Table 2 HCC cell models and healthy liver samples were taken for this study from various studies

DRR018792

HiSeq 2500

Huh7.5.1

HCC

1

ERR2619174, ERR2619175, ERR2619176, ERR2619177

HiSeq 2500

Hep3B

HCC

4

ERR2619178, ERR2619179, ERR2619180, ERR2619181

HepG2

HCC

4

ERR2619182, ERR2619183, ERR2619184, ERR2619185

HuH-7

HCC

4

ERR2619186, ERR2619187, ERR2619188, ERR2619189, ERR2619190, ERR2619191

HiSeq 2500

PHH

Healthy liver

6

SRR5104155

HiSeq 2500

LM3

HCC

1

SRR5576264, SRR5576288

HiSeq 2500

HepaRG

HCC

2

SRR8615310

HiSeq 2500

SNU-398

HCC

1

SRR8615311

SNU-387

HCC

1

SRR8615387

Li-7

HCC

1

SRR8615471

SNU-878

HCC

1

SRR8615472

SNU-886

HCC

1

SRR8615483

JHH-1

HCC

1

SRR8615650

SNU-475

HCC

1

SRR8615654

SNU-423

HCC

1

SRR8615655

SNU-449

HCC

1

SRR8615661

HuH-7

HCC

1

SRR8615664

HuH-1

HCC

1

SRR8615682

SK-HEP-1

HCC

1

SRR8615914

JHH-7

HCC

1

SRR8615918

JHH-2

HCC

1

SRR8615919

JHH-4

HCC

1

SRR8615920

JHH-5

HCC

1

SRR8615921

JHH-6

HCC

1

SRR8615932

SNU-182

HCC

1

SRR8615968

PLC/PRF/5

HCC

1

SRR8616023

SNU-761

HCC

1

SRR8616130

Hep 3B2.1–7

HCC

1

SRR8616135

HLF

HCC

1

SRR873426

HiSeq 2000

HKCI-1

HCC

1

SRR873427

HKCI-4

HCC

1

SRR873428

HKCI-7

HCC

1

SRR873429

HKCI-9

HCC

1

SRR873430

HKCI-11

HCC

1

SRR873836

HKCI-5B

HCC

1

EU-ToxRisk

PRJEB35350

ERR3668587, ERR3668588, ERR3668589, ERR3668591, ERR3668592, ERR3668593, ERR3668594, ERR3668595, ERR3668596, ERR3668597, ERR3668598, ERR3668600, ERR3668601, ERR3668602, ERR3668603, ERR3668604, ERR3668605, ERR3668606, ERR3668607, ERR3668609, ERR3668610, ERR3668611, ERR3668612, ERR3668613

NovaSeq 6000

Healthy in vivo liver

Healthy liver

24^a

PRJEB24482

ERR2259771, ERR2259772, ERR2259773, ERR2259774, ERR2259775, ERR2259776, ERR2259777, ERR2259778, ERR2259779

HiSeq 2500

Liver microtissues 3D

Healthy liver

9

PRJEB23590

ERR2203448, ERR2203449, ERR2203450, ERR2203451, ERR2203452, ERR2203453, ERR2203455, ERR2203456, ERR2203457, ERR2203458, ERR2203459

HiSeq 2500

Primary human hepatocytes (PHH)

Healthy liver

11^b

PRJEB24484

ERR2259780, ERR2259781, ERR2259782, ERR2259783

HiSeq 2500

Human precision-cut liver slices from HCC patients (hPCLiS)

HCC

4

PRJEB24487

ERR2260002, ERR2260003, ERR2260004, ERR2260005

HiSeq 2500

HepaRG 3D

HCC

4

PRJEB24466

ERR2259111, ERR2259112, ERR2259113

HiSeq 2500

HepG2

HCC

7

PRJEB24464

ERR2259092, ERR2259093, ERR2259094, ERR2259095