Aug 15, 2020
605.2 URMC HTC Human Lung BioSpecimen Ontology framework 081520
- Gloria S Pryhuber1,
- Jennifer Dutra1,
- Jeanne Holden-Wiltse1
- 1University of Rochester Medical Center
- LungMap2 Consortium
- URMC Pryhuber Lab
Document Citation: Gloria S Pryhuber, Jennifer Dutra, Jeanne Holden-Wiltse 2020. 605.2 URMC HTC Human Lung BioSpecimen Ontology framework 081520. protocols.io https://dx.doi.org/10.17504/protocols.io.bi9hkh36
License: This is an open access document 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
Created: August 01, 2020
Last Modified: August 15, 2020
Document Integer ID: 39945
LungMap HTC BRINDL Human Lung Biospecimen Inventory Ontology Framework
Sample primary derivative
Sample secondary derivative
Additive/Fixation
Sub-additive/Embedding
|- Organism: Homo sapiens
| |- Sex: Male/Female
| | |- Life Stage: (age or stage (fetal (up to 42 weeks gestation, neonatal up to 30 days, infant >30 days </= 1 yr, child >1yr </=11 years, adolescent >11yrs </=20 yrs, young adult >20yrs))
| | | | - Tissue Status/Diagnosis: (Healthy, Diseased)
| | | | |- Primary Tissue/Sample Type:
Left Upper Lung (LUL)
Left Lower Lung (LLL)
Right Upper Lung (RUL)
Right Middle Lung (RML)
Right Lower Lung (RLL)
Combined Lung Lobes (CBL)
Trachea, Unspecified (TRA)
Trachea Proximal, divided to left and right (TLP and TRP)
Trachea Distal, divided to left and right (TLD and TRD)
Bronchus Left (BRL) – extra pulmonary
Bronchus Right (BRR) – extra pulmonary
Lymph node, Paratracheal (LNT)
Lymph node, Hilar (LNH)
Thymus (THY)
Nerve (NRV)
Esophagus (ESO)
Extra pulmonary Vessel non-specific (VSL)
| | | | | |- Extra Pulmonary vein (VPV)
| | | | | |- Extra Pulmonary artery (VPA)
Spleen (SPL)
Blood (BLD)
| | | | | |- Sectioned Tissue:
OCT-PBS inflated frozen (OCTI) (* “OCT” may be other similar material, such as a methylcellulose)
| | | | | |- tissue slice (SLC)
| | | | I | |- tissue strip (STR)
| | | | I I I |- tissue block (BLK)
OCT (OCT) Embedded
| | | | | | | |- tissue block (BLD)
| | | | | | | | |- tissue slide (SLD)
| | | | | | | | | |- slide with H & E stain (H&E)
Flash Frozen, without inflation (FFr)
| | | | | |- tissue biopsy (BPS)
| | | | | |- tissue slice (SLC)
| | | | I | |- tissue strip (STR)
| | | | I I I |- tissue block (BLK)
| | | | | | | | |- FFb (OCT) embedded
| | | | | | | | |- FFb (CMC) embedded
| | | | | | | | |- FFb Non-embedded
| | | | | | | | |- Extracted RNA (XPA)
| | | | | | | | |- cDNA made from RNA (CDN)
| | | | | | | | |- Protein Lysate (PTN)
| | | | | | | | |- tissue slide (SLD)
| | | | | | | | | |- slide with H & E stain (H&E)
Fresh Tissue, air inflated without fixation (FSHAI)
| | | |- lobe (LUL, etc)
| | | | | |- tissue slice (SLC)
| | | | I | |- tissue strip (STR)
| | | | I I I |- tissue block (BLK)
| | | | | | | | |- Extracted RNA (XPA)
| | | | | | | | |- cDNA made from RNA (CDN)
| | | | | | | | |- Protein Lysate (PTN)
| | | | | | | | |- tissue slide (SLD)
| | | | | | | | | |- slide with H & E stain (H&E)
4% PFA Sucrose Frozen (PFAS)
OCT (OCT)
| | | | | |- tissue slice (SLC)
| | | | I | |- tissue strip (STR)
| | | | I I I |- tissue block (BLK)
| | | | | | | | | |- slide with H & E stain (H&E)
10% Formalin inflated (FFI)
| | | | | |- tissue slice (SLC)
| | | | I | |- tissue strip (STR)
| | | | I I I |- tissue block (BLK)
70% Ethanol (EtOH)
| | | | | |- tissue slice (SLC)
| | | | I | |- tissue strip (STR)
| | | | I I I |- tissue block (BLK)
Paraffin (PAR)
| | | | | | I |- tissue block (BLK)
| | | | | | | | |- tissue slide (SLD)
| | | | | | | | | |- slide with H & E stain (H&E)
10% Formalin (FF)
| | | | | |- tissue slice (SLC)
| | | | I | |- tissue strip (STR)
| | | | I I I |- tissue block (BLK)
70% Ethanol (EtOH)
| | | | | |- tissue slice (SLC)
| | | | I | |- tissue strip (STR)
| | | | I I I |- tissue block (BLK)
Paraffin (PAR)
| | | | | | I |- tissue block (BLK)
| | | | | | | | |- tissue slide (SLD)
| | | | | | | | | |- slide with H & E stain (H&E)
4% PFA inflated (PFAI)
| | | | | |- tissue slice (SLC)
| | | | I | |- tissue strip (STR)
| | | | I I I |- tissue block (BLK)
OCT (OCT)
| | | | | |- tissue slice (SLC)
| | | | I | |- tissue strip (STR)
| | | | I I I |- tissue block (BLK)
| | | | | | | | | |- slide with H & E stain (H&E)
4% PFA inflated sucrose (PFAIS)
| | | | | |- tissue slice (SLC)
| | | | I | |- tissue strip (STR)
| | | | I I I |- tissue block (BLK)
OCT (OCT)
| | | | |- tissue slice (SLC)
| | | | I | |- tissue strip (STR)
| | | | I I I |- tissue block (BLK)
| | | | | | | | | |- slide with H & E stain (H&E)
Agarose inflated (AGAI)
| | | | | |- tissue slice (SLC)
| | | | I | |- tissue strip (STR)
| | | | I I I |- tissue block (BLK)
| | | | I I I | |- Flash Frozen (FFr)
| | | | I I I | |- 10% Formalin (FORM)
| | | | I I I | |- 70% Ethanol (EtOH)
| | | | I I I | |- Paraffin (PAR)
| | | | | | | | | |- tissue slide (SLD)
| | | | | | | | | | |- slide with H & E stain (H&E)
| | | | I I I | |- 4% PFA Sucrose Frozen (PFAS)
| | | | I I I | | |- OCT Embedded (OCT)
| | | | | | | | | |- tissue slide (SLD)
| | | | | | | | | | |- slide with H & E stain (H&E)
| | | | I I I | | |- CMC Embedded (CMC)
| | | | | | | | | |- tissue slide (SLD)
| | | | | | | | | | |- slide with H & E stain (H&E)
| | | | | |- Dissociated Tissue Cells: (by enzymatic digestion with 1) Collagenase/Dnase I (C) or 2) Collagenase/Dnase I/Dispase II (CD) or 3) Collagenase/Dnase I /DispaseII/ Elastase (CDE) )
FBS DMSO (subadditive)
Possible sub-additives 1) Ammonium Bicarbonate or 2) Phosphatase Inhibitor cocktail
| | | | | |-Mixed lung tissue originating cells (MIX)
| | | | | | |- Mixed/unfractionated bone marrow derived immune cells (MIC): 7AAD+/singlets/CD45+
| | | | | | | |- CD4+ T cells (CD4): 7AAD-/singlets/CD14-/CD235a-/CD3+/CD4+/CD8-
| | | | | | | |- CD8+ T cells (CD8): 7AAD-/singlets/CD14-/CD235a-/CD3+/CD4-/CD8+
| | | | | | | |- B cells (BCL): 7AAD-/CD14-/singlets/CD235a-/CD3-/CD19+/CD56-
| | | | | | | |- NK cells (NKC): 7AAD-/singlets/CD14-/CD235a-/CD3-/CD19-/CD56+
| | | | | | | |- Macrophages (MCL): 7AAD-/singlets/CD235a-/CD14+
| | | | | | |- Epithelial cells (EPI) CD235a-/ 7-AAD-/CD45-/EpCAM+
| | | | | | | |- Type I epithelial cells (EP1) CD235a-/ 7-AAD-/CD45-/VE-Cadherin-/PECAM-/EpCam+/T1alpha+
| | | | | | | |- Mixture Type II and airway epithelial cells (EP2) CD235a-/ 7-AAD-/CD45-/VE-Cadherin-/PECAM-EpCam+/T1alpha-
| | | | | | |- Endothelial cells (END): CD235a-/ 7-AAD-/CD45-/VE-Cadherin+/PECAM+
| | | | | | |- Lymphatic cells (LYM): CD235a-/ 7-AAD-/CD45-/VE-Cadherin-/PECAM-/EpCam-/T1alpha+
| | | | | | |- Mesenchymal cells unspecified (MES): CD235a-/ 7-AAD-/CD45-/VE-Cadherin-/PECAM-/EpCam-/T1alpha-
| | | | | | | |- Mesenchymal fibroblast cells (MFI): CD235a-/ 7-AAD-/CD45-/VE-Cadherin-/PECAM-/EpCam-/T1alpha-/CD105-
| | | | | | | |- Mesenchymal stromal cells (MSC): CD235a-/ 7-AAD-/CD45-/VE-Cadherin-/PECAM-/EpCam-/T1alpha-CD105+/CD90+
| | | | | | |- Dissociated Tissue Cells Sub-derivatives: (following derivatives can be made from above dissociated cell populations):
| | | | | | |- Cytospin slide (SLS)
| | | | | | |- Extracted RNA (XPA)
| | | | | | |- cDNA made from RNA (CDN)
| | | | | | |- Protein taken from lysed cell pellet (PTN)
| | | | | | |- CD105+ (CD105)
| | | | |- Primary Sample Blood (BLD)
Heparin (HEP) or double dose of heparin (DHP)
| | | | | |- Serum (SER)
| | | | | |- Plasma (PL1)
| | | | | |- PBMC (CEL)
| | | | | | |- CD45+ mixed/unfractionated immune cells (MIC): 7AAD+/singlets/CD45+
| | | | | | | |- CD4+ T cells (CD4): 7AAD-/singlets/CD14-/CD235a-/CD3+/CD4+/CD8-
| | | | | | | |- CD8+ T cells (CD8): 7AAD-/singlets/CD14-/CD235a-/CD3+/CD4-/CD8+
| | | | | | | |- B cells (BCL): 7AAD-/CD14-/singlets/CD235a-/CD3-/CD19+/CD56-
| | | | | | | |- NK cells (NKC): 7AAD-/singlets/CD14-/CD235a-/CD3-/CD19-/CD56+
| | | | | | | |- Macrophages (MCL): 7AAD-/singlets/CD235a-/CD14+
| | | | | |- Nucleic Extraction Sub-derivatives: (following derivatives can be made from above PBMC cell populations):
| | | | | |- Extracted DNA (XDA)
| | | | | |- Extracted RNA (XPA)
| | | | | |- Extracted total nucleic acid (XTN)
| | | | | | |- Extracted pellet from DNA PCR for sequencing (XPD)
| | | | | | |- Extracted pellet from RNA RT PCR for sequencing (XPR)
| | | | | | |- Extracted pellet fluid from RNA RT PCR for sequencing (XFL)
| | | | | | | |- cDNA made from RNA (CDN)
| | | | | | | |- Protein taken from lysed cell pellet (PTN)