HIPC_Stanford {CytOpT}

HIPC_Stanford data

Description

HIPC T cell data set from HIPC program for patients 1228 and 1369 (replicate 1A from Stanford).

Usage

data(HIPC_Stanford)

Format

The data are composed of 4 objects:

HIPC_Stanford_1228_1A:

a data.frame of 31342 cells and 7 markers.

HIPC_Stanford_1228_1A_labels:

a factor vector with the cell type of each of the 31342 observed cells.

HIPC_Stanford_1369_1A:

a data.frame of 33992 cells and 7 markers.

HIPC_Stanford_1369_1A_labels:

a factor vector with the cell type of each of the 33992 observed cells.

Details

This immunophenotyping T cell panel from the Lyoplate HIPC dataset was used as part of the FlowCAP III Lyoplate challenge.

Flow cytometry data set from the HIPC T-cell panel study. In the HIPC T-cell panel study, Flow cytometry was measured in 3 samples for each 3 patients (IDs: 1228, 1349 and 1369) with 3 replicates each (1A, 2B and 3C) in 7 centers (NHLBI, Yale, UCLA, CIMR, Baylor, Stanford and Miami), i.e. 63 data sets in total. Manual gating was performed in the different centers to cluster te observed cells into one of 10 cellular populations:

1. CD8 Effector

2. CD8 Naive

3. CD8 Central Memory

4. CD8 Effector Memory

5. CD8 Activated

6. CD4 Effector

7. CD4 Naive

8. CD4 Central Memory

9. CD4 Effector Memory

10. CD4 Activated

Source

https://www.immuneprofiling.org/hipc/page/show https://www.immunespace.org/ https://www.immunespace.org/project/HIPC/Lyoplate/begin.view?pageId=study.DATA_ANALYSIS

References

Maecker HT, McCoy JP & Nussenblatt R (2012). Standardizing immunophenotyping for the human immunology project. Nature Reviews Immunology, 12(3):191–200. DOI: 10.1038/nri3158

Finak G, Langweiler M, Jaimes M, Malek M, Taghiyar J, Korin Y, Raddassi K, Devine L, Obermoser G, Pekalski ML, Pontikos N, Diaz A, Heck S, Villanova F, Terrazzini N, Kern F, Qian Y, Stanton R, Wang K, Brandes A, Ramey J, Aghaeepour N, Mosmann T, Scheuermann RH, Reed E, Palucka K, Pascual V, Blomberg BB, Nestle F, Nussenblatt RB, Brinkman RR, Gottardo R, Maecker H & McCoy JP (2016). Standardizing Flow Cytometry Immunophenotyping Analysis from the Human ImmunoPhenotyping Consortium. Scientific Reports. 10(6):20686. DOI: 10.1038/srep20686.