rna-seq data
Post on 04-Feb-2016
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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
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