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Series GSE62183 Query DataSets for GSE62183
Status Public on Nov 24, 2014
Title shRNA Sensor Analysis of DSIR Selected shRNAs
Organism synthetic construct
Experiment type Other
Summary Purpose: Generate a large, high quality database of paired shRNA efficacy/sequence datapoints.
Overall design Methods:Twelve shRNAs for each Refseq annotated human gene were selected based on the DSIR algorithm. Twelve batches of ~22K shRNAs (corresponding to 12 agilent chips) were then assessed for efficacy via the sensor method outlined in Fellmann et al, Mol Cell, 2011.
Conclusions: Neighboring nucleotide combinations are best at predicting shRNA efficacy.
Contributor(s) Knott SR
Citation(s) 25435137
Submission date Oct 08, 2014
Last update date May 15, 2019
Contact name Simon Robert Vincent Knott
Organization name Cold Spring Harbor Laboratory
Department Biology
Lab Hannon
Street address 1 Bungtown Rd
City Cold Spring Harbor
State/province NY
ZIP/Postal code 11724
Country USA
Platforms (1)
GPL9423 Illumina Genome Analyzer II (synthetic construct)
Samples (96)
GSM1521347 chip 3991 replicate A sort S0
GSM1521348 chip 3991 replicate A sort S1
GSM1521349 chip 3991 replicate A sort S3
This SubSeries is part of SuperSeries:
GSE62189 A computational algorithm to predict shRNA potency
BioProject PRJNA263390
SRA SRP048751

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
GSE62183_Initial_Sensor_Summary.txt.gz 7.2 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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