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
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 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.
|CVQb||CV of ABC|
|p10Qb||10th percentile ABC|
|p25Qb||25th percentile ABC|
|p75Qb||75th percentile ABC|
|p90Qb||90th percentile ABC|
|PEpos||Frequency of positive cells|
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,
Populations measured in all panels. In the project we use internal (CODE) names and DISPLAY names to be shown to users.
|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|
|Tgd||gamma delta T cells||2_B_T|
|TCD8RAdim||CD45RAdim CD27+ CD8 T cells||2_B_T|
|TCD4||CD4 T cells||2_B_T|
|TCD8||CD8 T 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|
|UnswtMem||Unswitched Memory B-cells||4_ton|
|SwtMem||Switched Memory B-cells||4_ton|
Gating of Panel 2 - Peripheral blood: B- and T-cell
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.