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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 10, 2007 |
| Title |
Genome-wide resources of endoribonucleotide-prepared short interfering RNAs for specific loss-of-function studies |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| Summary |
RNA interference (RNAi) has become an important technique for loss-of-gene functionstudies in mammalian cells. To achieve reliable results in an RNAi experiment, efficientand specific silencing triggers are required. Here we present genome-wide data sets forthe production of endoribonuclease-prepared short interfering RNAs (esiRNAs) for human, mouse and rat. We used an algorithm to predict the optimal region for esiRNA synthesis for every protein-coding gene of these three species. The database RiDDLE was installed for retrieval of target sequences and primer information. To test this in silico resource experimentally, we generated 16,242 esiRNAs that can be used for RNAi screening in human cells. Comparative analyses with chemically synthesized siRNAs demonstrated a high silencing efficacy of esiRNAs and a 12-fold reduction of downregulated off-target transcripts as detected by microarray analysis. Hence, the presented esiRNA libraries offer an efficient, cost-effective, and specific alternative to currently available mammalian RNAi resources.
Consensus gene lists used to generate the clusters appearing in the associated publication have been linked as supplementary files at the foot of the Series record. There is a consensus genelist for each gene in the study:
GSE6807_KIAA1387_ConsensusGeneList.txt
GSE6807_MAPK14_ConsensusGeneList.txt
Keywords: RNAi, off-target effects, esiRNA
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| Overall design |
Synthetic siRNAs or endoribonucleotide-prepared siRNAs were transfected into human cells in culture. RNA was isolated at 12 or 24 hours post-transfection and anaylzed by microarray for target gene silencing as well as silencing of unintented transcripts (off-target effects). siRNA pool profiles were clustered with all transcripts on the microarray. siRNA versus esiRNA clusters were generated with consensus gene lists.
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| Contributor(s) |
Kittler R, Surendranath V, Heninger A, Slabicki M, Theis M, Putz G, Franke K, Caldareli A, Grabner H, Kozak K, Wagner J, Rees E, Korn B, Sachse C, Sonnichsen B, Guo J, Schelter J, Burchard J, Linsley PS, Jackson AL, Habermann B, Buchholz F |
| Citation(s) |
17351622 |
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| Submission date |
Jan 19, 2007 |
| Last update date |
Nov 05, 2014 |
| Contact name |
Aimee Jackson |
| Organization name |
Regulus Therapeutics
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| Street address |
1896 Rutherford Rd
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| City |
Carlsbad |
| State/province |
CA |
| ZIP/Postal code |
92008 |
| Country |
USA |
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| Platforms (3) |
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| Samples (80)
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| GSM156686 |
HeLa, mock, 24 hr. vs. HeLa, MAPK14-1, 33nM, 24hr |
| GSM156687 |
HeLa, mock, 24 hr. vs. HeLa, MAPK14-1, 20nM, 24hr |
| GSM156688 |
HeLa, mock, 24 hr. vs. HeLa, MAPK14-1, 11nM, 24hr |
| GSM156689 |
HeLa, mock, 24 hr. vs. HeLa, MAPK14-1, 8.3nM, 24hr |
| GSM156690 |
HeLa, mock, 24 hr. vs. HeLa, Pool of siRNAs 1-3, 24hr |
| GSM156691 |
HeLa, mock, 24 hr. vs. HeLa, Pool of siRNAs 1-5, 24hr |
| GSM156692 |
HeLa, mock, 24 hr. vs. HeLa, Pool of siRNAs 1-9, 24hr |
| GSM156693 |
HeLa, mock, 24 hr. vs. HeLa, Pool of siRNAs 1-12, 24hr |
| GSM156962 |
HeLa, mock, 24 hr vs. HeLa, MAPK14 793, 10 nM, 24 hr |
| GSM156963 |
HeLa, mock, 12 hr vs. HeLa, KIAA1387 1512, 10 nM, 12 hr |
| GSM156964 |
HeLa, mock, 12 hr vs. HeLa, KIAA1387 2656, 10 nM, 12 hr |
| GSM156965 |
HeLa, mock, 12 hr vs. HeLa, KIAA1387 2473, 10 nM, 12 hr |
| GSM156966 |
HeLa, mock, 12 hr vs. HeLa, KIAA1387 esRNA-1, 10 nM, 12 hr |
| GSM156967 |
HeLa, mock, 12 hr vs. HeLa, KIAA1387 esRNA-2, 10 nM, 12 hr |
| GSM156968 |
HeLa, mock, 12 hr vs. HeLa, KIAA1387 esRNA-3, 10 nM, 12 hr |
| GSM156969 |
HeLa, mock, 12 hr vs. HeLa, MAPK14 793, 10 nM, 12 hr |
| GSM156970 |
HeLa, mock, 12 hr vs. HeLa, MAPK14 542, 10 nM, 12 hr |
| GSM156971 |
HeLa, mock, 12 hr vs. HeLa, MAPK14 569, 10 nM, 12 hr |
| GSM156972 |
HeLa, mock, 12 hr vs. HeLa, MAPK14 esRNA-1, 10 nM, 12 hr |
| GSM156973 |
HeLa, mock, 12 hr vs. HeLa, MAPK14 esRNA-2, 10 nM, 12 hr |
| GSM156974 |
HeLa, mock, 12 hr vs. HeLa, MAPK14 esRNA-3, 10 nM, 12 hr |
| GSM156975 |
HeLa, mock, 24 hr vs. HeLa, KIAA1387 1512, 10 nM, 24 hr |
| GSM156976 |
HeLa, mock, 24 hr vs. HeLa, KIAA1387 2656, 10 nM, 24 hr |
| GSM156977 |
HeLa, mock, 24 hr vs. HeLa, KIAA1387 2473, 10 nM, 24 hr |
| GSM156978 |
HeLa, mock, 24 hr vs. HeLa, KIAA1387 esRNA-1, 10 nM, 24 hr |
| GSM156979 |
HeLa, mock, 24 hr vs. HeLa, KIAA1387 esRNA-2, 10 nM, 24 hr |
| GSM156980 |
HeLa, mock, 24 hr vs. HeLa, KIAA1387 esRNA-3, 10 nM, 24 hr |
| GSM156981 |
HeLa, mock, 24 hr. vs. HeLa, MAPK14 793, 10nM, 24hr b |
| GSM156982 |
HeLa, mock, 24 hr vs. Hela, MAPK14 542, 10 nM, 24 hr |
| GSM156983 |
HeLa, mock, 24 hr vs. Hela, MAPK14 569, 10 nM, 24 hr |
| GSM156984 |
HeLa, mock, 24 hr vs. Hela, MAPK14 esRNA-1, 10 nM, 24 hr |
| GSM156985 |
HeLa, mock, 24 hr vs. Hela, MAPK14 esRNA-2, 10 nM, 24 hr |
| GSM156986 |
HeLa, mock, 24 hr vs. Hela, MAPK14 esRNA-3, 10 nM, 24 hr |
| GSM156987 |
HeLa, mock, 24 hr vs. HeLa, KIAA1387 esRNA-3, 10 nM, 24 hr (-DNase) |
| GSM156988 |
HCT116 Mock 24h a vs. HCT116 MAPK14-793 10nM 24h a |
| GSM156989 |
HCT116 Mock 24h a vs. HCT116 MAPK14-542 10nM 24h a |
| GSM156990 |
HCT116 Mock 24h a vs. HCT116 MAPK14-569 10nM 24h a |
| GSM156991 |
HCT116 Mock 24h a vs. HCT116 MAPK14-esiRNA1 10nM 24h a |
| GSM156992 |
HCT116 Mock 24h a vs. HCT116 MAPK14-esiRNA2 10nM 24h a |
| GSM156993 |
HCT116 Mock 24h a vs. HCT116 MAPK14-esiRNA3 10nM 24h a |
| GSM156994 |
HCT116 Mock 24h a vs. HCT116 KIAA1387-1512 10nM 24h a |
| GSM156995 |
HCT116 Mock 24h a vs. HCT116 KIAA1387-2656 10nM 24h a |
| GSM156996 |
HCT116 Mock 24h a vs. HCT116 KIAA1387-2473 10nM 24h a |
| GSM156997 |
HCT116 Mock 24h a vs. HCT116 KIAA1387-esiRNA1 10nM 24h a |
| GSM156998 |
HCT116 Mock 24h a vs. HCT116 KIAA1387-esiRNA2 10nM 24h a |
| GSM156999 |
HCT116 Mock 24h a vs. HCT116 KIAA1387-esiRNA3 10nM 24h a |
| GSM157000 |
HCT116 Mock 24h a2 vs. HCT116 MAPK14-793 10nM-24 a2 |
| GSM157001 |
HCT116 Mock 24h a2 vs. HCT116 MAPK14-542 10nM-24 a2 |
| GSM157002 |
HCT116 Mock 24h a2 vs. HCT116 MAPK14-569 10nM-24 a2 |
| GSM157003 |
HCT116 Mock 24h a2 vs. HCT116 MAPK14 esiRNA1 10nM-24 a2 |
| GSM157004 |
HCT116 Mock 24h a2 vs. HCT116 MAPK14 esiRNA2 10nM-24 a2 |
| GSM157005 |
HCT116 Mock 24h a2 vs. HCT116 MAPK14 esiRNA3 10nM-24 a2 |
| GSM157006 |
HCT116 Mock 24h a2 vs. HCT116 KIAA1387-1512 10nM-24 a2 |
| GSM157007 |
HCT116 Mock 24h a2 vs. HCT116 KIAA1387-2656 10nM-24 a2 |
| GSM157008 |
HCT116 Mock 24h a2 vs. HCT116 KIAA1387-2473 10nM-24 a2 |
| GSM157009 |
HCT116 Mock 24h a2 vs. HCT116 KIAA1387 esiRNA3 10nM-24 a2 |
| GSM157096 |
HCT116 Mock 24h b vs. HCT116 MAPK14-793 10nM 24h b |
| GSM157097 |
HCT116 Mock 24h b vs. HCT116 MAPK14-542 10nM 24h b |
| GSM157098 |
HCT116 Mock 24h b vs. HCT116 MAPK14-569 10nM 24h b |
| GSM157099 |
HCT116 Mock 24h b vs. HCT116 MAPK14-esiRNA1 10nM 24h b |
| GSM157100 |
HCT116 Mock 24h b vs. HCT116 MAPK14-esiRNA2 10nM 24h b |
| GSM157101 |
HCT116 Mock 24h b vs. HCT116 MAPK14-esiRNA3 10nM 24h b |
| GSM157102 |
HCT116 Mock 24h b vs. HCT116 KIAA1387-1512 10nM 24h b |
| GSM157103 |
HCT116 Mock 24h b vs. HCT116 KIAA1387-2656 10nM 24h b |
| GSM157104 |
HCT116 Mock 24h b vs. HCT116 KIAA1387-2473 10nM 24h b |
| GSM157105 |
HCT116 Mock 24h b vs. HCT116 KIAA1387-esiRNA1 10nM 24h b |
| GSM157106 |
HCT116 Mock 24h b vs. HCT116 KIAA1387-esiRNA2 10nM 24h b |
| GSM157107 |
HCT116 Mock 24h b vs. HCT116 KIAA1387-esiRNA3 10nM 24h b |
| GSM157108 |
HCT116 Mock 24h b2 vs. HCT116 MAPK14-793 10nM 24 b2 |
| GSM157109 |
HCT116 Mock 24h b vs. HCT116 MAPK14-542 10nM 24h b2 |
| GSM157110 |
HCT116 Mock 24h b vs. HCT116 MAPK14-569 10nM 24h b2 |
| GSM157111 |
HCT116 Mock 24h b vs. HCT116 MAPK14-esiRNA1 10nM 24h b2 |
| GSM157112 |
HCT116 Mock 24h b vs. HCT116 MAPK14-esiRNA2 10nM 24h b2 |
| GSM157113 |
HCT116 Mock 24h b vs. HCT116 MAPK14-esiRNA3 10nM 24h b2 |
| GSM157114 |
HCT116 Mock 24h b vs. HCT116 KIAA1387-1512 10nM 24h b2 |
| GSM157115 |
HCT116 Mock 24h b vs. HCT116 KIAA1387-2656 10nM 24h b2 |
| GSM157116 |
HCT116 Mock 24h b vs. HCT116 KIAA1387-2473 10nM 24h b2 |
| GSM157117 |
HCT116 Mock 24h b vs. HCT116 KIAA1387-esiRNA1 10nM 24h b2 |
| GSM157118 |
HCT116 Mock 24h b vs. HCT116 KIAA1387-esiRNA2 10nM 24h b2 |
| GSM157119 |
HCT116 Mock 24h b vs. HCT116 KIAA1387-esiRNA3 10nM 24h b2 |
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| Relations |
| BioProject |
PRJNA99211 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE6807_KIAA1387_ConsensusGeneList.txt |
1.4 Kb |
(ftp)(http) |
TXT |
| GSE6807_MAPK14_ConsensusGeneList.txt |
1.8 Kb |
(ftp)(http) |
TXT |
| GSE6807_RAW.tar |
180.0 Kb |
(http)(custom) |
TAR |
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