DAVID H. SHERMAN, PH.D.
DIRECTOR, CENTER FOR CHEMICAL GENOMICS
THE UNIVERSITY OF MICHIGAN, LIFE SCIENCES INSTITUTE
210 WASHTENAW AVENUE
ANN ARBOR, MICHIGAN 48109-2216
734-615-9317; FAX 734-763-6492
DATE
Dear name,
We are happy to assist you in your application for siRNA screening: title of proposal. Our staff has
extensive experience in assisting researchers with assay development and screening involving RNAi
technologies. This proposal involves the development and validation fill in details of assay here. The
staff has participated in several screening campaigns for University of Michigan faculty and from
institutions outside of U of M including: Case Western Reserve University, University of Virginia,
Wayne State University, Medical College of Wisconsin, Michigan State University and University of
Chicago.
With the experimental and administrative guidance of HTS director, Martha Larsen, the Center for
Chemical Genomics (CCG) will provide siRNA reagents, screening services, expert consultation, and
information sharing for researchers. You will be able to have screens performed with CCG staff
assistance and direction. In addition, CCG staff and faculty advisors are committed to working closely
with researchers both prior to and after the HTS screens. For RNAi screening projects, the HTS staff
provides consultation on assay design, transfection techniques, appropriate controls and assists in the
transition of your assay to HTS format. The HTS staff supervises the screening activities, collects and
archives data, and performs assay controls to insure quality results. If needed, the CCG has also
established collaboration with UM Center for Computational Medicine and Bioinformatics to use biology
network analysis of screening results to enrich genetic information from RNAi screens.
The CCG provides access to the Dharmacon siGenome SMART pool library of human and mouse genes.
This RNA library is designed for whole genome interference using HTS formats to identify and
investigate the targeted pathways and processes in biological systems. Our experience with this library
and techniques for whole genome screening give us confidence that we will be able to transition your
established protocols into HTS amenable platforms. The screening operation can be coordinated with
visits from your staff and students, giving them an opportunity to participate and observe HTS techniques
and assist in assay development.
The CCG enters all screening data into a database, MScreen, an effective tool to store, retrieve, archive
siRNA data and perform comparative analysis of screening targets to separate off-target effects from
genes of interest. This web-based system can be accessed from any computer, providing you and your lab
with up-to-date assay results and searching tools. For a full description of MScreen capabilities, a recent
publication is available (DOI:10.1177/1087057112450186).
We look forward to working with you on your project that involves siRNA high throughput screening.
Sincerely,
CCG Resources
Chemical and RNAi Libraries
150,000+
diverse small molecule compounds
2,446
FDA-approved drugs and known bioactives
1200+
focused libraries (autophagy, kinases, epigenetics)
2830
fragment library
30,000+
natural product extracts
20M
in silico library available for searching
siRNA
Dharmacon human and mouse druggable genomes
Liquid Handling Robotics
Mosquito X1 (TTP Labtech), a hit-picking liquid handler with 96- and 384-well plate formats,
25-1200 nL positive displacement tips for confirmation, serial dilutions and
reagent/sample transfers
Beckman Biomek FX multi/multi- 96-well pipetter head & 384 pipetter head
Beckman Biomek FX - 384-well nanoliter HDR (pin tool)
Sciclone ALH3000 – 384- and 1536-well nanoliter V&P pin tool
Thermo Multidrop and Micromultidrop 96-384 liquid dispensers
Thermo Combi Multidrops liquid dispensers
Thermo Combo nl liquid dispenser for 96, 384 & 1536 plates
Catalyst Express Robotic arm and plate storage
Bio-Tek ELx405 and 406 Plate Washers
CaliperLS Twister II plate hotel
Detection equipment
BMGLabtech PHERAstar high-speed, multifunction plate reader
Detection capabilities including 96-, 384-well: absorbance, fluorescence, fluorescence
polarization, time-resolved fluorescence, time-resolved FRET, and luminescence
Molecular Devices FlexStation3 with 5 assay formats: kinetic, endpoint, spectrum, well-scanning
and Flex mode for bottom read capacity in calcium mobilization and membrane potential
assays. Application technologies in 96-, 384-well: absorbance, fluorescence intensity,
fluorescence polarization, luminescence and time-resolved fluorescence with dual
monochromators.
HyperCyt/Accuri-The HyperCyt high throughput liquid handling front-end moves microliter
samples from 384-well plates and rapidly delivers them to the Accuri flow cytometer. Both
bead and cell samples can be used and a 384-well plate can be analyzed in 10 min providing a
throughput of over 2000 compounds per hour.
MDS Analytical Technologies-ImageXpress Micro Cellular Imaging and Analysis System for
automated acquisition and analysis of images for high throughput cell-based screening.
Includes Acuity Xpress Informatics and MDCStore database.
PE EnVision Multimode Plate Reader
Detection for all non-isotopic detection technologies, including fluorescence intensity,
fluorescence polarization, time-resolved fluorescence (TRF), luminescence (enhanced) and
absorbance (monochromator), BRET and AlphaScreen in 96-, 384 and 1536-well formats.
Informatics
Web database using Oracle:
Relational database of compounds, plate inventory, results
Results browsing or searching
Comparison of results among different screens
Structure similarity searches on external library to find compounds for SAR
Links to public databases for chemical and biological profiling
ICM Chemist (Molsoft LLC)
Chemical spreadsheet, Chemical structure clustering, SAR Analysis