 2.

3 Supplementary Fig 3. 236118_at ch7_138 chr18: chr7: NT_1 NT_1 NT_2 NT_2 Tumor_1 Tumor_1 Tumor_2 Tumor_2 Tumor_3 Tumor_3 SNU484 SNU484 SNU601 SNU601 SNU668 SNU668

4 236118_at SNU-620 SNU-216 SNU-484 SNU-668 KATOIII MKN-1 AGS AK123079
Supplementary Fig 4. 236118_at SNU-620 SNU-216 SNU-484 SNU-668 KATOIII MKN-1 AGS AK123079 BM742401 b-actin

5 ch7_138 chr7:138357000-138360000 R AK UP UP_AK098156_F + AK098156_R
Supplementary Fig 5. ch7_138 chr7: R AK UP UP_AK098156_F + AK098156_R UP2_AK098156_F + AK098156_R ZC3HAViL_F + AK098156_R UP2 AK098156_F + AK098156_R ZC

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

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

8 A B Cell viability BM742401 control BM742401 b-actin C Colony forming
Supplementary Fig 8. A B Cell viability BM742401 control BM742401 intensity b-actin C Colony forming control BM742401

9 Supplementary Fig 9. AGS Migration assay Control BM742401

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

11 Supplementary Fig 11. RT-PCR Immunoblot assay BM742401 control BM742401 control MMP9 236118_at MMP9 b-actin b-actin qRT-PCR ELISA p= 0.864 p = 0.631 DCt conc. (pg/ml) control BM742401


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