3174004b cxcr4 fluidigm Search Results


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antibody cd27 mouse monoclonal fluidigm  (fluidigm)
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Figure 4. Comparison of kNN latent cells reactivatable by different stimulations and from blood versus tissues using longitudinal specimens. (A) Atlas (gray) and kNN latent cells (red) from three blood specimens from the same donor (PID5003) spaced 2–3 months apart, where reactivation was induced by either PMA/ionomycin or Romidepsin/PEP005. Arrows highlight regions that harbor kNN latent cells in the PMA/ionomycin but not Romidepsin/ PEP005 samples. Red numbers indicate the number of kNN latent cells in each plot. (B) kNN latent cells reactivatable by PMA/ionomycin at two different time points are more similar to each other than to those reactivatable by Romidepsin/PEP005 at the same time point. The empirical cumulative distribution of median distances between kNN cells was calculated between (1) Time point 1 PMA/ionomycin and Time point 2 PMA/ ionomycin samples (red), and (2) Time point 2 Romidepsin/PEP005 and Time point 3 Romidepsin/PEP005 samples (pink), and (3) Time point 2 PMA/ ionomycin and Time point 2 Romidepsin/PEP005 samples (blue). (C) Atlases of memory CD4+ T cells from fine needle aspirates (FNAs) or the blood of the same donor (PID3010) with corresponding kNN latent cells (red). Red arrows point to regions of the FNA tSNEs that are concentrated in kNN latent cells. Bottom plots show each FNA atlas overlaid onto the blood atlas. Red numbers indicate the number of kNN latent cells in each plot. (D) Dot plots demonstrating that FNA but not blood kNN latent cells (red dots) express uniformly high levels of <t>CD27,</t> CD69, CXCR5, PD1, and ICOS. Atlas cells are Figure 4 continued on next page
Antibody Cd27 Mouse Monoclonal Fluidigm, supplied by fluidigm, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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antibody cd45ra mouse monoclonal fluidigm  (fluidigm)
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Figure 5. Design of tailored sort strategies to isolate three populations memory CD4+ PD1+ T cells harboring different frequencies of kNN latent cells. Sort strategies were designed for each of the four leukapheresis donors analyzed by PP-SLIDE. Shown are the CyTOF datasets, the unstimulated atlas cells are shown as gray contours and kNN latent cells shown as red contours. Gates in black correspond to upstream gates. Each sorting strategy isolates three populations of memory CD4+ PD1+ T cells: two disenriched (pink, purple), and one enriched (red). Results were pre-gated on live, singlet memory CD4+ T cells <t>(CD3+CD8-CD19-CD45RO+CD45RA-).</t> The three functional assays applied to sorted cells are listed. The gray inset on the right shows frequencies of kNN latent cells in the final enriched populations (per million memory CD4+ T cells) and the fold-enrichment of kNN latent cells in the final sorted enriched population relative to each of the disenriched populations. In instances where a disenriched population did not harbor any kNN cells, the fold-enrichment is listed as NA (not available) because the fold-enrichment is infinity when divided by zero.
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antibody cd69 mouse monoclonal fluidigm  (fluidigm)
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Figure 4. Comparison of kNN latent cells reactivatable by different stimulations and from blood versus tissues using longitudinal specimens. (A) Atlas (gray) and kNN latent cells (red) from three blood specimens from the same donor (PID5003) spaced 2–3 months apart, where reactivation was induced by either PMA/ionomycin or Romidepsin/PEP005. Arrows highlight regions that harbor kNN latent cells in the PMA/ionomycin but not Romidepsin/ PEP005 samples. Red numbers indicate the number of kNN latent cells in each plot. (B) kNN latent cells reactivatable by PMA/ionomycin at two different time points are more similar to each other than to those reactivatable by Romidepsin/PEP005 at the same time point. The empirical cumulative distribution of median distances between kNN cells was calculated between (1) Time point 1 PMA/ionomycin and Time point 2 PMA/ ionomycin samples (red), and (2) Time point 2 Romidepsin/PEP005 and Time point 3 Romidepsin/PEP005 samples (pink), and (3) Time point 2 PMA/ ionomycin and Time point 2 Romidepsin/PEP005 samples (blue). (C) Atlases of memory CD4+ T cells from fine needle aspirates (FNAs) or the blood of the same donor (PID3010) with corresponding kNN latent cells (red). Red arrows point to regions of the FNA tSNEs that are concentrated in kNN latent cells. Bottom plots show each FNA atlas overlaid onto the blood atlas. Red numbers indicate the number of kNN latent cells in each plot. (D) Dot plots demonstrating that FNA but not blood kNN latent cells (red dots) express uniformly high levels of CD27, <t>CD69,</t> CXCR5, PD1, and ICOS. Atlas cells are Figure 4 continued on next page
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antibody cd38 mouse monoclonal fluidigm  (fluidigm)
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Figure 4. Comparison of kNN latent cells reactivatable by different stimulations and from blood versus tissues using longitudinal specimens. (A) Atlas (gray) and kNN latent cells (red) from three blood specimens from the same donor (PID5003) spaced 2–3 months apart, where reactivation was induced by either PMA/ionomycin or Romidepsin/PEP005. Arrows highlight regions that harbor kNN latent cells in the PMA/ionomycin but not Romidepsin/ PEP005 samples. Red numbers indicate the number of kNN latent cells in each plot. (B) kNN latent cells reactivatable by PMA/ionomycin at two different time points are more similar to each other than to those reactivatable by Romidepsin/PEP005 at the same time point. The empirical cumulative distribution of median distances between kNN cells was calculated between (1) Time point 1 PMA/ionomycin and Time point 2 PMA/ ionomycin samples (red), and (2) Time point 2 Romidepsin/PEP005 and Time point 3 Romidepsin/PEP005 samples (pink), and (3) Time point 2 PMA/ ionomycin and Time point 2 Romidepsin/PEP005 samples (blue). (C) Atlases of memory CD4+ T cells from fine needle aspirates (FNAs) or the blood of the same donor (PID3010) with corresponding kNN latent cells (red). Red arrows point to regions of the FNA tSNEs that are concentrated in kNN latent cells. Bottom plots show each FNA atlas overlaid onto the blood atlas. Red numbers indicate the number of kNN latent cells in each plot. (D) Dot plots demonstrating that FNA but not blood kNN latent cells (red dots) express uniformly high levels of CD27, <t>CD69,</t> CXCR5, PD1, and ICOS. Atlas cells are Figure 4 continued on next page
Antibody Cd38 Mouse Monoclonal Fluidigm, supplied by fluidigm, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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antibody cd127 mouse monoclonal fluidigm  (fluidigm)
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Figure 4. Comparison of kNN latent cells reactivatable by different stimulations and from blood versus tissues using longitudinal specimens. (A) Atlas (gray) and kNN latent cells (red) from three blood specimens from the same donor (PID5003) spaced 2–3 months apart, where reactivation was induced by either PMA/ionomycin or Romidepsin/PEP005. Arrows highlight regions that harbor kNN latent cells in the PMA/ionomycin but not Romidepsin/ PEP005 samples. Red numbers indicate the number of kNN latent cells in each plot. (B) kNN latent cells reactivatable by PMA/ionomycin at two different time points are more similar to each other than to those reactivatable by Romidepsin/PEP005 at the same time point. The empirical cumulative distribution of median distances between kNN cells was calculated between (1) Time point 1 PMA/ionomycin and Time point 2 PMA/ ionomycin samples (red), and (2) Time point 2 Romidepsin/PEP005 and Time point 3 Romidepsin/PEP005 samples (pink), and (3) Time point 2 PMA/ ionomycin and Time point 2 Romidepsin/PEP005 samples (blue). (C) Atlases of memory CD4+ T cells from fine needle aspirates (FNAs) or the blood of the same donor (PID3010) with corresponding kNN latent cells (red). Red arrows point to regions of the FNA tSNEs that are concentrated in kNN latent cells. Bottom plots show each FNA atlas overlaid onto the blood atlas. Red numbers indicate the number of kNN latent cells in each plot. (D) Dot plots demonstrating that FNA but not blood kNN latent cells (red dots) express uniformly high levels of CD27, <t>CD69,</t> CXCR5, PD1, and ICOS. Atlas cells are Figure 4 continued on next page
Antibody Cd127 Mouse Monoclonal Fluidigm, supplied by fluidigm, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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antibody cxcr5 (rat monoclonal)  (Becton Dickinson)
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Figure 4. Comparison of kNN latent cells reactivatable by different stimulations and from blood versus tissues using longitudinal specimens. (A) Atlas (gray) and kNN latent cells (red) from three blood specimens from the same donor (PID5003) spaced 2–3 months apart, where reactivation was induced by either PMA/ionomycin or Romidepsin/PEP005. Arrows highlight regions that harbor kNN latent cells in the PMA/ionomycin but not Romidepsin/ PEP005 samples. Red numbers indicate the number of kNN latent cells in each plot. (B) kNN latent cells reactivatable by PMA/ionomycin at two different time points are more similar to each other than to those reactivatable by Romidepsin/PEP005 at the same time point. The empirical cumulative distribution of median distances between kNN cells was calculated between (1) Time point 1 PMA/ionomycin and Time point 2 PMA/ ionomycin samples (red), and (2) Time point 2 Romidepsin/PEP005 and Time point 3 Romidepsin/PEP005 samples (pink), and (3) Time point 2 PMA/ ionomycin and Time point 2 Romidepsin/PEP005 samples (blue). (C) Atlases of memory CD4+ T cells from fine needle aspirates (FNAs) or the blood of the same donor (PID3010) with corresponding kNN latent cells (red). Red arrows point to regions of the FNA tSNEs that are concentrated in kNN latent cells. Bottom plots show each FNA atlas overlaid onto the blood atlas. Red numbers indicate the number of kNN latent cells in each plot. (D) Dot plots demonstrating that FNA but not blood kNN latent cells (red dots) express uniformly high levels of CD27, <t>CD69,</t> CXCR5, PD1, and ICOS. Atlas cells are Figure 4 continued on next page
Antibody Cxcr5 (Rat Monoclonal), supplied by Becton Dickinson, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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antibody cd30 (mouse monoclonal)  (Becton Dickinson)
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Figure 4. Comparison of kNN latent cells reactivatable by different stimulations and from blood versus tissues using longitudinal specimens. (A) Atlas (gray) and kNN latent cells (red) from three blood specimens from the same donor (PID5003) spaced 2–3 months apart, where reactivation was induced by either PMA/ionomycin or Romidepsin/PEP005. Arrows highlight regions that harbor kNN latent cells in the PMA/ionomycin but not Romidepsin/ PEP005 samples. Red numbers indicate the number of kNN latent cells in each plot. (B) kNN latent cells reactivatable by PMA/ionomycin at two different time points are more similar to each other than to those reactivatable by Romidepsin/PEP005 at the same time point. The empirical cumulative distribution of median distances between kNN cells was calculated between (1) Time point 1 PMA/ionomycin and Time point 2 PMA/ ionomycin samples (red), and (2) Time point 2 Romidepsin/PEP005 and Time point 3 Romidepsin/PEP005 samples (pink), and (3) Time point 2 PMA/ ionomycin and Time point 2 Romidepsin/PEP005 samples (blue). (C) Atlases of memory CD4+ T cells from fine needle aspirates (FNAs) or the blood of the same donor (PID3010) with corresponding kNN latent cells (red). Red arrows point to regions of the FNA tSNEs that are concentrated in kNN latent cells. Bottom plots show each FNA atlas overlaid onto the blood atlas. Red numbers indicate the number of kNN latent cells in each plot. (D) Dot plots demonstrating that FNA but not blood kNN latent cells (red dots) express uniformly high levels of CD27, <t>CD69,</t> CXCR5, PD1, and ICOS. Atlas cells are Figure 4 continued on next page
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Figure 4. Comparison of kNN latent cells reactivatable by different stimulations and from blood versus tissues using longitudinal specimens. (A) Atlas (gray) and kNN latent cells (red) from three blood specimens from the same donor (PID5003) spaced 2–3 months apart, where reactivation was induced by either PMA/ionomycin or Romidepsin/PEP005. Arrows highlight regions that harbor kNN latent cells in the PMA/ionomycin but not Romidepsin/ PEP005 samples. Red numbers indicate the number of kNN latent cells in each plot. (B) kNN latent cells reactivatable by PMA/ionomycin at two different time points are more similar to each other than to those reactivatable by Romidepsin/PEP005 at the same time point. The empirical cumulative distribution of median distances between kNN cells was calculated between (1) Time point 1 PMA/ionomycin and Time point 2 PMA/ ionomycin samples (red), and (2) Time point 2 Romidepsin/PEP005 and Time point 3 Romidepsin/PEP005 samples (pink), and (3) Time point 2 PMA/ ionomycin and Time point 2 Romidepsin/PEP005 samples (blue). (C) Atlases of memory CD4+ T cells from fine needle aspirates (FNAs) or the blood of the same donor (PID3010) with corresponding kNN latent cells (red). Red arrows point to regions of the FNA tSNEs that are concentrated in kNN latent cells. Bottom plots show each FNA atlas overlaid onto the blood atlas. Red numbers indicate the number of kNN latent cells in each plot. (D) Dot plots demonstrating that FNA but not blood kNN latent cells (red dots) express uniformly high levels of CD27, <t>CD69,</t> CXCR5, PD1, and ICOS. Atlas cells are Figure 4 continued on next page
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antibody apc cd103 (mouse monoclonal)  (Becton Dickinson)
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Figure 4. Comparison of kNN latent cells reactivatable by different stimulations and from blood versus tissues using longitudinal specimens. (A) Atlas (gray) and kNN latent cells (red) from three blood specimens from the same donor (PID5003) spaced 2–3 months apart, where reactivation was induced by either PMA/ionomycin or Romidepsin/PEP005. Arrows highlight regions that harbor kNN latent cells in the PMA/ionomycin but not Romidepsin/ PEP005 samples. Red numbers indicate the number of kNN latent cells in each plot. (B) kNN latent cells reactivatable by PMA/ionomycin at two different time points are more similar to each other than to those reactivatable by Romidepsin/PEP005 at the same time point. The empirical cumulative distribution of median distances between kNN cells was calculated between (1) Time point 1 PMA/ionomycin and Time point 2 PMA/ ionomycin samples (red), and (2) Time point 2 Romidepsin/PEP005 and Time point 3 Romidepsin/PEP005 samples (pink), and (3) Time point 2 PMA/ ionomycin and Time point 2 Romidepsin/PEP005 samples (blue). (C) Atlases of memory CD4+ T cells from fine needle aspirates (FNAs) or the blood of the same donor (PID3010) with corresponding kNN latent cells (red). Red arrows point to regions of the FNA tSNEs that are concentrated in kNN latent cells. Bottom plots show each FNA atlas overlaid onto the blood atlas. Red numbers indicate the number of kNN latent cells in each plot. (D) Dot plots demonstrating that FNA but not blood kNN latent cells (red dots) express uniformly high levels of CD27, <t>CD69,</t> CXCR5, PD1, and ICOS. Atlas cells are Figure 4 continued on next page
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Image Search Results


Figure 4. Comparison of kNN latent cells reactivatable by different stimulations and from blood versus tissues using longitudinal specimens. (A) Atlas (gray) and kNN latent cells (red) from three blood specimens from the same donor (PID5003) spaced 2–3 months apart, where reactivation was induced by either PMA/ionomycin or Romidepsin/PEP005. Arrows highlight regions that harbor kNN latent cells in the PMA/ionomycin but not Romidepsin/ PEP005 samples. Red numbers indicate the number of kNN latent cells in each plot. (B) kNN latent cells reactivatable by PMA/ionomycin at two different time points are more similar to each other than to those reactivatable by Romidepsin/PEP005 at the same time point. The empirical cumulative distribution of median distances between kNN cells was calculated between (1) Time point 1 PMA/ionomycin and Time point 2 PMA/ ionomycin samples (red), and (2) Time point 2 Romidepsin/PEP005 and Time point 3 Romidepsin/PEP005 samples (pink), and (3) Time point 2 PMA/ ionomycin and Time point 2 Romidepsin/PEP005 samples (blue). (C) Atlases of memory CD4+ T cells from fine needle aspirates (FNAs) or the blood of the same donor (PID3010) with corresponding kNN latent cells (red). Red arrows point to regions of the FNA tSNEs that are concentrated in kNN latent cells. Bottom plots show each FNA atlas overlaid onto the blood atlas. Red numbers indicate the number of kNN latent cells in each plot. (D) Dot plots demonstrating that FNA but not blood kNN latent cells (red dots) express uniformly high levels of CD27, CD69, CXCR5, PD1, and ICOS. Atlas cells are Figure 4 continued on next page

Journal: eLife

Article Title: Phenotypic analysis of the unstimulated in vivo HIV CD4 T cell reservoir

doi: 10.7554/elife.60933

Figure Lengend Snippet: Figure 4. Comparison of kNN latent cells reactivatable by different stimulations and from blood versus tissues using longitudinal specimens. (A) Atlas (gray) and kNN latent cells (red) from three blood specimens from the same donor (PID5003) spaced 2–3 months apart, where reactivation was induced by either PMA/ionomycin or Romidepsin/PEP005. Arrows highlight regions that harbor kNN latent cells in the PMA/ionomycin but not Romidepsin/ PEP005 samples. Red numbers indicate the number of kNN latent cells in each plot. (B) kNN latent cells reactivatable by PMA/ionomycin at two different time points are more similar to each other than to those reactivatable by Romidepsin/PEP005 at the same time point. The empirical cumulative distribution of median distances between kNN cells was calculated between (1) Time point 1 PMA/ionomycin and Time point 2 PMA/ ionomycin samples (red), and (2) Time point 2 Romidepsin/PEP005 and Time point 3 Romidepsin/PEP005 samples (pink), and (3) Time point 2 PMA/ ionomycin and Time point 2 Romidepsin/PEP005 samples (blue). (C) Atlases of memory CD4+ T cells from fine needle aspirates (FNAs) or the blood of the same donor (PID3010) with corresponding kNN latent cells (red). Red arrows point to regions of the FNA tSNEs that are concentrated in kNN latent cells. Bottom plots show each FNA atlas overlaid onto the blood atlas. Red numbers indicate the number of kNN latent cells in each plot. (D) Dot plots demonstrating that FNA but not blood kNN latent cells (red dots) express uniformly high levels of CD27, CD69, CXCR5, PD1, and ICOS. Atlas cells are Figure 4 continued on next page

Article Snippet: DOI: https://doi.org/10.7554/eLife.60933 16 of 34 Continued Reagent type (species) or resource Designation Source or reference Identifiers Additional information Antibody OX40 (mouse monoclonal) Fluidigm Cat#3158012B (1 mg/100 mL) Antibody CCR7 (mouse monoclonal) Fluidigm Cat#3159003A (1 mg/100 mL) Antibody CD28 (mouse monoclonal) Fluidigm Cat#3160003B (1 mg/100 mL) Antibody CD45RO (mouse monoclonal) Biolegend Cat#304239 (1 mg/100 mL) Antibody CD69 (mouse monoclonal) Fluidigm Cat#3162001B (1 mg/100 mL) Antibody CRTH2 (rat monoclonal) Fluidigm Cat#3163003B (1 mg/100 mL) Antibody PD-1 (mouse monoclonal) Biolegend Cat#329941 (1 mg/100 mL) Antibody CD127 (mouse monoclonal) Fluidigm Cat#3165008B (1 mg/100 mL) Antibody CXCR5 (rat monoclonal) BD Biosciences Cat#552032 (1 mg/100 mL) Antibody CD27 (mouse monoclonal) Fluidigm Cat#3167006B (1 mg/100 mL) Antibody CD30 (mouse monoclonal) BD Biosciences Cat#555827 (1 mg/100 mL) Antibody CD45RA (mouse monoclonal) Fluidigm Cat#3169008B (1 mg/100 mL) Antibody CD3 (mouse monoclonal) Fluidigm Cat#3170001B (1 mg/100 mL) Antibody CD57 (mouse monoclonal) Biolegend Cat#359602 (1 mg/100 mL) Antibody CD38 (mouse monoclonal) Fluidigm Cat#3172007B (1 mg/100 mL) Antibody CD4 (mouse monoclonal) Fluidigm Cat#3174004B (1 mg/100 mL) Antibody CXCR4 (mouse monoclonal) Fluidigm Cat#3175001B (1 mg/100 mL) Antibody CD25 (mouse monoclonal) Biolegend Cat#356102 (1 mg/100 mL) Antibody PE-CF594 CD27 (mouse monoclonal) BD Biosciences Cat#562297 (1:25–1:200) Antibody BUV737 CD38 (mouse monoclonal) BD Biosciences Cat#564686 (1:25–1:200) Antibody BUV395 CD45RO (mouse monoclonal) BD Biosciences Cat#564291 (1:25–1:200) Antibody FITC CD57 (mouse monoclonal) BD Biosciences Cat#555619 (1:25–1:200) Antibody BV650 CD62L (mouse monoclonal) BD Biosciences Cat#563808 (1:25–1:200) Antibody APC CD69 (mouse monoclonal) Biolegend Cat#310910 (1:25–1:200) Antibody BV421 CD69 (mouse monoclonal) BD Biosciences Cat#562884 (1:25–1:200) Antibody APC CD103 (mouse monoclonal) BD Biosciences Cat#563883 (1:25–1:200) Continued on next page Neidleman et al. eLife 2020;9:e60933.

Techniques: Comparison

Figure 5. Design of tailored sort strategies to isolate three populations memory CD4+ PD1+ T cells harboring different frequencies of kNN latent cells. Sort strategies were designed for each of the four leukapheresis donors analyzed by PP-SLIDE. Shown are the CyTOF datasets, the unstimulated atlas cells are shown as gray contours and kNN latent cells shown as red contours. Gates in black correspond to upstream gates. Each sorting strategy isolates three populations of memory CD4+ PD1+ T cells: two disenriched (pink, purple), and one enriched (red). Results were pre-gated on live, singlet memory CD4+ T cells (CD3+CD8-CD19-CD45RO+CD45RA-). The three functional assays applied to sorted cells are listed. The gray inset on the right shows frequencies of kNN latent cells in the final enriched populations (per million memory CD4+ T cells) and the fold-enrichment of kNN latent cells in the final sorted enriched population relative to each of the disenriched populations. In instances where a disenriched population did not harbor any kNN cells, the fold-enrichment is listed as NA (not available) because the fold-enrichment is infinity when divided by zero.

Journal: eLife

Article Title: Phenotypic analysis of the unstimulated in vivo HIV CD4 T cell reservoir

doi: 10.7554/elife.60933

Figure Lengend Snippet: Figure 5. Design of tailored sort strategies to isolate three populations memory CD4+ PD1+ T cells harboring different frequencies of kNN latent cells. Sort strategies were designed for each of the four leukapheresis donors analyzed by PP-SLIDE. Shown are the CyTOF datasets, the unstimulated atlas cells are shown as gray contours and kNN latent cells shown as red contours. Gates in black correspond to upstream gates. Each sorting strategy isolates three populations of memory CD4+ PD1+ T cells: two disenriched (pink, purple), and one enriched (red). Results were pre-gated on live, singlet memory CD4+ T cells (CD3+CD8-CD19-CD45RO+CD45RA-). The three functional assays applied to sorted cells are listed. The gray inset on the right shows frequencies of kNN latent cells in the final enriched populations (per million memory CD4+ T cells) and the fold-enrichment of kNN latent cells in the final sorted enriched population relative to each of the disenriched populations. In instances where a disenriched population did not harbor any kNN cells, the fold-enrichment is listed as NA (not available) because the fold-enrichment is infinity when divided by zero.

Article Snippet: DOI: https://doi.org/10.7554/eLife.60933 16 of 34 Continued Reagent type (species) or resource Designation Source or reference Identifiers Additional information Antibody OX40 (mouse monoclonal) Fluidigm Cat#3158012B (1 mg/100 mL) Antibody CCR7 (mouse monoclonal) Fluidigm Cat#3159003A (1 mg/100 mL) Antibody CD28 (mouse monoclonal) Fluidigm Cat#3160003B (1 mg/100 mL) Antibody CD45RO (mouse monoclonal) Biolegend Cat#304239 (1 mg/100 mL) Antibody CD69 (mouse monoclonal) Fluidigm Cat#3162001B (1 mg/100 mL) Antibody CRTH2 (rat monoclonal) Fluidigm Cat#3163003B (1 mg/100 mL) Antibody PD-1 (mouse monoclonal) Biolegend Cat#329941 (1 mg/100 mL) Antibody CD127 (mouse monoclonal) Fluidigm Cat#3165008B (1 mg/100 mL) Antibody CXCR5 (rat monoclonal) BD Biosciences Cat#552032 (1 mg/100 mL) Antibody CD27 (mouse monoclonal) Fluidigm Cat#3167006B (1 mg/100 mL) Antibody CD30 (mouse monoclonal) BD Biosciences Cat#555827 (1 mg/100 mL) Antibody CD45RA (mouse monoclonal) Fluidigm Cat#3169008B (1 mg/100 mL) Antibody CD3 (mouse monoclonal) Fluidigm Cat#3170001B (1 mg/100 mL) Antibody CD57 (mouse monoclonal) Biolegend Cat#359602 (1 mg/100 mL) Antibody CD38 (mouse monoclonal) Fluidigm Cat#3172007B (1 mg/100 mL) Antibody CD4 (mouse monoclonal) Fluidigm Cat#3174004B (1 mg/100 mL) Antibody CXCR4 (mouse monoclonal) Fluidigm Cat#3175001B (1 mg/100 mL) Antibody CD25 (mouse monoclonal) Biolegend Cat#356102 (1 mg/100 mL) Antibody PE-CF594 CD27 (mouse monoclonal) BD Biosciences Cat#562297 (1:25–1:200) Antibody BUV737 CD38 (mouse monoclonal) BD Biosciences Cat#564686 (1:25–1:200) Antibody BUV395 CD45RO (mouse monoclonal) BD Biosciences Cat#564291 (1:25–1:200) Antibody FITC CD57 (mouse monoclonal) BD Biosciences Cat#555619 (1:25–1:200) Antibody BV650 CD62L (mouse monoclonal) BD Biosciences Cat#563808 (1:25–1:200) Antibody APC CD69 (mouse monoclonal) Biolegend Cat#310910 (1:25–1:200) Antibody BV421 CD69 (mouse monoclonal) BD Biosciences Cat#562884 (1:25–1:200) Antibody APC CD103 (mouse monoclonal) BD Biosciences Cat#563883 (1:25–1:200) Continued on next page Neidleman et al. eLife 2020;9:e60933.

Techniques: Functional Assay

Figure 4. Comparison of kNN latent cells reactivatable by different stimulations and from blood versus tissues using longitudinal specimens. (A) Atlas (gray) and kNN latent cells (red) from three blood specimens from the same donor (PID5003) spaced 2–3 months apart, where reactivation was induced by either PMA/ionomycin or Romidepsin/PEP005. Arrows highlight regions that harbor kNN latent cells in the PMA/ionomycin but not Romidepsin/ PEP005 samples. Red numbers indicate the number of kNN latent cells in each plot. (B) kNN latent cells reactivatable by PMA/ionomycin at two different time points are more similar to each other than to those reactivatable by Romidepsin/PEP005 at the same time point. The empirical cumulative distribution of median distances between kNN cells was calculated between (1) Time point 1 PMA/ionomycin and Time point 2 PMA/ ionomycin samples (red), and (2) Time point 2 Romidepsin/PEP005 and Time point 3 Romidepsin/PEP005 samples (pink), and (3) Time point 2 PMA/ ionomycin and Time point 2 Romidepsin/PEP005 samples (blue). (C) Atlases of memory CD4+ T cells from fine needle aspirates (FNAs) or the blood of the same donor (PID3010) with corresponding kNN latent cells (red). Red arrows point to regions of the FNA tSNEs that are concentrated in kNN latent cells. Bottom plots show each FNA atlas overlaid onto the blood atlas. Red numbers indicate the number of kNN latent cells in each plot. (D) Dot plots demonstrating that FNA but not blood kNN latent cells (red dots) express uniformly high levels of CD27, CD69, CXCR5, PD1, and ICOS. Atlas cells are Figure 4 continued on next page

Journal: eLife

Article Title: Phenotypic analysis of the unstimulated in vivo HIV CD4 T cell reservoir

doi: 10.7554/elife.60933

Figure Lengend Snippet: Figure 4. Comparison of kNN latent cells reactivatable by different stimulations and from blood versus tissues using longitudinal specimens. (A) Atlas (gray) and kNN latent cells (red) from three blood specimens from the same donor (PID5003) spaced 2–3 months apart, where reactivation was induced by either PMA/ionomycin or Romidepsin/PEP005. Arrows highlight regions that harbor kNN latent cells in the PMA/ionomycin but not Romidepsin/ PEP005 samples. Red numbers indicate the number of kNN latent cells in each plot. (B) kNN latent cells reactivatable by PMA/ionomycin at two different time points are more similar to each other than to those reactivatable by Romidepsin/PEP005 at the same time point. The empirical cumulative distribution of median distances between kNN cells was calculated between (1) Time point 1 PMA/ionomycin and Time point 2 PMA/ ionomycin samples (red), and (2) Time point 2 Romidepsin/PEP005 and Time point 3 Romidepsin/PEP005 samples (pink), and (3) Time point 2 PMA/ ionomycin and Time point 2 Romidepsin/PEP005 samples (blue). (C) Atlases of memory CD4+ T cells from fine needle aspirates (FNAs) or the blood of the same donor (PID3010) with corresponding kNN latent cells (red). Red arrows point to regions of the FNA tSNEs that are concentrated in kNN latent cells. Bottom plots show each FNA atlas overlaid onto the blood atlas. Red numbers indicate the number of kNN latent cells in each plot. (D) Dot plots demonstrating that FNA but not blood kNN latent cells (red dots) express uniformly high levels of CD27, CD69, CXCR5, PD1, and ICOS. Atlas cells are Figure 4 continued on next page

Article Snippet: DOI: https://doi.org/10.7554/eLife.60933 16 of 34 Continued Reagent type (species) or resource Designation Source or reference Identifiers Additional information Antibody OX40 (mouse monoclonal) Fluidigm Cat#3158012B (1 mg/100 mL) Antibody CCR7 (mouse monoclonal) Fluidigm Cat#3159003A (1 mg/100 mL) Antibody CD28 (mouse monoclonal) Fluidigm Cat#3160003B (1 mg/100 mL) Antibody CD45RO (mouse monoclonal) Biolegend Cat#304239 (1 mg/100 mL) Antibody CD69 (mouse monoclonal) Fluidigm Cat#3162001B (1 mg/100 mL) Antibody CRTH2 (rat monoclonal) Fluidigm Cat#3163003B (1 mg/100 mL) Antibody PD-1 (mouse monoclonal) Biolegend Cat#329941 (1 mg/100 mL) Antibody CD127 (mouse monoclonal) Fluidigm Cat#3165008B (1 mg/100 mL) Antibody CXCR5 (rat monoclonal) BD Biosciences Cat#552032 (1 mg/100 mL) Antibody CD27 (mouse monoclonal) Fluidigm Cat#3167006B (1 mg/100 mL) Antibody CD30 (mouse monoclonal) BD Biosciences Cat#555827 (1 mg/100 mL) Antibody CD45RA (mouse monoclonal) Fluidigm Cat#3169008B (1 mg/100 mL) Antibody CD3 (mouse monoclonal) Fluidigm Cat#3170001B (1 mg/100 mL) Antibody CD57 (mouse monoclonal) Biolegend Cat#359602 (1 mg/100 mL) Antibody CD38 (mouse monoclonal) Fluidigm Cat#3172007B (1 mg/100 mL) Antibody CD4 (mouse monoclonal) Fluidigm Cat#3174004B (1 mg/100 mL) Antibody CXCR4 (mouse monoclonal) Fluidigm Cat#3175001B (1 mg/100 mL) Antibody CD25 (mouse monoclonal) Biolegend Cat#356102 (1 mg/100 mL) Antibody PE-CF594 CD27 (mouse monoclonal) BD Biosciences Cat#562297 (1:25–1:200) Antibody BUV737 CD38 (mouse monoclonal) BD Biosciences Cat#564686 (1:25–1:200) Antibody BUV395 CD45RO (mouse monoclonal) BD Biosciences Cat#564291 (1:25–1:200) Antibody FITC CD57 (mouse monoclonal) BD Biosciences Cat#555619 (1:25–1:200) Antibody BV650 CD62L (mouse monoclonal) BD Biosciences Cat#563808 (1:25–1:200) Antibody APC CD69 (mouse monoclonal) Biolegend Cat#310910 (1:25–1:200) Antibody BV421 CD69 (mouse monoclonal) BD Biosciences Cat#562884 (1:25–1:200) Antibody APC CD103 (mouse monoclonal) BD Biosciences Cat#563883 (1:25–1:200) Continued on next page Neidleman et al. eLife 2020;9:e60933.

Techniques: Comparison