The Molecular Pathology and Imaging Core (MPIC)

Histological Services

All costs are listed under ‘Ordering and Pricing’

• Tissue Processing and Paraffin Embedding
• FFPE Sectioning
• Frozen Sectioning
• RNase free Processing, Embedding, and Sectioning
• Staining
  • H&E
  • Alcian Blue
  • Masson’s Trichrome
  • Oil Red O (not recommended for FFPE)
  • PAS
• Visium & Xenium Spatial Transcriptomics

Training

Training is available for all equipment. See ‘Equipment’ for further information

Reagents

No charge to members for reagents listed below:

• Secondary Antibodies
  • Cy2/Alexa Fluor 488
    • Bovine Anti-Digoxigenin
    • Donkey Anti-Goat
    • Donkey Anti-Guinea Pig
    • Donkey Anti-Mouse
    • Donkey Anti-Rabbit
    • Donkey Anti-Rat
    • Donkey Anti-Sheep
    • Goat Anti-Armenian Hamster
    • Mouse Anti-Chicken
  • Cy3
    • Anti-Digoxigenin
    • Bovine Anti-Goat
    • Donkey Anti-Chicken
    • Donkey Anti-Guinea Pig
    • Donkey Anti-Human
    • Donkey Anti-Mouse
    • Donkey Anti-Rabbit
    • Donkey Anti-Rat
    • Donkey Anti-Sheep
    • Goat Anti-Armenian Hamster
    • Goat Anti-Syrian Hamster
  • Cy5
    • Donkey Anti-Chicken
    • Donkey Anti-Goat
    • Donkey Anti-Guinea Pig
    • Donkey Anti-Mouse
    • Donkey Anti-Rabbit
    • Donkey Anti-Rat
    • Donkey Anti-Sheep
  • Biotinylated
    • Goat Anti-Chicken
    • Goat Anti-Guinea Pig
    • Goat Anti-Hamster
    • Goat Anti-Human
    • Goat Anti-Mouse
    • Goat Anti-Rabbit
    • Horse Anti-Goat
    • Horse Anti-Mouse
    • Rabbit Anti-Rat
    • Rabbit Anti-Sheep
• Kits
  • VectaStain Elite ABC kit (DAB reporter, Vector)
  • VectaStain Elite ABC kit (AP reporter, Vector)
  • Avidin / Biotin Blocking kit (Vector)
  • Peroxidase Substrate kit DAB (Vector)
• Additional Reagents
  • DAPI
  • Propidium Iodide
  • Protein Blocker
  • Sudan Black B
  • YoYo

Consultation Services

CPC Pathologists will provide consultations for Center investigators.  Each consultation will involve up to a 30-minute review of select slides, comments on the findings, and recommendations on possible interpretations and follow-up experiments.

How to Submit Samples

Please place an order using our online tissue order form here.  Specimen IDs should be unique and listed in vertical format with one ID per line

Formalin Fixed Paraffin Embedded (FFPE)

• Samples should be placed in individual histology cassettes that are labeled on the front and side with a unique Specimen ID in pencil
  • Chemical resistant marker is not recommended
  • All specimens sharing the same cassette will be embedded into the same block
  • Samples are batch processed and MPIC is not responsible for mix-ups due to duplicate identifiers between your samples and previously submitted samples, other lab members' samples, etc.  
  • Cassettes and biopsy sponges are provided free of charge and available in bay 931 for MPIC users
• Samples should be properly fixed in 10% neutral buffered formalin (NBF), rinsed in PBS, and fully submerged in a beaker of 70% ethanol labeled with “PI’s last name/Contact Name”
  • MPIC users are welcome to borrow beakers from bay 933. We will try to return your glassware, but we recommend borrowing from us
• Specialty tissue/processing:
  • Adipose tissue should be submitted in a separate beaker from other tissue types as it requires specific processing
  • Any tissue containing bone (sternum, spine, paws, etc.) should be properly decalcified prior to submission
• All beakers with samples to be processed, paraffin blocks, slides, and slide boxes can be dropped off on the MPIC labeled shelf in cold room 965
• With our standard 7 slides per sample, a large slide box can fit a maximum of 14 samples worth of slides. If providing slide boxes, please ensure a correct amount of slide boxes are dropped off to accommodate all your samples

Frozen Samples

• Frozen samples should be embedded in the center of a disposable plastic base mold, labeled with a unique Specimen ID, and fully encapsulated in OCT
• Frozen samples and slide boxes can be dropped off on the 3^rd or 4^th shelf of MPIC’s -80 C freezer across from cold room 965
  • Please do not put ice boxes or dry ice in the freezer
  • Separate slide boxes should be provided for frozen slides and stained slides

Completion

You will receive an email with pick-up instructions when your order is complete

• Our standard turnaround time is 1-3 weeks with a rush turnaround time of 7 business days for double the standard rate
• Our pick-up table is located opposite cold room 981 in the same hallway as the service elevator on the 9^th floor of BRB

Please contact an MPIC staff member if you have any questions or concerns

Molecular Pathology & Imaging Core Services are available at subsidized prices to AFCRI Members and Members of the Center for Molecular Studies in Digestive and Liver Diseases. Center Member Application (Word doc)

Visium Services and Pricing

Pricing includes the CytAssist, as well as all third-party reagents, consumables, and equipment.

$450 / run for Center and AFCRI members

$600 / run for Penn, CHOP, and other academic institutions

$800 / run for Industry

MPIC supports all steps of the workflow for H&E Visium samples up to and including the QC qPCR at the end of day 2.  The following steps involve library preparation and sequencing, and should be outsourced to a sequencing facility

Xenium Services and Pricing

MPIC offers a self-service Xenium Imager for you to conduct your own experiments on your own time. All reagents not sold by 10x Genomics will be provided by MPIC and are included in the daily fee. From now until December 31, 2023, email MPIC staff directly to schedule your Xenium run. More information regarding the launch of our Xenium booking calendar will be announced in the new year. 

Pricing:

• Processing and embedding = $7.50/sample
• Xenium Sectioning = $100/slide
• $240/day for Center and AFCRI members
• $360/day for CHOP, and Penn
• $500/day for Industry

Timeline:

• Schedule: Email MPIC staff to book your Xenium run

• Order with 10x: Place an order with 10x Genomics for your Xenium reagent kits if you haven't already

• Order with MPIC: 

       - For FFPE: we offer processing, embedding, and sectioning of your fixed samples onto your Xenium slides

       - For FF: we offer sectioning of your already OCT embedded FF tissue onto your Xenium slides

       - For paraffin embedded blocks: we offer sectioning onto your Xenium slides

• Xenium Day 1: MPIC staff will conduct Xenium training followed by benchwork 

• Xenium Day 2: Benchwork followed by the loading and running of the Xenium (2-4 days)

• Xenium Day 3 (when run is complete): Post-run cleanup, unload Xenium, collect data

• Optional post-run H&E: Email MPIC staff to book your optional post-run H&E

Reserve equipment here: Equipment Calendar

Microscopes

• Fluorescent & Brightfield
  • Nikon E600 microscopes with Brightfield, Nomarski and Fluorescent optics. Z-series and deconvolution
• Widefield Fluorescent
  • Nikon Eclipse Ti-U microscope with environmental chamber and warming plate for live-cell imaging. Capable of imaging DAPI, FITC, Cy3, Cy5, and brightfield color with an automated stage. Equipped with image stitching capabilities and Metamorph software
• Laser Capture Microdissection
  • Nikon Eclipse TE2000-S with Brightfield, Phase Contrast, Fluorescent optics and imaging
• Inverted Leica DM IRB microscope with Brightfield, Phase Contrast and Fluorescent optics
• Dissecting Microscope
  • Nikon SMZ-U dissecting microscope with imaging.
  • Nikon SMZ645 dissecting stereo microscope can be signed out
• Slide Scanner
  • Leica Aperio Slide Scanner
  • Brightfield and Fluorescent Imaging, Z-Stack capabilities
  • Images can be viewed, annotated, etc. with Leica's free software ImageScope

Spatial Biology Equipment

• Visium CytAssist
• Xenium In Situ
  • MPIC also has a C1000 Touch Thermocycler, the recommended model by 10x Genomics for their spatial biology assays

Other Equipment

• Leica BOND RXm Automatic slide stainer (IHC and IF staining)
• X-Clarity Tissue Clearing System
• Pressure Cooker
• Snap Freezer
• HybEZ II Hybridization Oven
• Cryostat Microm HM 505 E

Software

• Nikon NIS-Elements
• iVision
• Metamorph

Paraffin Sections 

• Immunofluorescence
• IHC
• Pepsin Digestion IHC
• Protease Digestion IHC
• Trypsin Digestion IHC

Frozen Sections 

• Immunofluorescence
• IHC

Staining

• H&E

Other Cores      

School of Medicine Cores

Educational Sites

Microscopy U - Extensive information about microscopy provided by Nikon
ImageJ User Guide - Helpful with learning to use ImageJ

Spectrum Viewers

Invitrogen Spectrum Viewer - Useful in determining the excitation and emission peaks of various fluorophores

Free Software

ImageJ - Imaging software provided by NIH.
Fiji - ImageJ with additional plug-ins

• Developmental Biology 8^th Edition, by Gilbert
• Mouse Development: Patterning, Morphogenesis, and Organogenesis, by Rossant and Tam
• The Anatomical Basis of Mouse Development, by Kaufman and Bard
• Under the Microscope, by Curry
• Advanced Laboratory Methods in Histology and Pathology, by Mikel
• Laboratory Methods in Histotechnology, by Prophet, Mills, Arrington, Sobin
• Techniques in Immunochemistry, by Bullock and Petrusz
• Analytical Morphology: Theory, Applications & Protocols, by Gu
• The Rat Brain, by Konig and Klippel
• Histopathological Methods and Color Atlas of Special Stains and Tissue Artifacts, by Luna
• Antibodies: A Laboratory Manual, by Lane and Harlow
• Color Atlas of Basic Histology 2^nd Edition, by Berman
• Atlas of Histology with Functional Correlations 8^th Edition, by Eroschenko
• Tumors of the Intestines - Second Series, by Fenoglio-Preiser
• Live Cell Imaging: A Laboratory Manual 2^nd Edition, by Goldman and Spector
• The Image Processing Handbook 4^th Edition, by Russ
• Fluorescence Microscopy 2^nd Edition, by Herman
• Handbook of Biological Confocal Microscopy 3^rd Edition, by Pawley
• Poly Scientific R&D Corp Reference Guide
• Fundamentals of Light Microscopy and Electronic Imaging, by Douglas B. Murphy
• Bancroft’s Theory and Practice of Histological Techniques 8^th Edition, by Suvarna, Layton, Bancroft