Below are the frequently asked questions and responses from within the Biorepository and Pathology CoRE, categorized by type of services required.
Following are questions and answers related to histology, special stains, and tissue microarray generation.
Q: How should the Investigator bring the samples to the Histology SRF group for tissue processing?
A: Samples should be brought to the Histology SRF laboratory in 4% or 10% Neutral Buffer Formalin fixative after they have been fixed in the solution for a period of approximately 24 hours.
Q: Does the Histology SRF have a form that lists pricing per service? And what kind of services do you provide?
A: Histology SRF has a digital form with an itemized list and description of all services including pricing. You can find the form on iLab or by contacting Alan Soto at extension 47582. The Histology SRF laboratory is located in Atran 6-10.
Q: How long does it take for a project to be completed by Histology SRF?
A: Generally, the turnaround time is 2 to 3 weeks after physically having received the samples (we operate on a first come, first serve basis). However, for urgent cases, the user should discuss directly with the Histology SRF personnel to accommodate deadlines.
Q: Can a project be rushed so it can be received earlier than the 2 to 3 weeks?
A: Yes, a project can be placed as Rush service which will accelerate the process and reduce the time of completion to 4 to 5 business days (when feasible) from the moment the specimen is physically received in the Histology SRF Laboratory in Atran 6-10 (Rush services are associated with an extra fee).
Q: Can a project be customized to meet specific instructions as far as processing, embedding, staining, and digital scanning?
A: Yes, all projects can be customized to meet the desired specification of the Principal Investigator. For a project to be handled as per specifications, a conversation needs to take place along with written instructions provided to the Histology SRF personnel. It is important that all custom-made projects are discussed in person and fully detailed to produce desired results for the requesting laboratory.
Q: How do we know when a project has been completed and is ready for pick-up?
A: When a project has been completed, an e-mail will be sent to the contact person provided on the Histology SRF form. There is a “Completed Projects Pick-Up Area” in the Histology SRF Lab in Atran 6-10 that is designated specifically for the research community. Each completed project is addressed by full (complete) names of the researchers who are in charge of the project. Projects can be picked up from Monday thru Friday from 8:00 AM to 6:00 PM with or without Histology SRF staff being present. When a researcher picks up the project, he/she will need to sign in a log book of “completed projects pick-up”.
Q: What is the cost of a project?
A: The cost of each project will appear once the electronic request form has been completed. As an alternative, the cost can be previously discussed with the Histology SRF personnel. If the Principal Investigator has any question regarding billing or invoices for any particular project, the SRF retains full records of the services we provide to our clients and can address any queries once they are billed at the beginning of each month. All Histology SRF projects are billed at the end of each month as per the practices of our Finance Department.
Q: Can prices be negotiated or discounts given to frequent customers?
A: As a matter of SRF policy, price discounts are not allowed. Please see Dr. Rachel Brody for any follow-up discussion.
Below we address the most frequently asked questions in immunohistochemical and immunofluorescent staining.
Q: How can the Immunostaining services help your research?
A: We facilitate immunohistochemical (IHC) as well as immunofluorescence (IF) detection in samples from human, mouse and other specimen types using commercial and in-house antibodies. The results support various biomarker and pathway analyses across multiple disease areas.
Q: What types of procedures are utilized in the Immunostaining service?
A: We offer both manual and Ventana Autostainer assay development activities. The user will decide the specific application type according to the antibody type, nature of the study and tissue type. After initial discussion, unstained sections on superfrost PLUS slides should be brought to Annenberg 24-16, between 9:00 am and 4:30 pm Monday-Friday. The tissue must be accompanied by a completed IHC service request form. If only fresh samples or paraffin blocks are available, they can be brought to the Histology SRF Lab (Atran 6-10) for sectioning along with appropriate paperwork
Q: Does the user need to provide positive control slides?
A: If The Investigator does not have their own positive control slides, the Immunostaining services can provide tissue from the Biorepository with an additional cost per slide. We will use a positive control for the characterization/titration of antibodies and in the final assay.
Q: How can the Immunostaining services help in protocol development for novel antibodies?
A: We can assist you in the development of protocols for novel antibodies. Users should meet with Dr. Rachel Brody (212-241-0678) to discuss this service. Investigator should provide the antibody, information from Western blot analyses, and both positive and negative tissue / cell line controls for analysis.
Q: Does the Immunostaining services provide the antibodies for your study?
A: We have a list of antibodies and standard protocols that have been developed for routine immunohistochemistry staining. The CoRE may provide a small aliquot for testing; however, the Investigator should provide antibodies of their interest to perform the final staining.
Q: With whom the Investigator is able to discuss the immunostaining application for their study?
A: Researchers are always welcome to discuss their study with Dr. Brody.
Q: How long will it take to complete a standard immunostaining project?
A: Generally, the turnaround time is two weeks. However, for urgent cases, the user should discuss directly with Dr.Tin Htwe Thin to accommodate deadlines.
Q: Are LMD services available?
A: Yes, the Pathology SRF is able to perform laser capture microdissection as well as provide assistance to a user to perform laser microdissection from tissue samples and cells. We also provide RNAse-free and protein-appropriate slides and sectioning capabilities for each investigator (cost of these slides is summarized in the electronic request form).
Q: Which LMD associated services are offered by the Biorepository and the Pathology CoRE?
A: We offer training, sectioning, rapid immunohistochemistry and rapid immunofluorescence staining. This includes RNase-free conditions, as well as extraction of DNA and RNA from LMD cut sections. The SRF is also able to provide a hands-free approach to LMD for all investigators upon request.
Q: What types of training do you need in order to use the LMD application?
A: There are two types of training courses that a user must complete. (1) laser safety training, which you can find on our website, and (2) demo training, which is an hour session with Biorepository and Pathology CoRE personnel who will teach how to operate the instrument as well as give you general technical advice for the preparation of a sample. There is a demo fee per hour (see electronic request form).
Q: What requirements are needed to use the LMD instrument?
A: After completing the two training courses, you must get approval from Tin Htwe Thin and send an e-mail for scheduling Whole Slide Scanning and Image Analysis
Below we respond to the most frequently asked questions concerning the Molecular DNA/RNA Extraction CoRE.
Q: How can Macromolecular pathology service help your research?
A: We are able to extract DNA/RNA from tissue or body fluids obtained in the Biorepository as well as from your own samples (i.e. fresh, snap-frozen, OCT, FFPE and, blood).
Q: Who should the Investigator contact when a service is needed?
Q: Can the Macromolecular CoRE help coordinate or design your project?
A: Yes, we can assist you in finding the best approach to ensure your project will be successful.
Q: How much DNA/RNA can you get from a sample?
A: It depends on the sample type. Human tissues usually vary in the amount of DNA/RNA which can be obtained (range: 1 to 30 µg, average: 5 to 10 µg). If the starting material is small, such as a needle biopsy, cytology specimen, decayed tissue, or stroma it may be difficult to extract more than 500 ng per sample.
Q: How is the quality of extracted DNA/RNA?
A: It depends on the sample type. FFPE DNA is sheared and FFPE RNA is generally not good (RIN: 2 or lower).
Q: How does the Molecular CoRE extract DNA/RNA?
A: We use QIAamp DNA mini kit or QIAamp DNA micro kit for tissue DNA; miRNeasy mini kit for tissue RNA; Maxwell CSC blood extraction (automated extraction) kit for blood DNA.
Q: How long does it take for a project to be completed?
A: Generally, the turnaround time is two weeks. However, for urgent cases, the user should discuss directly with Dr. Yayoi Kinoshita to accommodate deadlines.
Q: What is the cost of the macromolecular CoRE services?
Following are answers to the most frequently asked questions we receive about the Biorepository.
Q: What is the Biorepository?
A: The Biorepository is one of the CoRE services of the Pathology and Shared Research Facility (SRF) at Icahn School of Medicine at Mount Sinai. It is physically located in the Department of Pathology (Annenberg 15) and it collects surgical / procedural tissue specimens and body fluids for translational research.
Q: How does the Biorepository work?
A: The Biorepository identifies relevant surgical specimens based on project and or investigator requirements using IRB approved protocols. . When the specimen is available, the Biorepository personnel will coordinate acquisition, and after pathologist examination, the sample is released to Biorepository for processing, storage and subsequent release.
Q: How does the Biorepository store the tissue specimens?
A: The Biorepository collects the tissue specimens in formalin fixed paraffin embedded (FFPE), liquid nitrogen snap-freeze, OCT and RNA-later formats. The FFPE blocks are stored at room temperature. The snap frozen, OCT and RNA-later specimens are stored in a -80˚C freezer. Each specimen is registered in the Freezerworks database and the diagnosis / quality is confirmed histologically by Biorepository pathologists.
Q: What clinical data is provided with specimens from the Biorepository?
A: All specimens are provided with descriptive, de-identified clinical-pathology information. Specific patient data is only available with a confirmed IRB appropriate consent.
Q: How does an individual research group access the Biorepository services?
A: The PI of the research group should contact Dr. Rachel Brody with their proposal and project details.