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.

Cellecta Software

Barcode Analyzer and Deconvoluter

This software is required to convert raw HT sequencing data into a summary file for subsequent processing, and it includes annotation for every identified gene. Next, data can be processed, edited, normalized, and transformed using your data analysis tool of choice, such as SAS, SPSS, or, for simpler analyses, Microsoft Excel. The program requires the appropriate Module Library (BLIB) files, available via the links below, which you can download to the same directory where the Barcode Deconvoluter software resides. The software is freely available to anyone and can be used up to ten times without registration. Subsequently, registration is required to unlock the full functionality. A hardware-specific registration code is generated at the opening screen; email it to support@decipherproject.net to receive an activation code granting a single computer license.

 

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.

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 sales@cellecta.com or call 650-938-3910.

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.