TITLE: TMA-TNP  Section Map and Slide Processing - Phase 1
AUTHORS: Heidi Feiler, Koei Chin

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Human Tumor Atlas Tissue MicroArrary TNP  (TMA-TNP)</div><br/><div class = "text-block">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.</div><br/><div class = "text-block">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.</div><br/><div class = "text-block">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:  </div><div class = "text-block"><a href="https://dx.doi.org/10.17504/protocols.io.bn2fmgbn" style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":;">dx.doi.org/10.17504/protocols.io.bn2fmgbn</span></a></div><br/><div class = "text-block">This protocol describes the procedure by which the OHSU OMS Atlas HTAN Center distributed TMA sections for TMA-TNP Phase 1 analysis.</div><br/><br/></div>

[STEPS]
?. [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 1.
?. [Preparation]
Each slide was labeled with a  unique OHSU Slide ID corresponding to the FFPE section map (below).  ABCDE1&nbsp;Slide ID&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Section #DescriptionInstitutionThickness (μm)2OHSU_TMA1_0000QC H&E
  PantomicsOHSU43OHSU_TMA1_0011cmIF (G3B Panel) Cyclic IFOHSU44OHSU_TMA1_0022cmIF (G3A Panel ) Cyclic IFOHSU45OHSU_TMA1_0033H&EOHSU46OHSU_TMA1_0044t-CycIF (Tumor Panel)HMS47OHSU_TMA1_0055t-CycIF (Immune Panel)HMS48OHSU_TMA1_0066 mIHC (Discovery Panel) Multiplex IHCOHSU49OHSU_TMA1_0077cmIF (G3A Panel) Cyclic IFOHSU410OHSU_TMA1_0088cmIF (G3B Panel) Cyclic IFOHSU411OHSU_TMA1_0099H&EOHSU412OHSU_TMA1_01010t-CycIF (Tumor Panel)HMS413OHSU_TMA1_01111t-CycIF (Immune Panel)HMS414OHSU_TMA1_01212 mIHC (Discovery Panel) Multiplex IHCOHSU415OHSU_TMA1_01313cmIF (reserve) Cyclic IFOHSU416OHSU_TMA1_01414cmIF (reserve) Cyclic IFOHSU4
ABCDE1&nbsp;Slide ID&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Section #DescriptionInstitutionThickness (μm)2OHSU_TMA1_0000QC H&E
  PantomicsOHSU43OHSU_TMA1_0011cmIF (G3B Panel) Cyclic IFOHSU44OHSU_TMA1_0022cmIF (G3A Panel ) Cyclic IFOHSU45OHSU_TMA1_0033H&EOHSU46OHSU_TMA1_0044t-CycIF (Tumor Panel)HMS47OHSU_TMA1_0055t-CycIF (Immune Panel)HMS48OHSU_TMA1_0066 mIHC (Discovery Panel) Multiplex IHCOHSU49OHSU_TMA1_0077cmIF (G3A Panel) Cyclic IFOHSU410OHSU_TMA1_0088cmIF (G3B Panel) Cyclic IFOHSU411OHSU_TMA1_0099H&EOHSU412OHSU_TMA1_01010t-CycIF (Tumor Panel)HMS413OHSU_TMA1_01111t-CycIF (Immune Panel)HMS414OHSU_TMA1_01212 mIHC (Discovery Panel) Multiplex IHCOHSU415OHSU_TMA1_01313cmIF (reserve) Cyclic IFOHSU416OHSU_TMA1_01414cmIF (reserve) Cyclic IFOHSU4
?. [Sectioning]
Align block on microtome to minimize tissue loss.
?. [Sectioning]
Face into block at 4μm until full section of tissue is achieved.
?. [Sectioning]
Cut adequate ribbon at 4μm to cover all serial sections.
?. [Sectioning]
Mount tissue sections onto slides to maintain serial order and orientation of sections.  Thermo Fisher Superfrost Plus slides, Ref # 6776214 were utilized.  For Phase 1, sections #0-14 were cut.
?. 
?. [Slide Processing and Shipping]
Slides are baked in a  oven  (~45-48C) for 2 hours and shipped on ice packs via FedEx to OHSU.
45 °C
?. [Slide Processing and Shipping]
Slides were shipped on ice packs by express shipping to the institutions noted in step 2 above.
?. [Slide Processing and Shipping]
At OHSU,  the slides were baked in an oven at  , and then at    for Note: Slides should be baked at  for at least 30 minutes.The  slides are stored in  a   cold room until deparaffinization or shipping.
55 °C
[(12-16 hours)]
65 °C
[(30-45 min)]
65 °C
4 °C