CD Maps is a public portal presenting results of pilot study measuring 110 CD markers on 47 immune cell subsets. Using standardized approach across 4 laboratories, PE-conjugated CD antibodies were measured in 8-color panels allowing cell subset definition. Dataset was created from 12 replicate samples. Among other statistics the level of CD mAb bound was measured as an antibody binding capacity (ABC) using QuantiBRITE beads.


Our work is available as a pre-print: CD Maps – dynamic profiling of CD1 to CD100 surface expression on human leukocyte and lymphocyte subsets



Graphical Summary

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Expression of CD1 to CD100 on 42 human leukocyte subsets

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Figure big_picture. Overview of expession (as Fluorescence intensity [log10(Median ABC)]) of all CD markers (n = 115 including FMO controls) on 'end-point' cell subsets (n = 42). Selected populations are: TCD4naive - naïve CD4 T cells, TCD4EM - Effector Memory CD4 T cells, TCD4CM - Central Memory CD4 T cells, TCD4TEMRA - TEMRA CD4 T cells, TCD8naive - naïve CD8 T cells, TCD8EM - Effector Memory CD8 T cells, TCD8CM - Central Memory CD8 T cells , TCD8TEMRA - TEMRA CD8 T cells, Bdn - CD27- IgM- IgD- B cells, Bnaive - naïve B cells, BnatEff - Natural Effector B cells, BIgM - IgM only B cells, BswMem - Switched Memory B cells, B27high - plasma cells , Tgd - gamma delta T cells, TCD8RAdim - CD45RAdim CD27+ CD8 T cells , DN34p - CD34+ double negative, DN34m1ap - CD34+CD1a+ double negative, CD4ISP - CD4+ immature single positive, DP3m - Double positive CD3-, DP3p - Double positive CD3+, CD4SP1ap - CD4+ single positive CD1a+, CD4SP1am - CD4+ single positive, CD8SP1ap - CD8+ single positive CD1a+, CD8SP1am - CD8+ single positive, BnaiveTo - Naive B-cells Tonsil, CC - Centrocytes, CB - Centroblasts, UnswtMem - Unswitched Memory B-cells, SwtMem - Switched Memory B-cells, PC - Plasma cells, CD138negPC - CD138negPlasma cells, CD138posPC - CD138posPlasma cells, Eosin - Eosinophils, Neutro - Neutrophils, noncMono - non-classical monocytes, classMono - classical monocytes, interMono - intermediate monocytes, Baso - Basophils, pDC - plasmacytoid DC, NK - NK cells, mDC - myeloid DC. CD marker expression is colour coded (negativity = blue, positivity = red) and the size of dots coresponds to Frequency of PE positive cells as percentage, both variables are medians of all measured samples. Peripheral Blood - #FA7D7D, Thymus - #CF0404, Tonsil - #942626.





Variables

Variables used throughout the project are in the table below. Those mainly used will be MedQb: PE intensity Median (in QB units, that is recalculated to Quantibright beads) or PEpos: % of positive cells of the gated subset.

CODE_NAME DISPLAY_NAME
CVQb CV of ABC
MeanQb Mean ABC
MedQb Median ABC
ModeQb Mode ABC
p10Qb 10th percentile ABC
p25Qb 25th percentile ABC
p75Qb 75th percentile ABC
p90Qb 90th percentile ABC
count Count
PEpos Frequency of positive cells
MedPE Median PE

CD markers

Measured CD markers with links to HCMD web: CD10, CD100, CD11a, CD11b, CD11c, CD13, CD15, CD16, CD18, CD19, CD1a, CD1b, CD1d, CD2, CD20, CD21, CD22, CD23, CD24, CD25, CD26, CD27, CD28, CD29, CD3, CD30, CD31, CD32, CD33, CD34, CD35, CD36, CD37, CD38, CD39, CD4, CD40, CD41, CD42a, CD42b, CD43, CD44, CD45, CD45RA, CD45RB, CD45RO, CD46, CD47, CD48, CD49a, CD49b, CD49c, CD49d, CD49e, CD49f, CD5, CD50, CD51, CD52, CD53, CD54, CD55, CD56, CD57, CD58, CD59, CD6, CD61, CD62E, CD62L, CD62P, CD63, CD64, CD66a_c_d_e, CD66b, CD66c, CD68, CD69, CD7, CD70, CD71, CD72, CD73, CD74, CD75, CD79a, CD79b, CD8, CD80, CD81, CD82, CD83, CD84, CD85d, CD85j, CD85k, CD86, CD87, CD88, CD89, CD9, CD90, CD91, CD93, CD95, CD96, CD97, CD98, CD99,


Cell subsets

Populations measured in all panels. In the project we use internal (CODE) names and DISPLAY names to be shown to users.

CODE_NAME DISPLAY_NAME panel
TCD4naive naïve CD4 T cells 2_B_T
TCD4EM Effector Memory CD4 T cells 2_B_T
TCD4CM Central Memory CD4 T cells 2_B_T
TCD4TEMRA TEMRA CD4 T cells 2_B_T
TCD8naive naïve CD8 T cells 2_B_T
TCD8EM Effector Memory CD8 T cells 2_B_T
TCD8CM Central Memory CD8 T cells 2_B_T
TCD8TEMRA TEMRA CD8 T cells 2_B_T
Bdn CD27- IgM- IgD- B cells 2_B_T
Bnaive naïve B cells 2_B_T
BnatEff Natural Effector B cells 2_B_T
BIgM IgM only B cells 2_B_T
BswMem Switched Memory B cells 2_B_T
B27high plasma cells 2_B_T
Tgd gamma delta T cells 2_B_T
TCD8RAdim CD45RAdim CD27+ CD8 T cells 2_B_T
Lymphs Lymphocytes 2_B_T
T T cells 2_B_T
TCD4 CD4 T cells 2_B_T
TCD8 CD8 T cells 2_B_T
B B cells 2_B_T
DN34p CD34+ double negative 5_thy
DN34m1ap CD34+CD1a+ double negative 5_thy
CD4ISP CD4+ immature single positive 5_thy
DP3m Double positive CD3- 5_thy
DP3p Double positive CD3+ 5_thy
CD4SP1ap CD4+ single positive CD1a+ 5_thy
CD4SP1am CD4+ single positive 5_thy
CD8SP1ap CD8+ single positive CD1a+ 5_thy
CD8SP1am CD8+ single positive 5_thy
BnaiveTo Naive B-cells Tonsil 4_ton
CC Centrocytes 4_ton
CB Centroblasts 4_ton
UnswtMem Unswitched Memory B-cells 4_ton
SwtMem Switched Memory B-cells 4_ton
PC Plasma cells 4_ton
CD138negPC CD138negPlasma cells 4_ton
CD138posPC CD138posPlasma cells 4_ton
Eosin Eosinophils 1_inn
Neutro Neutrophils 1_inn
noncMono non-classical monocytes 1_inn
classMono classical monocytes 1_inn
interMono intermediate monocytes 1_inn
Baso Basophils 1_inn
pDC plasmacytoid DC 1_inn
NK NK cells 1_inn
mDC myeloid DC 1_inn

Panel design, protocols and gating strategy

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  • panels 1 and 2 used same protocol for leukocyte isolation.

Gating of Panel 2 - Peripheral blood: B- and T-cell

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How CD markers change during maturation?




Save selected data









What is CD markers expression on a subset of cells?










Which markers are significantly different between cell populations?


Group - A

Group - B












Barplots in a table.












CD marker expression profile across cell subsets.












Single cell subset.











Hierarchical clustering analysis


Download Heatmap









A)

B)

Principal Component Analysis










Download table


This site was created by Karel Fišer as part of CD Maps project team effort.

I have done all work in R, using RStudio. From raw flow cytometry exported values through data pre-processing, transformations and corrections to sigmoidal and knee fitting modeling to all figures in the publication. The application itself is pure R shiny framework. The pre-print is Rmarkdown.

Please do not hesitate to contact me should you have any type of feedback.




Participating laboratories

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Our sponsors and supporters


Grant agencies

  • TK was supported by Ministry of Health of the Czech Republic project no. 15-26588A.
  • KF was supported by Ministry of Health of the Czech Republic project no. NV18-08-00385.


Other supporters