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. Author manuscript; available in PMC: 2013 Feb 5.
Published in final edited form as: Annu Rev Biochem. 2010;79:37–64. doi: 10.1146/annurev-biochem-060408-092949

Table 1.

Results of genome-scale,a cell-based RNAi high-throughput screens in mammalian or Drosophila cells

Cell type Screen type Reagent Primary hits Secondary hitsb Field of study References
Human cells
HeLa Plate reader & imaging esiRNA 275 37 Cell division 120, 121
U2OS Imaging siRNA 1,152 18 Cell cycle 114
NCI-H1155 Plate reader siRNA 87 6 Cancer biology 103
NIH3T3 Pooled shRNA 15 3 Stress resistance 43
293T Plate reader siRNA — 295 Host-pathogen interactions 79
293T, HeLa, MCF-7 Pooled shRNA 30 8 Cell death 42
DLD1 Plate reader siRNA 740 268 Signal transduction 50
HEK293 Pooled shRNA 13,140 21 Cell adhesion 40
HeLa Imaging siRNA 305 124 Host-pathogen interactions 180
HeLa Plate reader siRNA 530 23 Signal transduction 156
HeLa-derived TZM-b1 Plate reader siRNA 386 273 Host-pathogen interactions 78
HeLa P4/R5 Plate reader siRNA 931 232 Host-pathogen interactions 80
Jurkat Pooled shRNA 11 5 Cancer biology 46
MCF-10Ac Pooled shRNA 201 166 Cancer biology 45
MNT-1 Plate reader siRNA 98 35 Pigmentation 142
RDG3 Imaging siRNA — 171 Stress resistance 133
BJtsLT Pooled shRNA 100 37 Cancer biology 126
DLD-1 Pooled shRNA 368 83 Cancer biology 48
Huh7/Rep-Feo Plate reader siRNA 236 96 Host-pathogen interactions 181
Jurkat Pooled shRNA 252 7 Host-pathogen interactions 47
Huh 7.5.1 Imaging siRNA 521 262 Host-pathogen interactions 182
Mouse cells
NIH 3T3 Pooled shRNA — 28 Cancer biology 104
L929 Plate reader siRNA 666 432 Cell death 122
B16-F0 Pooled shRNA 78 22 Cancer biology 41
Oct4-Gip ESCs FACSd & imaging esiRNA 296 21 Stem cell biology 109
Oct4-Gip ESCs FACS siRNA 148 104 Stem cell biology 107
Drosophila cells
Kc167, S2R+ Imaging dsRNA 438 — Viability 97
S2 Imaging dsRNA — 121 Host-pathogen interactions 164
Clone 8 Plate reader dsRNA 238 213 Signal transduction 152
Clone 8 Plate reader dsRNA 509 96 Signal transduction 147
Kc167 Plate reader dsRNA — 90 Signal transduction 149
S2 Plate reader dsRNA 474 121 Signal transduction 190
S2 Imaging dsRNA — 86 Host-pathogen interactions 167
S2 Imaging dsRNA 305 ~190 Host-pathogen interactions 169
S2 Imaging dsRNA 210 112 Host-pathogen interactions 176
S2 Plate reader dsRNA — 14 Host-pathogen interactions 163, 191
S2 Plate reader dsRNA 1,133 284 Protein secretion 139
S2 FACS dsRNA 488 — Cell cycle and/or cell size 115
S2 Imaging dsRNA — — Signal transduction 130
S2 FACS dsRNA 66 23 RNA biology 157
S2 Plate reader dsRNA 75 4 Ion transport 129
S2R+ Plate reader dsRNA 138 7 RNA biology 158
S2R+ Plate reader dsRNA 1,168 331 Signal transduction 144
S2R+ Imaging dsRNA 699 — Signal transduction 131
S2R+ Imaging dsRNA 1,500 27 Signal transduction 132
S2 Imaging dsRNA 90 24 RNA biology 162
Kc167 Plate reader dsRNA 81 47 Cell death 123
S2 Plate reader dsRNA 47 1 RNA biology 159
S2* Plate reader dsRNA 18 5 Chromatin regulation 140
S2R+ Imaging dsRNA 346 — Signal transduction 145a
S2 Imaging dsRNA 162 54 Host-pathogen interactions 173
DL1 Plate reader dsRNA 176 110 Host-pathogen interactions 178
Kc167 Imaging dsRNA 526 — Lipids 82
Kc167 Plate reader dsRNA 265 120 Transcription and/or translation 141
Primary neurons Imaging dsRNA 336 104 Neural outgrowth 136
S2 Plate reader dsRNA 821 152 Mitochondria 138
S2 Plate reader dsRNA — — Phagocytosis 128
S2 Imaging dsRNA — — Centrioles and/or centrosomes 119
S2 Imaging dsRNA 847 227 Lipids 83
S2 Imaging dsRNA 292 133 Cancer biology 117
S2 Imaging dsRNA 23 — Transcription and/or translation 85
S2-derived RZ-14 Plate reader dsRNA 177 — RNA biology 160
S2R+ Imaging dsRNA 119 39 Centrioles and/or centrosomes 118
S2R+ Imaging dsRNA 133 72 RNA biology 161
S2R+ Imaging dsRNA ~500 1 Mitochondria 137
S2R+ Plate reader dsRNA 303 173 Circadian rhythms 125
Clone 8 Plate reader dsRNA ~100 11 Signal transduction 155
S2 Plate reader dsRNA 218 116 Host-pathogen interactions 37
Kc167 Plate reader dsRNA 996 202 Cell cycle and/or cell size 116
S2R+ Plate reader dsRNA 42 33 Cell death 124
S2R+ Imaging dsRNA — — Signal transduction 154
S2R+ Imaging dsRNA 15 7 Cell cycle and/or cell size 134
a

For this summary, we defined genome-scale with a cutoff of approximately 5000 genes (mammalian cell screens) or at least 70% of the genome (Drosophila cell screens).

b

Here, we use secondary hits to refer to the largest set of primary hits that passed an additional test verifying the result at the reagent level (retest after re-synthesis or with another assay or cell type) or in most cases, at the gene level (retest with another reagent or single reagents from a pool, for example). In some cases, only a subset of primary hits were tested in secondary assays. For most reports, only a small number of genes (typically, one to five) were confirmed with a rigorous test, such as rescue of the RNAi effect with a cDNA, or were confirmed at the level of biological significance with another type of assay or an in vivo analysis.

c

Additional cell types tested with smaller shRNA pools.

d

FACS, fluorescence-activated cell sorter.