Feb 15, 2023
Version 1
TMA-TNP Section Map and Slide Processing - Phase 4 V.1
Forked from a private protocol
- Heidi S Feiler1,2
- 1Oregon Health & Science University (OHSU), Portland, OR [Department of Biomedical Engineering];
- 2Oregon Health & Science University (OHSU) [Knight Cancer Institute]
- NCIHTAN
Protocol Citation: Heidi S Feiler 2023. TMA-TNP Section Map and Slide Processing - Phase 4. protocols.io https://dx.doi.org/10.17504/protocols.io.ewov1o7wolr2/v1
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: February 15, 2023
Last Modified: February 15, 2023
Protocol Integer ID: 77069
Keywords: biospecimen, FFPE, tissue processing, spatial mapping, TMA, Nanostring GeoMx, DSP, human tumor atlas tissue microarrary tnp, breast tumor tma, breast tumor sample, tma section, anonymized breast tumor tma, tma sections for phase, tma design, custom tma design, tissue microarray, pantomics for custom tma ffpe block generation, custom tma design for this project, tma, custom tma ffpe block generation, basic clinical data, clinical sample description, tnp characterization
Funders Acknowledgements:
NCI Human Tumor Atlas Network
Grant ID: U2C CA233280
Abstract
Human Tumor Atlas Tissue MicroArrary TNP (TMA-TNP)
The Tissue MicroArray (TMA) TNP will extend the SARDANA-TNP characterization and analytics methodologies for evaluation and validation on a large array of breast tumor samples that provide a broad spectrum of disease state and subtype. A commercially available anonymized breast tumor TMA was purchased and sections distributed to participating HTAN Centers. Some deidentified basic clinical data will also be provided. The participating HTAN Centers will characterize the FFPE specimens (e.g. by imaging) and generate a spatially resolved cell type/state census using each Center’s method of choice. Data will then be recorded in a common repository to enable joint analysis.
This TNP has two specific Aims focused on (i) Data Collection and (ii) Data Coordination and Analysis. Individual Centers can participate in one or both aims.
The custom TMA design for this project was generated by Dr. Koei Chin (OHSU) and sent to Pantomics for custom TMA FFPE block generation and sectioning. The TMA design and clinical sample descriptions can be found here:
This protocol describes the procedure by which the OHSU OMS Atlas HTAN Center sectioned and distributed TMA sections for Phase 4 analysis.
Materials
MATERIALS
Thermo Fisher Superfrost Plus microscope slides: Catalog No.12-550-15
Troubleshooting
Preparation
Verify the identity of the FFPE block to be cut against written request for sectioning. The FFPE block (TMA1) will be utilized for TMA-TNP Phase 4.
Each slide was labeled with a unique OHSU Slide ID corresponding to the FFPE section map (below).
| A | B | C | D | E | |
| Slide Label Name | Slide # | Description | Institution | Thickness (μm) | |
| OHSU_TMA1_037 | 37 | GeoMx DSP Assay (Nanostring) protein ½ TMA (top 4 rows) | OHSU | 5 | |
| OHSU_TMA1_038 | 38 | GeoMx DSP Assay (Nanostring) WTA ½ TMA (top 4 rows) | OHSU | 5 | |
| OHSU_TMA1_039 | 39 | GeoMx DSP Assay (Nanostring) protein ½ TMA (bottom 4 rows) | OHSU | 5 | |
| OHSU_TMA1_040 | 40 | missing - bad section - Pantomics did not send to OHSU | 5 | ||
| OHSU_TMA1_041 | 41 | GeoMx DSP Assay (Nanostring) WTA ½ TMA (bottom 4 rows) | OHSU | 5 |
Sectioning
Align block on microtome to minimize tissue loss.
Face into block at 5μm until full section of tissue is achieved.
Cut adequate ribbon at 5μm to cover all serial sections.
Mount tissue sections onto ThermoFisher Superfrost Plus slides to maintain serial order and orientation of sections. Sections for Nanostring must be placed in a shifted orientation to capture the cores of interest (2 sections/slides to be combined for full representation of TMA1).
Slide Processing and Shipping
12h 30m
All Slides are immediately baked in a 45 °C oven (~45-48C) for 2 hours prior to distribution.
In the lab, the slides are baked in an oven at 55 °C Overnight (12-16 hours) (except for #30-33 for Nanostring) , and then at 65 °C for 00:30:00 (30-45 min)
Note: Slides should be baked at 65 °C for at least 30 minutes.
The slides are stored in a 4 °C cold room until deparaffinization or shipping.
12h 30m
Slides were shipped on 4 °C ice packs by express shipping per the FFPE spatial map noted above.