DECIPHER Data Analysis Software
The following software tools to aid in data analysis and sequences of functional shRNA are available as part of the DECIPHER Project. Please refer to the NIH Data and Resource Sharing Policy for terms and conditions of use.
DECIPHER Project Software
Barcode Analyzer and Deconvoluter
The Barcode Deconvoluter software has been discontinued, and support for the software will end on December 31, 2017. We sincerely appreciate your support and regret any inconvenience this necessary action causes you.
We now recommend the following procedure for deconvolution of DECIPHER shRNA Libraries.
When sequencing is completed, demultiplex the run to into separate FASTQ (*.bcl files) files. This can be done using the Illumina BaseSpace Hub or, alternatively, demultiplexing and FASTQ file generation may be done faster using a UNIX server and the Illumina bcl2fastq software. Using the bcl2fastq software also avoids the rather slow step of downloading FASTQ files from BaseSpace. You can obtain the bcl2fastq program on the Illumina website.
- The Bioinformatics I/O Blog on the University of Glasgow’s Centre for Viral Research website (for instance, see blog articles How to generate a Sample Sheet from sample/index data in BaseSpace and How to demultiplex Illumina data and generate FASTQ files using bcl2fastq).
- The BaseSpace Sequence Hub Help Center from Illumina. In particular, see How to download data from Run.
After demultiplexing the data, the barcode sequence reads should be aligned with the library reference file (see Complete shRNA and Barcode Sequences for all DECIPHER libraries in pRSI9 or pRSI12) and counted using appropriate software.
Barcode Trimmer Tool (Third Party software, not supported by Cellecta)
Author: Indranil Sinha, Karolinska Institutet
Description: Automatically trims the output sequences from the TAB file to the 18nt barcode sequence. Trimming is required before proceeding to the second step of the Deconvoluter software.
- Request Barcode Trimmer Tool (PC only)
RNAi Generator Tool (Third Party software, not supported by Cellecta)
Author: Gus Frangou, Fred Hutchinson Cancer Research Institute
Description: Generate a list of optimal shRNA target sequences for a given input sequence or sequences. The software is extremely customizable.
- Request RNAi Generator Tool (Mac only)
Cellecta NGS Services
Cellecta’s Functional shRNA Project
As a result of NIH SBIR grants HG003355 and RR024323, Cellecta has compiled a database of ~120,000 functionally validated shRNA for human and mouse genes. Under the NIH Data and Resource Sharing Plan, the shRNA sequences are freely available to all academic and commercial researchers. For information on how the shRNA were experimentally tested and functionally confirmed, please see the Reporter Assay technology page.
Registration on the DECIPHER Project website is required to access and download the sequence file. As part of the registration process, users must (1) agree to the conditions of use governing access to the data, including restrictions to commercial use and redistribution of the information to third parties, and (2) provide proper acknowledgment of the data resources and NIH as a supporting organization for this project.
Sequences of Validated shRNA
Receive the list of functionally validated shRNAs upon submission of the Resource Request Form. A valid institution email address is required.
Cellecta offers Custom shRNA Construct and Pooled shRNA Library services which utilize these validated shRNA. For pricing and ordering information, please email email@example.com or call 650-938-3910.