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Published byKaylee Bird
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A B Supplementary Fig 1. RNA-seq data Mapping with Tophat/BowtieGet 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
Supplementary Fig 2.
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
236118_at SNU-620 SNU-216 SNU-484 SNU-668 KATOIII MKN-1 AGS AK123079Supplementary Fig 4. 236118_at SNU-620 SNU-216 SNU-484 SNU-668 KATOIII MKN-1 AGS AK123079 BM742401 b-actin
ch7_138 chr7:138357000-138360000 R AK UP UP_AK098156_F + AK098156_RSupplementary 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
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
A B C Supplementary Fig 7. MKN-1 siControl siRNA #1 siRNA #2 AK098156b-actin B Relative intensity C # of colonies colony size
A B Cell viability BM742401 control BM742401 b-actin C Colony formingSupplementary Fig 8. A B Cell viability BM742401 control BM742401 intensity b-actin C Colony forming control BM742401
Supplementary Fig 9. AGS Migration assay Control BM742401
Supplementary Fig 10. Invasion assay MKN-1 Control BM742401
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
RNA-Seq Primer Understanding the RNA-Seq evidence tracks on the GEP UCSC Genome Browser Wilson Leung08/2014.
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