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27 lncRNAs(predictive of subtype)
10 lncRNAs(TS & Onc.)
8 lncRNAs
4 lncRNAs(BALR-1, BALR-2,
BALR-6, LINC00958)
114 lncRNAs
2 lncRNAs(BALR-2, BALR-6)
Microarray
Nearest shrunken centroid analysis
81 lncRNAs
Expression in leukemia > or < than pro-B cells
17 lncRNAs
GenBank ESTs and mRNAs
Available transcript models
2 lncRNAs
Expression >in leukemic samples
4 lncRNAs(TS)
FC > 2 adj. p < 0.01
Clinicopathologicalparameters
2 lncRNAs
BALR-2
Prednisone responseSubcellular localization
Futurestudies
Supplemental Figure 1
c
e f
a
d
bM
iscl
ass
ifica
tion
Err
or
Value of Threshold
0.8
0.2
0.4
0.6
0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
Number of genes
miss
class
ifica
tion
erro
r
Value of Threshold
1112
4Number of Genes
2 4 6 8 10 12
6886
1
Supplemental Figure 2
Value of Threshold
Mis
cla
ssifi
catio
n E
rro
rNumber of Genes
2596
322
099
1377
368
8635
6219
3811
1266
237
824
116
511
376 54 41 31 25 20 17 11 9 6 4 4 3 2 2 1 1 0
0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
Number of genes
Miss
clas
sifica
tion
erro
r
Value of threshold
ALL1
ALL2
ALL3
Number of genes
2 4 6 8 10 12
0.8
0.2
0.4
0.668
8611
12
4 1
TEL-AML1E2A-PBXMLL
Number of lincRNAs
Mis
cla
ssifi
catio
n E
rro
r
7419
7002
5832
4345
2887
1791
1022
618
389
249
168
123
87 62 50 34 27 18 15 14 12 11 8 7 6 6 4 4 3 0
0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0
0.24
6
0.49
2
0.73
9
0.98
5
1.23
1
1.47
7
1.72
3
1.97
2.21
6
2.46
2
2.70
8
2.95
4
3.2
3.44
7
3.69
3
3.93
9
4.18
5
4.43
1
4.67
8
4.92
4
5.17
5.41
6
5.66
2
5.90
9
6.15
5
6.40
1
6.64
7
6.89
3
0.8
0.2
0.4
0.6
2 4 6Value of Threshold
27618
44345
TEL-AML1E2A-PBXMLL
Value of Threshold
7419 7002 5832 4345 2887 1791 1022 618 389 249 168 123 87 62 50 34 27 18 15 14 12 11 8 7 6 6 4 4 3 0
0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
Mis
cla
ssifi
catio
n E
rro
r
2 4 6
27 4
Number of lincRNAs
0.8
0.2
0.4
0.6
618
4345
ALL Cases
0.2
0.6
1
00 5 10 15 20 25
TEL-AML1E2A-PBXMLL
ALL Cases
0
0.2
0.6
1
0 5 10 15 20 25
Pro
ba
bili
ty o
f co
rre
ct
cla
ssifi
catio
n
Pro
ba
bili
ty o
f co
rre
ct c
lass
ifica
tion TEL-AML1
E2A-PBXMLL
0
5000
10000
15000
20000
25000
30000
0 2 4 6 8 10 12 14
Threshold
Nu
mb
er
of
ge
ne
s
01000
2000
3000
4000
5000
6000
7000
8000
0 1 2 3 4 5 6 7 8
Threshold
Nu
mb
er
of
lincR
NA
g h
a b
c d
e f
g
Supplemental Figure 3
Time (days)
Cu
mu
lati
ve
Su
rviv
al
0 100 300 500
1.0
0.6
0.2
0
0.8
0.4
High BALR-6
Low BALR-6
Time (days)
Cu
mu
lati
ve
Su
rviv
al
0 100 300 500
1.0
0.6
0.2
0
0.8
0.4
High BALR-1
Low BALR-1
Time (days)
Cu
mu
lati
ve
Su
rviv
al
0 100 300 500
1.0
0.6
0.2
0
0.8
0.4
High LINC00958
Low LINC00958
BALR-2
Fre
qu
en
cy
40
10
0
30
20
0 0.2 0.4 0.6 0.8
LINC00958F
req
ue
nc
y
30
10
0
20
0 1.0 10.0 100.0
BALR-1F
req
ue
nc
y50
10
0
40
30
0 1.0 10.0
20
BALR-6
Fre
qu
en
cy
15
10
0
0 1.0 10.0 100.0 1000.0
5
RASSF10
LINC0095811q15.2
mRNA: NR_038904
Probe set on microarray
qPCR primers
TEAD1
RACE product
LOC100506305
BALR-63p24.3
mRNA: NM_001257177
Probe set on microarray
qPCR primers
LOC339862 SATB1TBC1D5
RACE product
14q32.2
C14orf132
mRNA: NM_001252507
Probe seton microarray
qPCR primers
LINC00617 BDKRB2
BALR-1a b
c
Supplemental Figure 4
BALR-2
5’ RACE product 1
3’ RACE product
5’ RACE primerUn-annotated exon
AAAAA
5’ RACE product 2
5’ RACE product 3
80kb
Balr-2
3’ RACE product 1
3’ RACE primer
3’ RACE product 2
d
e
5’ RACE 3’ RACE1000 bp
500 bp
1000 bp
500 bp
3’ RACE NC
VECTOR
siRNA 2
0.0
0.5
1.0
1.5
BA
LR
-2(f
old
Ch
ang
e) **
VECTOR
siRNA 2
0
5
10
15
FO
S(f
old
ch
ang
e) **
VECTOR
siRNA 2
0
2
4
6
8JU
N(f
old
ch
ang
e)**
Supplemental Figure 5
VECTOR
siRNA2
0.0
0.5
1.0
1.5
2.0
2.5
SG
K1
(fol
d c
han
ge)
*
VECTOR
siRNA2
0
1
2
3
4
5
SE
RP
INE
1(f
old
ch
ang
e) **
f g
h
FO
S(f
old
ch
ang
e)
UNT
PRED
DEXADOX
UNT
PRED
DEXADOX
0
5
10
15RS4;11NALM-6*** **
p=0.06**
**
*
JUN
(fol
d c
han
ge)
UNT
PRED
DEXADOX
UNT
PRED
DEXADOX
0
5
10
15
20RS4;11NALM-6
******
******
**
****
BIM
(fol
d c
han
ge)
UNT
PRED
DEXADOX
UNT
PRED
DEXADOX
0
2
4
6
8RS4;11NALM-6**
***
***
**
*
a b c
d e
VECTOR
sispli
ce1
0.0
0.5
1.0
1.5
BA
LR
-2(f
old
ch
ang
e) ***
VECTOR
sispli
ce1
0.00
0.05
0.10
0.15
0.20
casp
ase-
3 a
ctiv
ity (
A4
05)
*
VECTOR
siRNA3
0.0
0.5
1.0
1.5
BA
LR
-2(f
old
ch
ang
e) **
VECTOR
siRNA3
0.00
0.01
0.02
0.03
0.04
0.05
Cas
pas
e-3
act
ivity
(A
40
5)
*
fold
ch
ang
e
VECTOR
siRNA3
VECTOR
siRNA3
0.0
0.5
1.0
1.5
2.0
2.5FOSJUN
p = 0.09
*
VECTOR
siRNA3
0.0
0.5
1.0
1.5
BA
LR
-2(f
old
ch
ang
e) **
fold
ch
ang
e
VECTOR
sispli
ce1
VECTOR
sispli
ce1
VECTOR
sispli
ce1
0
5
10
15FOSJUN
p = 0.07
***BIM
***
fold
ch
ang
e
VECTOR
siRNA3
VECTOR
siRNA3
0.0
0.5
1.0
1.5
2.0FOSJUN
**
**
BA
LR-2
(fold
cha
nge)
0.0
0.5
1.0
1.5F
old
Ch
ang
e
VECTOR
siRNA1
siRNA2
siRNA3
VECTOR
siRNA1
siRNA2
siRNA3
VECTOR
siRNA1
siRNA2
siRNA3
0
1
2
3
4
5FOSJUNBIM
p=0.06
p=0.07
***
** *
Time (hours)
cell
pro
lifer
atio
n(f
old
ch
ang
e)
0 24 48 72 960
2
4
6
8
10
12
14
VECTORsiRNA1siRNA2siRNA3
Supplemental Figure 6
% o
f apo
ptot
ic c
ells
0
5
10
15
20 125 g/mL250 g/mL
*
**
**
VECTOR
siRNA3
0
5
10
15
20
25
% a
pop
totic
cel
ls *
a b c
d
e f g
h i j
k l m
Supplemental Figure 7
PRED
GR
BIM
BALR-2
JUN JUN
FOS
Cytokines/survival genes
?
Caspase-3 APOPTOSIS
FOS