Tripathi et al., Fig-S2A abc - PLOS

TUBB

TTK

TOP2B

TMEM30A

SUV39H1

STMN1

SSBP4

SRPK2

SPC25

SPC24

SMC4

SMC2

H2AFY2

HDAC2

HAUS8

GTSE1

GINS4

GINS3

FOXM1

FEN1

FBXO5

PPARG

PCNA

PARP1

NUP205

NUP153

NUP133

NUP107

MCM7

LMNB2

HNRNPH1

HNRNPD

HNRNPM

HNRNPK

c

SMARCC2

SKP2

SKIV2L2

SKA1

RFC5

RFC4

RPA1

RAD51

RAD21

0 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 BARD1

FANCG

FAM64A

DUT

CLK1

CKS2

CKAP2

CEP55

CENPN

CENPM

CENPK

CENPF

CENPA

CDKN3

CDC25C

CDC25B

CDCA3

CDCA2

CCNB2

CCL2

CASP6

BUB3

BCL2L12

b

PSIP1

FANCI

0

scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2

Relative Fold RNA levels scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2

0

PRP31

Relative Fold RNA levels

Relative Fold RNA levels

a 1.2

1.0

0.8

0.6

0.4

0.2

1.2

1.0

0.8

0.6

0.4

0.2

1.2

1.0

0.8

0.6

0.4

0.2

Tripathi et al., Fig-S2A

0

PCNA-II PCNA-III

**

GMNN

MALAT1-si1

control-si

MALAT1-si1

control-si

MALAT1-si1

control-si

**

AS2

E2F2

AS1

scr

CDT1

AS2

MALAT1-si1

control-si

0.4

AS1

CDK1

scr

CCNA2 MALAT1-si1

***

AS2

control-si

MALAT1-si1

Relative Fold RNA levels

0.2

AS1

e control-si

0

scr

Relative Fold RNA levels

d 1.2

1.0

0.8

0.6

** **

***

ORC1

1.2

1.0

0.8

0.6

0.4

0.2

PCNA-IV

Tripathi et al., Fig-S2A

0

vector

MYBL2

hMALAT1

vector

CCNA2

hMALAT1

vector

CENPE

AS1

**

scr

**

scr

1.4

AS1

1.6

AS1

0.4

scr

TRIB3

TP53INP1

SNHG11

SETDB2

SAT1

PTBP2

PRP4

PPP3CC

MDM2

PDRG1

NEK6

MAPK13

LRDD

IL-11

IL-8

IL-6

GADD45B

GADD45A

FOSB

FBXO31

DDIT3

CDKN1A

CCNB1IP1

p53 signaling

VDR/RXR Activation

iNOS Signaling

Xenobiotic Metabolism Signaling

AMPK Signaling

p13K Signaling in B Lymphocytes

Atherosclerosis Signaling

B Cell Receptor Signaling

p38 MAPK Signaling

LPS/IL-1 Mediated Inhibition of RXR Function

IL-10 Signaling

PI3K/AKT Signaling

ATM Signaling

NRF2-mediated Oxidative Stress Response

12

AS1

scr

BCL2L1

IL-17A Signaling in Fibroblasts

4.0 3.5 3.0 2.5 2.0 1.5 1.0 0.5 0.0

AS1

0.6

BANP

-log [p-value]

Cellular Function & Maintenance

Cell Morphology

Cellular Assembly & Organization

Drug Metabolism

Molecular Transport

Cell Cycle

Amino Acid Metabolism

Cellular Development

Cellular Growth & Proliferation

Cell-To-Cell Signaling and Interaction

Cellular Compromise

DNA Replication, Recombination & Repair

Small Molecule Biochemistry

Lipid Metabolism

Cell Death

-log [p-value] 1 0

scr

0 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2 scr AS1 AS2

c

AS1

d

ADARB1

Relative Fold RNA Levels

b

scr

Relative Fold RNA Levels

a 6

5

4

3

2

10

8

6

4

2

*

1.2

1.0

0.8

0.2

**

hMALAT1

Tripathi et al., Fig-S2B