Translational Pathology Shared Resource

Note: Slide-Scanner Upgrade: TPSR has replaced its 5-slide Leica Aperio CS2 with a 1,000-slide 3DHISTECH Pannoramic P1000 at no added cost to users. For SKCCC members, standard 20× scans are $5 per slide, falling to $4.75 (101–200 slides), $4.50 (201–300), $4.25 (301–400), and $4.00 (401+). High-resolution 40× scans are $10 per slide with the same discount tiers: $9.50, $9.00, $8.50, and $8.00.

Note: Immunohistochemistry Service Upgrade: New Ventana Discover Ultra Autostainer: TPSR has replaced the Biocare autostainer with the Ventana Discovery system, delivering sharper signals and lower background via polymer‑based amplification (see Fig. 1). A service cost increase from $31 to $34 per slide (SKCCC members) has been implemented to cover higher reagent expenses. This upgrade was funded by Dr. Haifeng Yang’s S10 grant, which many Jefferson and Drexel faculty members graciously supported.

Note: Longer turn-around times: We are working to fill the Research Assistant position vacated by the promotion of Natalie Dougherty, MS, to Manager. Our turn-around times will likely remain longer than usual until that position is filled and the new hire is trained. Thank you for your patience.

 

TPSR Sample Drop-Off and Pick-Up Procedures: 

For routine requests submitted through iLab, walk-in drop-offs/pick-ups are welcome during our work hours (Mon-Fri, 8:30 am to 4:30 pm). 

For consultation requests, please contact the Shared Resource (Tel: 215-503-3858/215-503-8826 or Email natalie.dougherty@jefferson.edu) to schedule an appointment. 

When dropping off:

• Please label the sample container(s)/package with the request ID and the client's name.
• Please print a hard copy of your request sheet and submit it with the other materials.
• Please talk to one of our staff when dropping off samples so we can check the samples and request details, safely store/secure the submitted materials, and verify and update your request status.

NEVER drop off samples without communicating with our staff. Un-notified materials might jeopardize the research request/project.

 

About us:

The Translational Pathology Shared Resource provides a full range, state-of-the-art, detail-orientated, outstanding array of experimental histopathology services complemented by molecular pathology and digital pathology services to SKCC members, TJU, and the local research community in the greater Philadelphia area. In collaboration with our internal labs at TJU, we also facilitate the interactions between investigators and the SKCC Biorepository and Pathology Department to access human tissue samples and perform Laser Capture Microdissection of tissues to capture individual cells. Over one hundred principal investigators use the Translational Pathology Shared Resource, and the core has provided vital data that support many publications and grant applications.

Our Instruments

 

Work Offered

1. Full range of experimental histopathology services including paraffin and frozen tissue processing, slide preparation, histochemical staining (H&E and Special Stains)

2. Immunohistochemistry (IHC) staining is performed on paraffin sections, frozen tissue, or cytological preparations. It utilizes a broad range of optimized commercial antibodies or antibodies provided by the investigator with an automatic staining platform (Biocare Medical IntelliPATH FLX®).

3. TUNEL 

4. Bright-field whole slide scanning (20X and 40X) with Aperio CS2 ScanScope. Link to our Image server: SKCC TPSR eSlideManager Server Link

Procedures to Utilize This Shared Resource:

For all first-time users, please watch iLab user tutorials videos.

The procedures are:

1. PI and lab members planning to use SKCC shared resources under iLab must register in the iLab system.

2. Internal users will use their Jefferson campus credentials to log in after registering.

3. External users can generate their username and password. The PI should register first so their lab members can register under the PI’s lab.

4. Both internal and external PIs need to review and accept/approve the lab member’s membership request in the iLab system before the lab member can join and utilize the iLab portal.

See instruction: How to manage membership request and charge codes (for PI) 

See iLab registration link: https://skcc-pa.ilabsolutions.com/landing/2792

5. For internal users, PI needs to set up payment information with our IT expert Ryan Smalley (Tel: 3-9692, Email: Ryan.Smalley@jefferson.edu) after registration. 

6. For external users, please generate a PO (Purchase Order) before submitting the request to us.

    No request will go through the iLab system to us without payment information.

7. For internal users, PI needs to assign a charge code to their lab members to allow them to access the charge code. See instructions How to manage membership request and charge codes (for PI)

8. After PI assigns the charge code, the lab member can submit a request to us in the iLab portal under the Request Service tab. 

a. When filling out the 'Describe Work Requested in FULL DETAIL', please include at a minimum the following information, and consider adding other essential relevant information:

• Description of the Submitted Materials: such as species, organ/tissue type, fixative type and duration, current solution samples are stored in, etc.;
• Trimming/Grossing and any Special Handling Requirements;
• Processing and Embedding Requirement: such as oversized tissues need a longer program to process, special embedding and sectioning orientation, etc.;
• Sectioning Requirement: number of slides/sample, number of sections/slides, the thickness of the section (our default thickness is 4 µm; cut into different levels, etc.;
• Staining Requirement: Routine H&E, special stain, IHC, ISH, TUNEL, Multiplex staining, etc.;
• Digital Scanning Requirement: 20X or 40X, attach sample information collection form if available;
• Any additional requirements were not mentioned above.

b. Enter the sample "label” in the request form:

• The label will show up on your slides. Please ensure the labels on the request form match the cassette labels.
• Type in the material type or select from the drop-down menu. If the material type is the same, drag to fill in the rest of the area. This form operates similarly to an Excel worksheet.

c. Enter the Charge Code or Purchase Order under payment information.

d. Check all information entered above to make sure it is correct.

e. If you are ready, click the Submit button to submit the request to this shared resource. Otherwise, click "save a draft of the form" at the end of "Forms and Request Details" to save it under your account.

f. Use the printer icon"" under "Forms and Request Details" to download a PDF file and print it out.

g. Please submit the request sheet together with the samples to us.

9. For Training/Consultation Requests, Frozen Requests, and IHC/ISH Requests, please always call 215-503-3858/8826 or email us to schedule an appointment before submitting the samples/request to this shared resource.

10. No appointment is needed to submit samples for routine paraffin processing or blocks. 

11. We will review, update, and confirm the request details with users and process the request once we receive the hard copy of the request sheet and all related materials.

12. Once we complete the request and update the request status to "completed," an automatic email (from no-reply@ilabsolutions.com titled "NOTIFICATION: XXXX The Service request TR/PSR-XX-XXXX has been completed") will be sent to you. This means you can come and pick up your completed work during our work hours; no appointment is needed unless there are temperature- or time-sensitive materials involved.

Leadership

Hallgeir Rui, MD, PhD | Director

Haifeng Yang, PhD | Co-Director

Natalie Dougherty, MS | Laboratory Manager

Hours of Operation, Location and Telephone

Hours:  8:30 AM - 4:30 PM Monday - Friday except Holidays	Address:  233 S. 10th Street Room 815, Bluemle Life Sciences Building        Philadelphia, PA 19107
Telephone: 215-503-3858/8826/2237

Useful Links and Resources

1. iLab user tutorials videos

2. How to manage membership request and charge codes(for PI)

3. SKCC Translational Research Shared Resource - List of Services & Price Schedule

4. Sidney Kimmel Cancer Center Shared Resources

5. Sample preparation instruction for paraffin embedding

6. Sample preparation instruction for frozen embedding

7. Preparing Gel Block from Cell Lines or Cell Suspensions

8. Aperio eSlideManager Server

9. Policy for Aperio CS2 Digital Slide Scanning and Access of the eSlide Manager

10. Aperio eSlide Manager User Account Request Form 

11. Aperio CS2 Digital Image Scanning Sample Information Collection Form

12. Aperio eSlideManager Operator Guide

13. Aperio ImageScope User Guide

14. Aperio WebScope User Guide

15. Revised guides for organ sampling and trimming in rats and mice: Parts 1 – 3(A joint publication of the RITA and NACAD groups)

16. The Internet Pathology Laboratory for Medical Education (Hosted By University of Utah Eccles Health Sciences Library)

17. The Human Protein Atlas

18. Sidney Kimmel Cancer Center

Contacts

Name	Role	Phone	Email	Location
Hallgeir Rui, MD, PhD	Director	(215) 503-9881	hallgeir.rui@jefferson.edu	Bluemle Life Sciences Building, Rm 1008
Haifeng Yang, PhD	Co-Director	(215) 503-6163	haifeng.yang@jefferson.edu	Jefferson Alumni Hall, 336D
Natalie Dougherty, MS	Manager	(215) 503-3858/8826/2237	natalie.dougherty@jefferson.edu	Bluemle Life Sciences Building, Rm 815
Ruiyan Jing, BA	Research Assistant Senior	(215) 503-3858/8826/2237	ruiyan.jing@jefferson.edu	Bluemle Life Sciences Building, Rm 815
Naheed Perez, MS	Research Assistant Intermediate	(215) 503-3858	naheed.perez@jefferson.edu	Bluemle Life Sciences Building, Rm 1008
Linna Ge	Lab Specialist		linna.ge@jefferson.edu	Bluemle Life Sciences Building, Rm 815
Yunguang Sun, MD, PhD	Digital Pathology		yunguang.sun@jefferson.edu	Bluemle Life Sciences Building, Rm 1020

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