Policies
Patient samples
Prior to transferring specimens to the LSP Tissue Profiling Service (TPS), Clinical Research Coordinator (CRC) Crystal Chiu will confirm that all necessary IRBs, Material Transfer Agreements, and General Data Protection Regulation compliance are in place. All tissue samples must be de-identified prior to onboarding by the CRC. All de-identified samples are catalogued in our internal Experiment Tracker database, along with detailed staining plans.
Do NOT section samples until first reading about our sample standards. We will refuse samples which do not adhere to these guidelines.
Deliverables
CyCIF and OrionTM Imaging
TPS scientists will work with collaborators to understand the project scope and unique needs followed by development of an appropriate experimental plan. Staff will perform slide preparation, imaging, and will use our MCMICRO analysis pipeline to perform downstream image stitching, segmentation, and quantification, delivering raw image data (.rcpnl), stitched images (.ome-tif), and feature tables (.csv) to service users.
Note that processing data via MCMICRO does not in and of itself generate scientific results and discoveries. Collaborators will need to combine careful inspection of images with quantitative analysis of single cell data to arrive at an understanding of the images and the biology they reveal.
GeoMx DSP
In order to maximize the value of each experiment, TPS scientists will work with collaborators to understand their unique goals and tissue types. Staff will probe samples with the Nanostring Whole transcriptome atlas RNA probe set, and work together with you to define regions of interest for transcript collection. Once the transcript information has been sequenced, we will perform quality control of the data before handoff for deep analysis. Deliverables include an image file (ome.tif) of the tissue stained with fluorescent morphology markers, and a matrix of transcript count values of each area of interest collected. Users may also be granted access to our GeoMx DSP analysis server which provides a graphic user interface to the data, though traditional single cell analysis techniques are applicable to this data type as well.
Data management
Please note that data may be very large. In particular, stitched CyCIF image files may be up to 1Tb in size. The LSP TPS does not have space or funding to maintain large datasets for more than a short time. Individual research groups retain the responsibility for long-term data management and deposition and will be expected to transfer data to their own spaces using Harvard Medical School’s Globus Connect file transfer platform within one year of experiment completion unless an extended timeline has been approved.
Acknowledgments/Publications
If the support provided by TSP staff meets the generally accepted criteria for academic collaborations, then that TPS staff member should be considered for authorship on the publication. Regardless of the type of support, we request acknowledgement in all publications and presentations. Proper acknowledgment of our facility enables us to obtain financial and other support so we may continue to provide essential services. Please send a link of newly published work to the TPS Director.
If rates are subsidized, please talk with the TPS Director to determine how to appropriately acknowledge funding sources.