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Additional reagents associated with doi: 10.1101/2024.02.28.582563
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Reagents used in paper:  M. Vierhout et al., "A Novel Ex Vivo Approach
for Investigating Profibrotic Macrophage Polarization Using Murine
Precision-Cut Lung Slices", bioRxiv, 2024.
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zivy committed Aug 27, 2024
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9 changes: 8 additions & 1 deletion data/reagent_resources.csv
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Expand Up @@ -1198,4 +1198,11 @@ A0A8C6KR86,Primary Antibody,Peripherin 2,Turquoise Killifish,Rabbit,IgG,Polyclon
O42583,Primary Antibody,Peripherin 2,African Clawed Frog (Xenopus laevis),Rabbit,IgG,Polyclonal,Proteintech,18109-1-AP,Unconjugated,AB_10665364,Stock,IBEX2D Manual,4% PFA Fixed Frozen,Retina,NA,0.1% Triton-X-100,pH 6 (10 mM Sodium Citrate) for 20 minutes in a pressure cooker,NA,Yes,0009-0000-2047-4228,NA,0009-0000-2047-4228
NA,Primary Antibody,Zpr-1,Turquoise Killifish,Mouse,IgG1,Monoclonal,ZIRC,ZDB-ATB-081002-43,Unconjugated,AB_10013803,Stock,IBEX2D Manual,4% PFA Fixed Frozen,Retina,NA,0.1% Triton-X-100,pH 6 (10 mM Sodium Citrate) for 20 minutes in a pressure cooker,NA,Yes,0009-0000-2047-4228,NA,0009-0000-2047-4228
NA,Primary Antibody,Zpr-3,African Clawed Frog (Xenopus laevis),Mouse,IgG1,Monoclonal,ZIRC,ZDB-ATB-081002-45,Unconjugated,AB_10013805,Stock,IBEX2D Manual,4% PFA Fixed Frozen,Retina,NA,0.1% Triton-X-100,pH 6 (10 mM Sodium Citrate) for 20 minutes in a pressure cooker,NA,Yes,0009-0000-2047-4228,NA,0009-0000-2047-4228
NA,Primary Antibody,Zrf-1,Turquoise Killifish,Mouse,IgG1,Monoclonal,ZIRC,ZDB-ATB-081002-46,Unconjugated,AB_10013806,Stock,IBEX2D Manual,4% PFA Fixed Frozen,Retina,NA,0.1% Triton-X-100,pH 6 (10 mM Sodium Citrate) for 20 minutes in a pressure cooker,NA,Yes,0009-0000-2047-4228,NA,0009-0000-2047-4228
NA,Primary Antibody,Zrf-1,Turquoise Killifish,Mouse,IgG1,Monoclonal,ZIRC,ZDB-ATB-081002-46,Unconjugated,AB_10013806,Stock,IBEX2D Manual,4% PFA Fixed Frozen,Retina,NA,0.1% Triton-X-100,pH 6 (10 mM Sodium Citrate) for 20 minutes in a pressure cooker,NA,Yes,0009-0000-2047-4228,NA,0009-0000-2047-4228
P24788,Primary Antibody,CD11b,Mouse,Rat,IgG2b,M1/70,BD Biosciences,557397,PE,AB_396680,Stock,IBEX2D Manual,1:4 Cytofix/Cytoperm Fixed Frozen,Lung,NA,0.3% Triton-X-100,NA,1 mg/ml LiBH4 15 minutes,Yes,0000-0001-5813-2581,NA,0000-0001-5813-2581
Q9QXH4,Primary Antibody,CD11c,Mouse,Armenian Hamster,IgG,N418,Thermo Fisher Scientific,MCD11c20,AF488,AB_10373244,Stock,IBEX2D Manual,1:4 Cytofix/Cytoperm Fixed Frozen,Lung,NA,0.3% Triton-X-100,NA,1 mg/ml LiBH4 15 minutes,Yes,0000-0001-5813-2581,NA,0000-0001-5813-2581
P06800,Primary Antibody,CD45,Mouse,Rat,IgG2b,30-F11,BioLegend,103144,AF594,AB_2563458,Stock,IBEX2D Manual,1:4 Cytofix/Cytoperm Fixed Frozen,Lung,NA,0.3% Triton-X-100,NA,NA,Yes,0000-0001-5813-2581,NA,0000-0001-5813-2581
Q920G3,Primary Antibody,SiglecF,Mouse,Rat,IgG2a,E50-2440,BD Biosciences,552126,PE,AB_394341,Stock,IBEX2D Manual,1:4 Cytofix/Cytoperm Fixed Frozen,Lung,NA,0.3% Triton-X-100,NA,1 mg/ml LiBH4 15 minutes,Yes,0000-0001-5813-2581,NA,0000-0001-5813-2581
P62737,Primary Antibody,Alpha smooth muscle actin,Mouse,Mouse,IgG2a,1A4,Thermo Fisher Scientific,50-9760-82,eF660,AB_2574362,Stock,IBEX2D Manual,1:4 Cytofix/Cytoperm Fixed Frozen,Lung,NA,0.3% Triton-X-100,NA,1 mg/ml LiBH4 15 minutes,Yes,0000-0001-5813-2581,NA,0000-0001-5813-2581
P05089,Primary Antibody,Arginase-1,Mouse,Rabbit,IgG,D4E3M,Cell Signaling Technology,93668,Unconjugated,AB_2800207,Stock,IBEX2D Manual,1:4 Cytofix/Cytoperm Fixed Frozen,Lung,NA,0.3% Triton-X-100,NA,1 mg/ml LiBH4 15 minutes,Yes,0000-0001-5813-2581,NA,0000-0001-5813-2581
Q61830,Primary Antibody,CD206,Mouse,Rat,IgG2a,C068C2,BioLegend,141709,AF488,AB_10933252,Stock,IBEX2D Manual,1:4 Cytofix/Cytoperm Fixed Frozen,Lung,NA,0.3% Triton-X-100,NA,1 mg/ml LiBH4 15 minutes,Yes,0000-0001-5813-2581,NA,0000-0001-5813-2581
20 changes: 20 additions & 0 deletions docs/supporting_material/Alpha_smooth_muscle_actin_eF660/0000-0001-5813-2581.md
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layout: default
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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 |
|:---------------------------|:-----------------|:----------------------------------|:-----------------|:----------------|:----------|:------------|:-------------------------|:-----------------|:------------|:-----------|:---------------|:--------------|:----------------------------------|:----------------|:---------------|:------------------|:-------------------------------|:------------------------------|:------------|:----------------------------------------------------------------------------------|:-----------|:-------------------------------------------------------------|:------------|
| P62737 | Primary Antibody | Alpha smooth muscle actin | Mouse | Mouse | IgG2a | 1A4 | Thermo Fisher Scientific | 50-9760-82 | eF660 | AB_2574362 | Stock | IBEX2D Manual | 1:4 Cytofix/Cytoperm Fixed Frozen | Lung | NA | 0.3% Triton-X-100 | NA | 1 mg/ml LiBH4 15 minutes | Yes | [0000-0001-5813-2581](https://orcid.org/0000-0001-5813-2581) [[1](#publications)] | NA | [0000-0001-5813-2581](https://orcid.org/0000-0001-5813-2581) | [1](#notes) |

# Publications

<a name="publications"></a>
1. M. Vierhout et al., "A Novel Ex Vivo Approach for Investigating Profibrotic Macrophage Polarization Using Murine Precision-Cut Lung Slices", *bioRxiv*, 2024, [doi: 10.1101/2024.07.05.602278](https://doi.org/10.1101/2024.07.05.602278).


# Additional Notes

<a name="notes"></a>
1. 1:200 dilution on precision-cut lung slices, see methods details in associated preprint.
20 changes: 20 additions & 0 deletions docs/supporting_material/Arginase-1_Unconjugated/0000-0001-5813-2581.md
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layout: default
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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 |
|:---------------------------|:-----------------|:----------------------------------|:-----------------|:----------------|:----------|:------------|:--------------------------|-----------------:|:-------------|:-----------|:---------------|:--------------|:----------------------------------|:----------------|:---------------|:------------------|:-------------------------------|:------------------------------|:------------|:----------------------------------------------------------------------------------|:-----------|:-------------------------------------------------------------|:------------|
| P05089 | Primary Antibody | Arginase-1 | Mouse | Rabbit | IgG | D4E3M | Cell Signaling Technology | 93668 | Unconjugated | AB_2800207 | Stock | IBEX2D Manual | 1:4 Cytofix/Cytoperm Fixed Frozen | Lung | NA | 0.3% Triton-X-100 | NA | 1 mg/ml LiBH4 15 minutes | Yes | [0000-0001-5813-2581](https://orcid.org/0000-0001-5813-2581) [[1](#publications)] | NA | [0000-0001-5813-2581](https://orcid.org/0000-0001-5813-2581) | [1](#notes) |

# Publications

<a name="publications"></a>
1. M. Vierhout et al., "A Novel Ex Vivo Approach for Investigating Profibrotic Macrophage Polarization Using Murine Precision-Cut Lung Slices", *bioRxiv*, 2024, [doi: 10.1101/2024.07.05.602278](https://doi.org/10.1101/2024.07.05.602278).


# Additional Notes

<a name="notes"></a>
1. 1:50 dilution on precision-cut lung slices, see methods details in associated preprint.
20 changes: 20 additions & 0 deletions docs/supporting_material/CD11b_PE/0000-0001-5813-2581.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 |
|:---------------------------|:-----------------|:----------------------------------|:-----------------|:----------------|:----------|:------------|:---------------|-----------------:|:------------|:----------|:---------------|:--------------|:----------------------------------|:----------------|:---------------|:------------------|:-------------------------------|:------------------------------|:------------|:----------------------------------------------------------------------------------|:-----------|:-------------------------------------------------------------|:------------|
| P24788 | Primary Antibody | CD11b | Mouse | Rat | IgG2b | M1/70 | BD Biosciences | 557397 | PE | AB_396680 | Stock | IBEX2D Manual | 1:4 Cytofix/Cytoperm Fixed Frozen | Lung | NA | 0.3% Triton-X-100 | NA | 1 mg/ml LiBH4 15 minutes | Yes | [0000-0001-5813-2581](https://orcid.org/0000-0001-5813-2581) [[1](#publications)] | NA | [0000-0001-5813-2581](https://orcid.org/0000-0001-5813-2581) | [1](#notes) |

# Publications

<a name="publications"></a>
1. M. Vierhout et al., "A Novel Ex Vivo Approach for Investigating Profibrotic Macrophage Polarization Using Murine Precision-Cut Lung Slices", *bioRxiv*, 2024, [doi: 10.1101/2024.07.05.602278](https://doi.org/10.1101/2024.07.05.602278).


# Additional Notes

<a name="notes"></a>
1. 1:100 dilution on precision-cut lung slices, see methods details in associated preprint.
20 changes: 20 additions & 0 deletions docs/supporting_material/CD11c_AF488/0000-0001-5813-2581.md
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layout: default
---

# 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 |
|:---------------------------|:-----------------|:----------------------------------|:-----------------|:-----------------|:----------|:------------|:-------------------------|:-----------------|:------------|:------------|:---------------|:--------------|:----------------------------------|:----------------|:---------------|:------------------|:-------------------------------|:------------------------------|:------------|:----------------------------------------------------------------------------------|:-----------|:-------------------------------------------------------------|:------------|
| Q9QXH4 | Primary Antibody | CD11c | Mouse | Armenian Hamster | IgG | N418 | Thermo Fisher Scientific | MCD11c20 | AF488 | AB_10373244 | Stock | IBEX2D Manual | 1:4 Cytofix/Cytoperm Fixed Frozen | Lung | NA | 0.3% Triton-X-100 | NA | 1 mg/ml LiBH4 15 minutes | Yes | [0000-0001-5813-2581](https://orcid.org/0000-0001-5813-2581) [[1](#publications)] | NA | [0000-0001-5813-2581](https://orcid.org/0000-0001-5813-2581) | [1](#notes) |

# Publications

<a name="publications"></a>
1. M. Vierhout et al., "A Novel Ex Vivo Approach for Investigating Profibrotic Macrophage Polarization Using Murine Precision-Cut Lung Slices", *bioRxiv*, 2024, [doi: 10.1101/2024.07.05.602278](https://doi.org/10.1101/2024.07.05.602278).


# Additional Notes

<a name="notes"></a>
1. 1:200 dilution on precision-cut lung slices, see methods details in associated preprint.
20 changes: 20 additions & 0 deletions docs/supporting_material/CD206_AF488/0000-0001-5813-2581.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 |
|:---------------------------|:-----------------|:----------------------------------|:-----------------|:----------------|:----------|:------------|:----------|-----------------:|:------------|:------------|:---------------|:--------------|:----------------------------------|:----------------|:---------------|:------------------|:-------------------------------|:------------------------------|:------------|:----------------------------------------------------------------------------------|:-----------|:-------------------------------------------------------------|:------------|
| Q61830 | Primary Antibody | CD206 | Mouse | Rat | IgG2a | C068C2 | BioLegend | 141709 | AF488 | AB_10933252 | Stock | IBEX2D Manual | 1:4 Cytofix/Cytoperm Fixed Frozen | Lung | NA | 0.3% Triton-X-100 | NA | 1 mg/ml LiBH4 15 minutes | Yes | [0000-0001-5813-2581](https://orcid.org/0000-0001-5813-2581) [[1](#publications)] | NA | [0000-0001-5813-2581](https://orcid.org/0000-0001-5813-2581) | [1](#notes) |

# Publications

<a name="publications"></a>
1. M. Vierhout et al., "A Novel Ex Vivo Approach for Investigating Profibrotic Macrophage Polarization Using Murine Precision-Cut Lung Slices", *bioRxiv*, 2024, [doi: 10.1101/2024.07.05.602278](https://doi.org/10.1101/2024.07.05.602278).


# Additional Notes

<a name="notes"></a>
1. 1:100 dilution on precision-cut lung slices, see methods details in associated preprint.
20 changes: 20 additions & 0 deletions docs/supporting_material/CD45_AF594/0000-0001-5813-2581.md
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layout: default
---

# 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 |
|:---------------------------|:-----------------|:----------------------------------|:-----------------|:----------------|:----------|:------------|:----------|-----------------:|:------------|:-----------|:---------------|:--------------|:----------------------------------|:----------------|:---------------|:------------------|:-------------------------------|:------------------------------|:------------|:----------------------------------------------------------------------------------|:-----------|:-------------------------------------------------------------|:------------|
| P06800 | Primary Antibody | CD45 | Mouse | Rat | IgG2b | 30-F11 | BioLegend | 103144 | AF594 | AB_2563458 | Stock | IBEX2D Manual | 1:4 Cytofix/Cytoperm Fixed Frozen | Lung | NA | 0.3% Triton-X-100 | NA | NA | Yes | [0000-0001-5813-2581](https://orcid.org/0000-0001-5813-2581) [[1](#publications)] | NA | [0000-0001-5813-2581](https://orcid.org/0000-0001-5813-2581) | [1](#notes) |

# Publications

<a name="publications"></a>
1. M. Vierhout et al., "A Novel Ex Vivo Approach for Investigating Profibrotic Macrophage Polarization Using Murine Precision-Cut Lung Slices", *bioRxiv*, 2024, [doi: 10.1101/2024.07.05.602278](https://doi.org/10.1101/2024.07.05.602278).


# Additional Notes

<a name="notes"></a>
1. 1:20 dilution on precision-cut lung slices, see methods details in associated preprint.
5 changes: 4 additions & 1 deletion docs/supporting_material/CD68_AF647/0000-0001-5813-2581.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 |
|:---------------------------|:-----------------|:----------------------------------|:-----------------|:----------------|:----------|:------------|:----------|-----------------:|:------------|:-----------|:---------------|:--------------|:----------------------------------|:----------------|:---------------|:------------------|:-------------------------------|:------------------------------|:------------|:--------------------|:-----------|:--------------------|:------------|
| P31996 | Primary Antibody | CD68 | Mouse | Rat | IgG2a | FA-11 | BioLegend | 137004 | AF647 | AB_2044002 | Stock | IBEX2D Manual | 1:4 Cytofix/Cytoperm Fixed Frozen | Lung | NA | 0.3% Triton-X-100 | NA | 1 mg/ml LiBH4 15 minutes | Yes | [0000-0001-5813-2581](https://orcid.org/0000-0001-5813-2581) | NA | [0000-0001-5813-2581](https://orcid.org/0000-0001-5813-2581) | [1](#notes) |
| P31996 | Primary Antibody | CD68 | Mouse | Rat | IgG2a | FA-11 | BioLegend | 137004 | AF647 | AB_2044002 | Stock | IBEX2D Manual | 1:4 Cytofix/Cytoperm Fixed Frozen | Lung | NA | 0.3% Triton-X-100 | NA | 1 mg/ml LiBH4 15 minutes | Yes | [0000-0001-5813-2581](https://orcid.org/0000-0001-5813-2581) [[1](#publications)] | NA | [0000-0001-5813-2581](https://orcid.org/0000-0001-5813-2581) | [1,2](#notes) |

# Publications

<a name="publications"></a>
1. M. Vierhout et al., "A Novel Ex Vivo Approach for Investigating Profibrotic Macrophage Polarization Using Murine Precision-Cut Lung Slices", *bioRxiv*, 2024, [doi: 10.1101/2024.07.05.602278](https://doi.org/10.1101/2024.07.05.602278).


# Additional Notes

<a name="notes"></a>
1. Validated by colocalization with macrophage markers F4/80 and CD206.
2. 1:100 dilution on precision-cut lung slices, see methods details in associated preprint.
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