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.

Supplementary Fig 2.

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

Supplementary Fig 4.

236118_at

-actin

BM742401

SN

U-6

20

SN

U-2

16

SN

U-4

84

AG

S

KA

TO

III

MK

N-1

SN

U-6

68

AK123079

AK

09

8156

_F +

A

K0981

56_R

UP_A

K0

9815

6_F

+

AK

0981

56_R

UP2_A

K0

9815

6_F

+

AK

0981

56_R

ZC

3H

AV

iL_F

+ A

K09

815

6_R

chr7:138357000-138360000ch7_138

R AK

UP

UP2

ZC

Supplementary Fig 5.

p = 0.326

rfsGSE6532

Breast

rfs

p = 0.045

GSE9195mfs

p = 0.009

GSE20711ovs

p = 0.257

Supplementary Fig 6.

GSE2658Multiple Myeloma

p = 0.428

mfsGSE19234Melanoma

p = 0.383

ovsGSE31210

Lung adenocarcinoma

p = 0. 196

ovs

-actin

AK098156

siC

ontr

ol

siR

NA

#1

siR

NA

#2MKN-1

A

B

C

Rela

tive inte

nsi

ty#

of

colo

nie

sco

lony s

ize

Supplementary Fig 7.

-actin

BM742401

contr

ol

BM

74240

1

contr

ol

BM

74240

1

Supplementary Fig 8.

Cell viability

Colony forming

inte

nsi

ty

C

A B

Supplementary Fig 9.

Migration assayControl

BM742401

AGS

Invasion assay

Control

BM742401

Supplementary Fig 10.

MKN-1

-actin

236118_at

MMP9

contr

ol

BM

74

24

01

control BM742401

Ct

a b

-30

-28

-26

-24

-22

p= 0.864

-actinMMP9

contr

ol

BM

74

24

01

p = 0.631

conc.

(pg/m

l)

Supplementary Fig 11.

RT-PCR

qRT-PCR

Immunoblot assay

ELISA