RNA-seq data

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

Supplementary Fig 2.

Supplementary Fig 3. 236118_at ch7_138 chr18:18000500-18003000 chr7:138357000-138360000 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

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

Supplementary Fig 5. ch7_138 chr7:138357000-138360000 R AK UP UP_AK098156_F + AK098156_R ZC3HAViL_F + AK098156_R UP2_AK098156_F + AK098156_R AK098156_F + AK098156_R UP2 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 GSE2658 GSE19234 GSE31210 ovs ovs mfs p = 0.428 p = 0.383 p = 0.196

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

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

RNA-seq data

RNA-seq data

Presentation Transcript

How to store and visualize RNA-seq data

RNA-Seq

Expression A nalysis of RNA - seq Data

RNA- seq Analysis

RNA- Seq Lab

RNA seq (I)

Identifying differentially expressed genes from RNA- seq data

Biases in RNA- Seq data

Le RNA-seq

Biases in RNA- Seq data October 30, 2013 NBIC Advanced RNA- Seq course

“BIG DATA” from RNA- Seq Experiments

Bioinformatics for DNA - seq and RNA- seq experiments

RNA-Seq and transcriptome analysis

RNA-Seq datasets

Supplemental Data Figure 1. RNA-seq data analysis pipeline.

Bioinformatics Pipelines for RNA- Seq Data Analysis

Applications of RNA-Seq

RNA-SEQ