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Series GSE6807 Query DataSets for GSE6807
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
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
 
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.
 
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
Submission date Jan 19, 2007
Last update date Nov 05, 2014
Contact name Aimee Jackson
Organization name Regulus Therapeutics
Street address 1896 Rutherford Rd
City Carlsbad
State/province CA
ZIP/Postal code 92008
Country USA
 
Platforms (3)
GPL3991 Human 3.0 A1
GPL3992 Functional ID v2.0 Array 1
GPL4372 Rosetta/Merck Human 44k 1.1 microarray
Samples (80)
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
Relations
BioProject PRJNA99211

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

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
Raw data included within Sample table

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