Bioinformatics and Computing Core Facility

Services include:
Microarray Data- Gene expression, copy number and genotyping
Sequence Analysis- Genomes and proteins
Phylogenetic Analysis
Functional Annotation
Data Manipulation
Let us take the repetitive out of your “repetitive tasks”. No job is too small!
Desktop hardware support
In-house back-up and storage (in progress)

Contacts:
Charlie Whittaker
charliew@mit.edu, x4-0337, E18-366
Sebastian Hoersch
hoersch@mit.edu, x4-1728, E18-366
Michael Moran
mmoran@mit.edu, x4-1728, E17-321
http://web.mit.edu/ki/facilities/bioinformatics/index.html
http://luria.mit.edu/CCR_BCC/

Biopolymers Core Facility

Services:
Standard Sanger DNA sequencing,single sample and plate format (24-48h turnaround)
Peptide synthesis
- small (multipep) scale (5-10 umole, up to 192 at once)
- large scale (250 umole)
cellulose membrane arrays (384 spots, up to 12-mers), evaluating 40-mer instrument
HPLC
Purification, analysis, training and self-use
Mass spectrometry
MALDI- peptide QC, small molecule analysis
ESI- >35KDa protein (not currently in service)
Solexa Genome Analyzer (HHMI PIs- Jacks/Horvitz/Amon/Bell/Tonegawa/Hynes)
- Very high throughput DNA sequencing
Preparaive HPLC (improved capability for purifications)

Contact:
Dick Cook for info
cook@mit.edu,
E17-415, x3-1685
http://web.mit.edu/ki/facilities/biopolymers/index.html
http://web.mit.edu/biopolymers/www/

Cell Sorting (Flow Cytometry) Core Facility

Services:
Assisted high-performance cell sorting (4 instruments)
Training and self-use of benchtop analyzers (6 instruments) FACSCalibur analyzer- high throughput (Hynes/HHMI)
Soon: 561nm yellow/orange laser upgrade to LSRII (HTS)- RFP fruit protein
Soon: red/yellow laser on MoFlo (both 3 laser)- RFP and red-excited dyes
computer upgrade to MoFlo sorters- improved data acquisition

Contact:
Glenn Paradis for info and training
gap@mit.edu,
E17-440 (office), x2-4132
E18-463 (sorting lab), x3-6454
http://web.mit.edu/ki/facilities/flowcytometry/index.html
http://web.mit.edu/flowcytometry/www/

ES Cell/Transgenic Core Facility

Services Include:
Embryonic Stem Cell Culture – gene targeting, assistance with vector design, importation and testing of lines from outside sources, generation of feeders and more.
Microinjection – mouse ES cells into blastocysts, DNA into pronucleus of fertilized mouse eggs, and lentivirus into fertilized eggs.
Repository of Reagent Mice – containing Cre, Flp, EGFP, Luciferase, LacZ and other useful strains.

Contact:
Aurora Burds Connor
aaburds@mit.edu,
NEW LOCATION: E18-218
x2-3658
http://web.mit.edu/ki/facilities/transgenic/index.html

Glassware Preparation Facility

Glasswash services:
In-lab pick-up: dirty glassware and pipettes, solid biohazard waste
Sterile glassware and media bottles
Non-sterile glass and labware
Sterile pipettes (volumetric, Pasteur, tissue culture)
Sterile Milli-Q water

Contact:
Suzan Stevens, suzan@mit.edu, E18-375
http://web.mit.edu/ki/facilities/glassware/index.html

Histology Core Facility

Services:
Paraffin embedding and sectioning
Frozen and resin sections
Serial sectioning
H&E and specialized stains (carbohydrate, connective tissue, nerve, hematologic)

Contact:
Denise Crowley
dencrowl@mit.edu,
E17-427 (lab), x8-8183
http://web.mit.edu/ki/facilities/histology/index.html

Media Preparation Facility

Media Prep services:
Custom-made bacterial, yeast and tissue culture media

Contact:
Bong Kim, bongkim@mit.edu, E17-323, x8-7372
Ann Thompson, annthomp@mit.edu, E17-323, x3-6415
http://web.mit.edu/ki/facilities/mediaprep/index.html

Microarray Technologies Core Facility (BioMicro Center)

Services:
Commercial microarray scanners- Affymetrix, Agilent and ArrayWoRx
Custom array generation
High-throughput PCR
Real-time PCR

Joint effort: KI, Center for Environmental Health Sciences, Biology, Biological Engineering

Location: 68-316

Contacts:
Rebecca Fry: rfry@mit.edu, x2-2015
Manlin Luo: manlin@mit.edu, x2-2563
http://web.mit.edu/ki/facilities/microarray/index.html
http://web.mit.edu/biomicro/

Microscopy and Imaging Core Facility

Services:
(assisted, training and self-use)
Fluorescence microscopy- Zeiss
Live cell video microscopy- Deltavision
Laser capture microscopy
Electron microscopy (assisted)
Image processing (training or assisted)- SoftWorx, Imaris, OpenLab, ImageJ Second Deltavision (Gertler)
Spinning disk confocal microscope (Gertler)
SKY, FISH- detection of chromosomal instability, specific sequences on chromosomes
TIRF- live cell imaging on confocal (cell-cell contacts and PM processes)
Critical point drying and vacuum deposition system (Gertler)- EM cell surface imaging
Color camera on Zeiss

Contact:
Eliza Vasile for info and training
evasile@mit.edu,
E18-376, x4-3804
http://web.mit.edu/ki/facilities/microscopy/index.html

Preclinical Testing/Animal Imaging Core Facility- in development

Services:
NightOwl system- fluorescent & bioluminescent whole mouse imaging
Whole animal microCT
High-resolution mouse ultrasound

Contact :
Eliza Vasile for NightOwl and microCT
evasile@mit.edu,
E18-376, x4-3804

Susan Erdman (DCM) for ultrasound
serdman@mit.edu,
x2-1804

Proteomics Core Facility

Instrumentation:
ThermoFisher LTQ ion trap mass spectrometer (2004)
High sensitivity
Protein identification
Post-translational modification identification
Agilent 1100 nano HPLC
Compatible with LTQ high sensitivity nano-ESI source

Applied Biosystems QSTAR quadrupole-time-of-fight mass spectrometer (2007)
High resolution and mass accuracy
Protein identification
Post-translational modification identification
Quantitation of differential protein expression using isotopic (SILAC, ICAT) or isobaric (iTRAQ) labels
Applied Biosystems/Eksigent Tempo 2D nano-HPLC
Compatible with QSTAR high sensitivity nano-ESI source
Instrument capable of supporting multidimensional peptide separations (ion exchange followed by reversed phase - MudPIT)

Mascot™ database search software
Mascot is the most widely used search engine in proteomics
Probability based algorithm
Compatible with data from all mass spectrometers
Fast and flexible
Capable of error-tolerant searches for discovery of post-translational modifications
Integrated feature for estimating false positive rates

Sequest™ database search software
Sequest is the ThermoFisher proprietary software for analysis of LTQ data

ProteinPilot™ database search software
ProteinPilot is the Applied Biosystems proprietary software for analysis of QSTAR data, including ICAT, SILAC and iTRAQ quantitation

Contact:
Ioannis A. Papayannopoulos
Office: E17-354 (at the end of the corridor connecting to the bridgeto building E25)
Lab: E18-313 (across from office)
Telephone: x4-2609
E-mail: ioannis@mit.edu

Shared Research Resources

Services:
building operations (cold/warm rooms, vacuum and compressed air systems, temperature, R/O water)
shared equipment (ice machines, film developers, autoclaves, etc)
CO2 system
biosafety cabinet testing and repair
EHS management system

Contacts:
Barry Hughes, Operations Administrator, abhughes@mit.edu
E17-110
x3-3168
Barry’s Pager: 617-546-2359

Jennifer Lynn, EHS Coordinator, jlynn@mit.edu
E17-110
x3-2463

Virus Production Core Facility

BL2+ safety level room, E17-127A, for self-use
One containment hood
Equipment (inverted fluorescent scope, ultracentrifuge, incubators, minus 80C freezer, etc)
Disposable plastics & supplies

Contact:
Carol McKinley for info and training
camck@mit.edu

Tech Time calendar for scheduling
http://calendar.mit.edu/techtime
Resource calendars: BL2+ containment hood, BL2+ ultracentrifuge