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Merge pull request #141 from zivy/harmonizeLYVE1Spelling
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Harmonizing the naming of LYVE1 vs. LYVE-1.
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zivy authored Apr 29, 2024
2 parents e6978d2 + bcc0801 commit 09e0ebc
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26 changes: 13 additions & 13 deletions data/reagent_resources.csv
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4 changes: 2 additions & 2 deletions ...terial/LYVE1_AF532/0000-0003-4379-8967.md → ...erial/LYVE-1_AF532/0000-0003-4379-8967.md
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| UniProt Accession Number | Reagent Type | Target Name / Protein Biomarker | Target Species | Host Organism | Isotype | Clonality | Vendor | Catalog Number | Conjugate | RRID | Availability | Method | Tissue Preservation | Target Tissue | Tissue State | Detergent | Antigen Retrieval Conditions | Dye Inactivation Conditions | Recommend | Agree | Disagree | Contributor | Notes |
|:---------------------------|:-----------------|:----------------------------------|:-----------------|:----------------|:----------|:------------|:------------|:----------------------|:------------|:-----------|:---------------|:--------------|:----------------------------------|:----------------|:--------------------|:------------------|:-------------------------------|:------------------------------|:------------|:-------------------------------------------------------------|:-----------|:--------------------|:------------|
| Q9Y5Y7 | Primary Antibody | LYVE1 | Human | Goat | IgG | Polyclonal | R&D Systems | AF2089 (Unconjugated) | AF532 | AB_2892756 | Custom | IBEX2D Manual | 1:4 Cytofix/Cytoperm Fixed Frozen | Lymph Node | NA | 0.3% Triton-X-100 | NA | 1 mg/ml LiBH4 15 minutes | Yes | [0000-0003-4379-8967](https://orcid.org/0000-0003-4379-8967) [[3](#publications), [1](#publications)] | NA | [0000-0003-4379-8967](https://orcid.org/0000-0003-4379-8967) | [1](#notes) |
| Q9Y5Y7 | Primary Antibody | LYVE1 | Human | Goat | IgG | Polyclonal | R&D Systems | AF2089 (Unconjugated) | AF532 | AB_2892756 | Custom | IBEX2D Manual | 1:4 Cytofix/Cytoperm Fixed Frozen | Lymph Node | Follicular Lymphoma | 0.3% Triton-X-100 | NA | 1 mg/ml LiBH4 15 minutes | Yes | [0000-0003-4379-8967](https://orcid.org/0000-0003-4379-8967) [[2](#publications)] | NA | [0000-0003-4379-8967](https://orcid.org/0000-0003-4379-8967) | [1](#notes) |
| Q9Y5Y7 | Primary Antibody | LYVE-1 | Human | Goat | IgG | Polyclonal | R&D Systems | AF2089 (Unconjugated) | AF532 | AB_2892756 | Custom | IBEX2D Manual | 1:4 Cytofix/Cytoperm Fixed Frozen | Lymph Node | NA | 0.3% Triton-X-100 | NA | 1 mg/ml LiBH4 15 minutes | Yes | [0000-0003-4379-8967](https://orcid.org/0000-0003-4379-8967) [[3](#publications), [1](#publications)] | NA | [0000-0003-4379-8967](https://orcid.org/0000-0003-4379-8967) | [1](#notes) |
| Q9Y5Y7 | Primary Antibody | LYVE-1 | Human | Goat | IgG | Polyclonal | R&D Systems | AF2089 (Unconjugated) | AF532 | AB_2892756 | Custom | IBEX2D Manual | 1:4 Cytofix/Cytoperm Fixed Frozen | Lymph Node | Follicular Lymphoma | 0.3% Triton-X-100 | NA | 1 mg/ml LiBH4 15 minutes | Yes | [0000-0003-4379-8967](https://orcid.org/0000-0003-4379-8967) [[2](#publications)] | NA | [0000-0003-4379-8967](https://orcid.org/0000-0003-4379-8967) | [1](#notes) |

# Publications

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0 ...LYVE1_RD_AF2089_Desmin_Abcam_Ab185033.jpg → ...LYVE1_RD_AF2089_Desmin_Abcam_Ab185033.jpg
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2 changes: 1 addition & 1 deletion ...LYVE1_Unconjugated/0000-0001-9561-4256.md → ...YVE-1_Unconjugated/0000-0001-9561-4256.md
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| UniProt Accession Number | Reagent Type | Target Name / Protein Biomarker | Target Species | Host Organism | Isotype | Clonality | Vendor | Catalog Number | Conjugate | RRID | Availability | Method | Tissue Preservation | Target Tissue | Tissue State | Detergent | Antigen Retrieval Conditions | Dye Inactivation Conditions | Recommend | Agree | Disagree | Contributor | Notes |
|:---------------------------|:-----------------|:----------------------------------|:-----------------|:----------------|:----------|:------------|:------------|:-----------------|:-------------|:----------|:---------------|:-----------------------|:----------------------|:----------------|:---------------|:------------------|:-------------------------------------------------------------------|:------------------------------|:------------|:----------------------------------------------------------------------------------|:-----------|:-------------------------------------------------------------|:------------|
| F7AVS7 | Primary Antibody | LYVE1 | Rhesus Macaque | Goat | IgG | Polyclonal | R&D Systems | AF2089 | Unconjugated | AB_355144 | Stock | Multiplexed 2D Imaging | FFPE | Lymph Node | Infected | 0.3% Triton-X-100 | pH 9.5 for 15 minutes in a pressure cooker (Borg Decloaker BD1000) | NA | Yes | [0000-0001-9561-4256](https://orcid.org/0000-0001-9561-4256) [[1](#publications)] | NA | [0000-0001-9561-4256](https://orcid.org/0000-0001-9561-4256) | [1](#notes) |
| F7AVS7 | Primary Antibody | LYVE-1 | Rhesus Macaque | Goat | IgG | Polyclonal | R&D Systems | AF2089 | Unconjugated | AB_355144 | Stock | Multiplexed 2D Imaging | FFPE | Lymph Node | Infected | 0.3% Triton-X-100 | pH 9.5 for 15 minutes in a pressure cooker (Borg Decloaker BD1000) | NA | Yes | [0000-0001-9561-4256](https://orcid.org/0000-0001-9561-4256) [[1](#publications)] | NA | [0000-0001-9561-4256](https://orcid.org/0000-0001-9561-4256) | [1](#notes) |

# Publications

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2 changes: 1 addition & 1 deletion ...LYVE1_Unconjugated/0000-0003-0666-4804.md → ...YVE-1_Unconjugated/0000-0003-0666-4804.md
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| UniProt Accession Number | Reagent Type | Target Name / Protein Biomarker | Target Species | Host Organism | Isotype | Clonality | Vendor | Catalog Number | Conjugate | RRID | Availability | Method | Tissue Preservation | Target Tissue | Tissue State | Detergent | Antigen Retrieval Conditions | Dye Inactivation Conditions | Recommend | Agree | Disagree | Contributor | Notes |
|:---------------------------|:-----------------|:----------------------------------|:-----------------|:----------------|:----------|:------------|:--------------------------|-----------------:|:-------------|:-------|:---------------|:----------|:------------------------|:----------------|:---------------|:-----------------------|:-------------------------------|:------------------------------|:------------|:--------------------|:-----------|:--------------------|:--------|
| Q8BHC0 | Primary Antibody | LYVE1 | Mouse | Rabbit | IgG | E3L3V | Cell Signaling Technology | 67538 | Unconjugated | NA | Stock | Opal-plex | 10% Formalin for 7 Days | Lymph Node | Infected | Akoya Antibody Diluent | Akoya AR6 | NA | Yes | [0000-0003-0666-4804](https://orcid.org/0000-0003-0666-4804) | NA | [0000-0003-0666-4804](https://orcid.org/0000-0003-0666-4804) | |
| Q8BHC0 | Primary Antibody | LYVE-1 | Mouse | Rabbit | IgG | E3L3V | Cell Signaling Technology | 67538 | Unconjugated | NA | Stock | Opal-plex | 10% Formalin for 7 Days | Lymph Node | Infected | Akoya Antibody Diluent | Akoya AR6 | NA | Yes | [0000-0003-0666-4804](https://orcid.org/0000-0003-0666-4804) | NA | [0000-0003-0666-4804](https://orcid.org/0000-0003-0666-4804) | |

# Publications

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20 changes: 16 additions & 4 deletions docs/supporting_material/LYVE-1_Unconjugated/0000-0003-4379-8967.md
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# Configurations

| UniProt Accession Number | Reagent Type | Target Name / Protein Biomarker | Target Species | Host Organism | Isotype | Clonality | Vendor | Catalog Number | Conjugate | RRID | Availability | Method | Tissue Preservation | Target Tissue | Tissue State | Detergent | Antigen Retrieval Conditions | Dye Inactivation Conditions | Recommend | Agree | Disagree | Contributor | Notes |
|:---------------------------|:-----------------|:----------------------------------|:-----------------|:----------------|:----------|:------------|:------------|:-----------------|:-------------|:----------|:---------------|:-----------------------|:----------------------|:----------------|:--------------------|:------------------|:-------------------------------------------------------------------------------------------|:------------------------------|:------------|:-------------------------------------------------------------|:-----------|:-------------------------------------------------------------|:------------|
| Q9Y5Y7 | Primary Antibody | LYVE-1 | Human | Goat | IgG | Polyclonal | R&D Systems | AF2089 | Unconjugated | AB_355144 | Stock | Multiplexed 2D Imaging | FFPE | Lymph Node | Follicular Lymphoma | 0.3% Triton-X-100 | pH 6 for 30 minutes ER1 (AR9961) and pH 9 for 30 minutes ER2 (AR9640) using the Leica Bond | NA | Yes | [0000-0003-4379-8967](https://orcid.org/0000-0003-4379-8967) | NA | [0000-0003-4379-8967](https://orcid.org/0000-0003-4379-8967) | [1](#notes) |
| UniProt Accession Number | Reagent Type | Target Name / Protein Biomarker | Target Species | Host Organism | Isotype | Clonality | Vendor | Catalog Number | Conjugate | RRID | Availability | Method | Tissue Preservation | Target Tissue | Tissue State | Detergent | Antigen Retrieval Conditions | Dye Inactivation Conditions | Recommend | Agree | Disagree | Contributor | Notes |
|:---------------------------|:-----------------|:----------------------------------|:-----------------|:----------------|:----------|:------------|:------------|:-----------------|:-------------|:----------|:---------------|:-----------------------|:----------------------------------|:----------------|:--------------------|:------------------|:-------------------------------------------------------------------------------------------|:------------------------------|:------------|:-------------------------------------------------------------|:-----------|:--------------------|:------------|
| Q9Y5Y7 | Primary Antibody | LYVE-1 | Human | Goat | IgG | Polyclonal | R&D Systems | AF2089 | Unconjugated | AB_355144 | Stock | IBEX2D Automated | 1:4 Cytofix/Cytoperm Fixed Frozen | Jejunum | NA | 0.3% Triton-X-100 | NA | NA | Yes | [0000-0003-4379-8967](https://orcid.org/0000-0003-4379-8967) [[1](#publications)] | NA | [0000-0003-4379-8967](https://orcid.org/0000-0003-4379-8967) | |
| Q9Y5Y7 | Primary Antibody | LYVE-1 | Human | Goat | IgG | Polyclonal | R&D Systems | AF2089 | Unconjugated | AB_355144 | Stock | IBEX2D Manual | 1:4 Cytofix/Cytoperm Fixed Frozen | Liver | NA | 0.3% Triton-X-100 | NA | NA | Yes | [0000-0003-4379-8967](https://orcid.org/0000-0003-4379-8967) [[2](#publications), [1](#publications)] | NA | [0000-0003-4379-8967](https://orcid.org/0000-0003-4379-8967) | |
| Q9Y5Y7 | Primary Antibody | LYVE-1 | Human | Goat | IgG | Polyclonal | R&D Systems | AF2089 | Unconjugated | AB_355144 | Stock | IBEX2D Automated | 1:4 Cytofix/Cytoperm Fixed Frozen | Lymph Node | NA | 0.3% Triton-X-100 | NA | NA | Yes | [0000-0003-4379-8967](https://orcid.org/0000-0003-4379-8967) [[1](#publications)] | NA | [0000-0003-4379-8967](https://orcid.org/0000-0003-4379-8967) | |
| Q9Y5Y7 | Primary Antibody | LYVE-1 | Human | Goat | IgG | Polyclonal | R&D Systems | AF2089 | Unconjugated | AB_355144 | Stock | Multiplexed 2D Imaging | FFPE | Lymph Node | Follicular Lymphoma | 0.3% Triton-X-100 | pH 6 for 30 minutes ER1 (AR9961) and pH 9 for 30 minutes ER2 (AR9640) using the Leica Bond | NA | Yes | [0000-0003-4379-8967](https://orcid.org/0000-0003-4379-8967) | NA | [0000-0003-4379-8967](https://orcid.org/0000-0003-4379-8967) | [1](#notes) |
| Q9Y5Y7 | Primary Antibody | LYVE-1 | Human | Goat | IgG | Polyclonal | R&D Systems | AF2089 | Unconjugated | AB_355144 | Stock | Multiplexed 2D Imaging | FFPE | Lymph Node | Follicular Lymphoma | 0.3% Triton-X-100 | pH 6 for 30 minutes ER1 (AR9961) and pH 9 for 30 minutes ER2 (AR9640) using the Leica Bond | NA | Yes | [0000-0003-4379-8967](https://orcid.org/0000-0003-4379-8967) | NA | [0000-0003-4379-8967](https://orcid.org/0000-0003-4379-8967) | [2](#notes) |

# Publications

<a name="publications"></a>
1. A. J. Radtke et al., "IBEX: an iterative immunolabeling and chemical bleaching
method for high-content imaging of diverse tissues", *Nat. Protoc.*, 17(2):378-401, 2022, [doi: 10.1038/s41596-021-00644-9](https://doi.org/10.1038/s41596-021-00644-9).

A. J. Radtke et al., "Accompanying dataset for: IBEX: An iterative immunolabeling and chemical bleaching method for high-content imaging of diverse tissues", [doi: 10.5281/zenodo.5244550](https://doi.org/10.5281/zenodo.5244551).

2. A. J. Radtke et al., "IBEX: A versatile multiplex optical imaging approach for deep phenotyping and spatial analysis of cells in complex tissues", *Proc Natl Acad Sci*, 117(52):33455–33465, 2020, [doi:10.1073/pnas.2018488117](https://doi.org/10.1073/pnas.2018488117)


# Additional Notes

<a name="notes"></a>
1. Antibody labels lymphatic endothelial cells and vessels in FFPE tissues. Excellent antibody used throughout many studies. Used at a dilution of 1:100 with an anti-goat AF555 secondary antibody (Thermo Fisher Scientific catalog number A-21432).
1. Antibody labels lymphatic endothelial cells and macrophages as expected.
2. Antibody labels lymphatic endothelial cells and vessels in FFPE tissues. Excellent antibody used throughout many studies. Used at a dilution of 1:100 with an anti-goat AF555 secondary antibody (Thermo Fisher Scientific catalog number A-21432).

| Human follicular lymphoma FFPE: LYVE-1 (yellow, catalog number AF2089) and Hoechst (blue, catalog number 40046) |
|:-------:|
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# Configurations

| UniProt Accession Number | Reagent Type | Target Name / Protein Biomarker | Target Species | Host Organism | Isotype | Clonality | Vendor | Catalog Number | Conjugate | RRID | Availability | Method | Tissue Preservation | Target Tissue | Tissue State | Detergent | Antigen Retrieval Conditions | Dye Inactivation Conditions | Recommend | Agree | Disagree | Contributor | Notes |
|:---------------------------|:-----------------|:----------------------------------|:-----------------|:----------------|:----------|:------------|:-------------------------|:-----------------|:------------|:-----------|:---------------|:--------------|:----------------------------------|:----------------|:---------------|:------------------|:-------------------------------|:------------------------------|:------------|:-----------------------------------------|:-----------|:--------------------|:------------|
| Q8BHC0 | Primary Antibody | LYVE-1 | Mouse | Rat | IgG1 | ALY7 | Thermo Fisher Scientific | 41-0443-82 | eF570 | AB_2573596 | Stock | IBEX2D Manual | 1:4 Cytofix/Cytoperm Fixed Frozen | Lung | NA | 0.3% Triton-X-100 | NA | 1 mg/ml LiBH4 15 minutes | Yes | [0000-0003-4379-8967](https://orcid.org/0000-0003-4379-8967) [[1](#publications)] | NA | [0000-0003-4379-8967](https://orcid.org/0000-0003-4379-8967) | [1](#notes) |
| Q8BHC0 | Primary Antibody | LYVE-1 | Mouse | Rat | IgG1 | ALY7 | Thermo Fisher Scientific | 41-0443-82 | eF570 | AB_2573596 | Stock | IBEX2D Manual | 1:4 Cytofix/Cytoperm Fixed Frozen | Small Intestine | NA | 0.3% Triton-X-100 | NA | 1 mg/ml LiBH4 15 minutes | Yes | [0000-0003-4379-8967](https://orcid.org/0000-0003-4379-8967) [[1](#publications)] | NA | [0000-0003-4379-8967](https://orcid.org/0000-0003-4379-8967) | [1](#notes) |
| Q8BHC0 | Primary Antibody | LYVE-1 | Mouse | Rat | IgG1 | ALY7 | Thermo Fisher Scientific | 41-0443-82 | eF570 | AB_2573596 | Stock | IBEX2D Manual | 1:4 Cytofix/Cytoperm Fixed Frozen | Lymph Node | NA | 0.3% Triton-X-100 | NA | 1 mg/ml LiBH4 15 minutes | Yes | [0000-0003-4379-8967](https://orcid.org/0000-0003-4379-8967) [[1](#publications)] | NA | [0000-0003-4379-8967](https://orcid.org/0000-0003-4379-8967) | |

# Publications

<a name="publications"></a>
1. A. J. Radtke et al., "IBEX: A versatile multiplex optical imaging approach for deep phenotyping and spatial analysis of cells in complex tissues", *Proc Natl Acad Sci*, 117(52):33455–33465, 2020, [doi:10.1073/pnas.2018488117](https://doi.org/10.1073/pnas.2018488117)


# Additional Notes

<a name="notes"></a>
1. Validated by Evelyn Kandov (No ORCID)
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