Table 1

Primary screen

Pool

Insert

Gene name

Gene symbol

Freq

Cons per Gene

Library location


3

v2HS_63142

keratin associated protein 5-9

KRTAP5-9

3/9

1

match

v2HS_119967

LOC155004

LOC155004

4/9

2

pool 52

v2HS_56766

acyl-CoA synthetase medium-chain family member 3

ACSM3

1/9

2

match

v2HS_59294

glycoprotein hormone alpha 2

GPHA2

1/9

1

match


v2HS_53974

PRO0255 protein

PRO0255

5/8

1

match

v2HS_63482

paired box gene 1

PAX1

2/8

1

match


4

v2HS_119967

LOC155004

LOC155004

2/10

2

pool 52

v2HS_66751

LOC344082

LOC344082

4/10

1

match

v2HS_70011

serum amyloid A-like 1

SAAL1

2/10

2

match

v2HS_98079

human solute carrier family 22

SLC22A3

1/10

2

pool 79


5

v2HS_108647

LOC349868

LOC349868

3/8

1

pool 79

v2HS_70473

polymerase (DNA directed), mu

POLM

2/8

v2HS_71958

human olfactory receptor, family 5, subfamily P, member 3

OR5P3

3/8

1

match


v2HS_119967

LOC155004

LOC155004

7/12

2

pool 52

v2HS_66652

protein phosphatase 3, catalytic subunit, β isoform

PPP3CB

1/12

1

match

v2HS_70473

polymerase (DNA directed), mu

POLM

4/12


7

v2HS_112910

human cyclin-dependent kinase 8

CDK8

1/10

3

match

v2HS_98079

solute carrier family 22, member3

SLC22A3

1/10

2

pool 79

v2HS_97017

sterile alpha motif containing 4a

SAMD4A

1/10


v2HS_69776

cytochrome P450, family 4, subfamily Z, polypeptide

CYP4Z2P

1/10

2

match

2 pseudogene


9

v2HS_108647

LOC349868

LOC349868

1/8

1

pool 79

v2HS_119967

LOC155004

LOC155004

1/8

2

pool 52

v2HS_62506

family with sequence similarity 181, member B

FAM181B

1/8

1

match


v2HS_55950

prostate stem cell antigen

PSCA

2/13

1

match

v2HS_119967

LOC155004

LOC155004

3/13

2

pool 52

v2HS_70312

TRK-fused gene

TFG

4/13

3

match

v2HS_71740

ataxin 10

ATXN10

1/13

1

match

v2HS_98079

solute carrier family 22, member 3

SLC22A3

1/13

2

pool 79

v2HS_65121

sorting nexin 12

SNX12

1/13

1

match


v2HS_64384

amyloid beta precursor protein binding family A member 2

APBA2

1/6

1

match

v2HS_97017

sterile alpha motif containing 4A

SAMD4A

1/6


12

v2HS_119967

LOC155004

LOC155004

5/11

2

pool 52

v2HS_58950

signal-regulatory protein beta 2

SIRPB2

3/11

2

match


protein tyrosine phosphatase, non-receptor type 13

PTPN13

1/10

v2HS_119967

LOC155004

LOC155004

5/10

2

pool 52


13

v2HS_55731

phenylalanine-tRNA synthetase-like, beta subunit

FARSLB

1/12

2

match

v2HS_59258

dynein, light chain, roadblock-type 1

DYNLRB1

3/12

1

match

v2HS_59891

TAO kinase 1

TAOK1

5/12

3

match

v2HS_162164

iodotyrosine deiodinase

IYD

1/12

cell cycle exit and neuronal differentiation 1

CEND1

1/12


transmembrane protein 168

TMEM168

2/5

v2HS_68714

abl-interactor 1

ABL1

3/5

3

match


cell cycle exit and neuronal differentiation 1

CEND1

4/6

v2HS_58952

signal regulatory protein gamma

SIRPG

1/6

2

pool 14

v2HS_59653

LOC342404

LOC342404

1/6

1

match


v2HS_55731

phenylalanyl-tRNA synthetase like, beta subunit

FARSLB

1/15

2

match

v2HS_64320

Smith-Magenis syndrome chromosome region, candidate 7

SMCR7

1/15

1

match

v2HS_71174

peroxisome proliferator-activated receptor, gamma

PPARGC1A

3/15

1

match

v2HS_71453

similar to IAP-associated factor VIAF1; phosducin-like

2/15

1

match


16

v2HS_68478

CD28 antigen

CD28

8/12

2

pool 13

v2HS_63107

dopamine beta hydoxylase

DBH

2/12

1

match


v2HS_61750

LOC100129230

LOC100129230

7/13

3

match

LOC9142

LOC9142

2/13

V2HS_62831

membrane bound O-acyltransferase domain containing 1

MBOAT1

3/13

2

match


18

v2HS_63989

STAR-related lipid transfer (START) domain containing 6

STARD6

1/14

2

match

LOC730256

LOC730256

1/14


19

v2HS_58958

TMEM9 domain family, member B/C11orf15

TMEM9B

3/10

1

match

v2HS_57051

RNA binding motif, single stranded interacting protein 1

RBMS1

5/10

1

match

v2HS_106158

LOC345672

LOC345672

1/10

2

pool 82


v2HS_59560

chromosome 13 open reading frame 15

C13orf15

10/10

1

match


21

v2HS_55312

glucosamine-phosphate N-acetyltransferase 1

GNPNAT1

6/9

2

match

v2HS_68437

LOC157503

LOC157503

2/9

3

match


30

v2HS_119967

LOC155004

LOC155004

6/14

2

pool 52

v2HS_34338

protein phosphatase 4, regulatory subunit 2

PPP4R2

7/14

3

match


v2HS_119967

LOC155004

LOC155004

1/13

2

pool 52

v2HS_36467

solute carrier family 33 (acetyl-CoA transporter), member 1

SLC33A1

8/13

3

match

v2HS_46793

ubiquitin-like modifier activating enzyme 3

UBA3

1/13

1

match


32

v2HS_42104

citrate lyase beta like (CLYBL), transcript variant 1

CLYBL

5/7

1

match

LOC100129563

LOC 10012956

1/7


41

v2HS_48278

choline kinase-like

CHKL

6/6

1

match


54

v2HS_112629

basic transcription factor 3, like 1

BTF3L1

1/5

1

match

v2HS_121153

LOC221399

LOC221399

2/5

1

match

v2HS_125538

LOC350103

LOC350103

1/5

1

match


v2HS_129527

LOC351851

LOC351851

6/6

1

match


v2HS_112629

basic transcription factor 3, like 1

BTF3L1

2/6

1

match


55

v2HS_117465

SH3 domain binding glutamic acid-rich protein like 2

SH3BGRL2

2/6

1

match

v2HS_119051

LOC90841

LOC90841

1/6

1

match


v2HS_116174

YTH domain containing 2

YTHDC2

1/7

2

pool 58

v2HS_119120

hypothetical protein FLJ20032

FLJ20032

6/7

2

match


56

V2HS_120429

six-twelve leukemia (STL), non-coding RNA

STL

5/6

1

match


v2HS_115231

rab23, member RAS oncogene family

RAB23

4/6

4

match

v2HS_117914

transketolase-like 2

TKTL2

2/6

1

match


v2HS_117239

chromosome 9 open reading frame 58

C9orf58

3/6

1

match

v2HS_120429

six-twelve leukemia (STL), non-coding RNA

STL

1/6

1

match

v2HS_119206

lon peptidase 2, peroxisomal

LONP2

2/6

1

pool 146


58

v2HS_116174

YTH domain containing 2

YTHDC2

1/4

2

match

v2HS_118722

layilin

LAYN

2/4

2

match


v2HS_112838

ectonucleoside triphosphate diphosphohydrolase 3

ENTPD3

3/7

4

match

v2HS_112982

chromodomain helicase DNA binding protein 3

CHD3

1/7

3

match

v2HS_116174

YTH domain containing 2

YTHDC2

1/7

2

match


v2HS_112838

ectonucleoside triphosphate diphosphohydrolase 3

ENTPD3

1/12

4

match

v2HS_118254

WD repeat and FYVE domain containing 2

WDFY2

1/12

1

match

v2HS_122548

similar to ribosomal protein S3A

RPS3A

4/12

1

pool 53

v2HS_120982

coiled coil domain containing 129

CCDC129

5/12

2

match


59

v2HS_111554

interleukin 2

IL2

8/10

2

match

v2HS_115544

DEAD (Asp-Glu-Ala-Asp) box polypeptide 47

DDX47

2/10

4

match


v2HS_116377

transmemembrane protein 135

TMEM135

1/9

2

match

v2HS_117064

CD1E molecule

CD1E

3/9

1

match

v2HS_119967

LOC155004

LOC155004

4/9

2

pool 52

v2HS_120757

olfactory receptor, family 8, subfamily K, member 1

OR8K1

1/9

2

match


v2HS_108647

LOC349868

LOC349868

1/8

1

pool 79

v2HS_115544

DEAD (Asp-Glu-Ala-Asp) box polypeptide 47

DDX47

3/8

4

match

v2HS_116833

intermediate filament protein syncoilin

SYNC

1/8

2

match


60

v2HS_121585

dual specificity phosphatase 3

DUSP3

10/11

1

match


v2HS_117903

glutamine rich 2

QRICH2

4/11

1

match

v2HS_119967

LOC155004

LOC155004

1/11

2

pool 52

v2HS_121585

dual specificity phosphatase 3

DUSP3

2/11

1

match

v2HS_128131

LOC351061

LOC351061

2/11

1

match

v2HS_98079

solute carrier family 22 member 3

SLC22A3

1/11

2

pool 79


v2HS_119967

LOC155004

LOC155004

8/10

2

pool 52

v2HS_121585

dual specificity phosphatase 3

DUSP3

2/10

1

match


64

v2HS_119967

LOC155004

LOC155004

10/11

2

pool 52


v2HS_121013

protease serine 54

PRSS54

3/12

1

match


66

v2HS_117675

latent transforming growth factor β binding protein 2/3

LTBP2/3

15/15


v2HS_118530

RNA exonuclease 1 homolog like 1

REXO1L1

5/13

3

match

v2HS_117675

latent transforming growth factor β binding protein 2/3

LTBP2/3

8/13


v2HS_118530

REX1, RNA exonuclease 1 homolog-like 2

REXO1L1

1/11

3

match


71

v2HS_103818

LOC284804

LOC284804

2/16

1

pool 78

v2HS_119967

LOC155004

LOC155004

9/16

2

pool 52

v2HS_97981

LOC51152

LOC51152

5/16

2

pool 79


72

v2HS_119967

LOC155004

LOC155004

9/10

2

pool 52


74

v2HS_119967

LOC155004

LOC155004

11/12

2

pool 52


77

v2HS_119967

LOC155004

LOC155004

12/12

2

pool 52


78

v2HS_94763

paired related homeobox 1

PRRX1

1/8

1

match

v2HS_99138

solute carrier family 25

SLC25A21

7/8

2

match


v2HS_102207

transmembrane protein 63B

TMEM63B

1/12

1

match

v2HS_103818

LOC284804

LOC284804

4/12

1

match

V2HS_95356

armadillo repeat containing, X-linked 2

ARMCX2

2/12

2

match

v2HS_98650

mitochondrial ribosomal protein 63

MRP63

1/12

1

match


v2HS_102155

similar to hypothetical protein KIAA0286 (HA6800)

KIAA0286

1/8

1

match

v2HS_108506

LOC349839

LOC349839

1/8

2

match


v2HS_96236

zinc finger and BTB domain containing 1

ZBTB1

2/8

1

match

v2HS_184999

eukaryotic initiation factor 4A isoform 1

EIF4A1

3/10

v2HS_96236

zinc finger and BTB domain containing 1

ZBTB1

1/10

1

match


79

v2HS_105974

LOC345597

LOC345597

3/11

1

match

v2HS_184999

eukaryotic initiation factor 4A isoform 1

EIF4A1

3/11

v2HS_98079

solute carrier family 22, member 3

SLC22A3

4/11

2

match


v2HS_108647

LOC349868

LOC349868

2/7

1

match

v2HS_98079

solute carrier family 22, member 3

SLC22A3

5/7

2

match


v2HS_101943

anthrax toxin receptor-like

ANTXRL

1/11

3

match

v2HS_105093

human solute carrier family 35, member F4

SLC35F4

2/11

1

match

v2HS_106472

LOC345713

LOC345713

1/11

1

match

v2HS_107395

LOC346589

LOC346589

1/11

1

match

v2HS_91777

nuclear receptor co-repressor N-Cor 1

NCOR1

4/11

2

match

Non-protein coding RNA 282

NCRNA00282

1/11


80

v2HS_102441

adenylate cyclase 1

ADCY1

5/11

1

match

v2HS_130882

glutamate receptor, metabotropic 3

GRM3

1/11

3

pool 91

v2HS_97368

yippee-like 5

YPEL5

2/11

1

match


v2HS_102441

adenylate cyclase 1

ADCY1

5/10

1

match


82

v2HS_184999

eukaryotic initiation factor 4A isoform 1

EIF4A1

1/11

v2HS_101845

human prickle-like 2 (Drosophila)

PRICKLE2

3/11

1

match

v2HS_109096

LOC349975

LOC349975

1/11

1

pool 84

v2HS_99423

coiled coil domain containing 70

CCDC70

1/11

1

match


v2HS_109596

1/14

v2HS_108399

LOC349811

LOC349811

3/14

1

match

v2HS_184999

eukaryotic initiation factor 4A isoform 1

EIF4A1

1/14

v2HS_93536

proteolipid protein 1

PLP1

5/14

1

match

v2HS_97017

sterile alpha motif domain containing 4A

SAMD4A

1/14


v2HS_106158

LOC345672

LOC345672

3/14

2

match

v2HS_93615

p53

TP53

3/14

1

match

v2HS_95112

RAS p21 protein activator 4

RASA4

1/14

1

match

v2HS_99525

BCL2 like 12

BCL2L12

1/14

2

match

v2HS_97017

sterile alpha motif domain containing 4A

SAMD4A

4/14


v2HS_94640

aryl hydrocarbon receptor nuclear translocator-like

ARNTL

3/10

2

match

v2HS_100174

desmoglein 4

DSG4

2/10

2

pool 145

v2HS_96026

adnp homeobox 2

ADNP2

3/10

1

match

v2HS_100819

Rho GTPase activating protein 20

ARHGAP20

2/10

1

match


84

v2HS_106409

LOC345700

LOC345700

1/11

1

match

v2HS_95019

zinc finger protein 16

ZNF16

9/11

1

match

v2HS_97152

ubiquitin-conjugating enzyme E2, J1

UBE2J1

1/11

1

match


v2HS_95019

zinc finger protein 16

ZNF16

10/11

1

match


94

v2HS_141495

zinc finger protein 454

ZNF454

7/12

2

pool 96


95

v2HS_130457

radial spoke head 10 homolog B (Chlamydomonas)

RSPH10B

6/7

3

match

v2HS_131154

potassium inwardly-rectifying channel, subfamily J

KCNJ2

1/7

3

match


v2HS_184999

eukaryotic initiation factor 4A isoform 1

EIF4A1

1/3


96

chromosome 9 open reading frame 123

C9orf123

5/13


98

v2HS_141367

cDNA FLJ37626/LOC285500

FLJ37626

10/10

2

match


v2HS_119967

LOC155004

LOC155004

2/11

2

pool 52

v2HS_133299

insulin-like growth factor binding protein 6

IGFBP6

3/11

2

match

v2HS_135564

chromosome X open reading frame 57

CXORF57

5/11

1

match


For each candidate the DNA pool from which it was isolated, the insert reference, target gene, frequency of isolation, as well as the number of shRNAmir constructs for that gene within the SM2 library are indicated. The last column shows if the recovered insert was a match to a hair pin in that particular pool ("match") or if it was from another pool ("pool X").

Rovillain et al. BMC Genomics 2011 12:355   doi:10.1186/1471-2164-12-355

Open Data