Data dissemination

Originality and quality of the dataset

Our mass cytometry dataset is composed of macaque blood samples collected at steady state, before or long after immunization, outnumbered by samples collected very early after immunization, during acute inflammation.

To ensure a high quality of the dataset, we controlled the quality of each staining and acquisition and their reproducibility. We used the same batches of antibody all along the longitudinal study and we included the same two control samples each time to allow us to exclude samples or markers from the analysis because of a batch effect.

Data accessibility

We provide full access to our mass cytometry data here (pre-processed and processed data).

Data are also available from Flowrepository (ID FR-FCM-ZYBG) , which also provides full experimental and acquisition metadata.

Data are also accessible from Cytobank under accession number 68443 and 68590. Cytobank Community allows new analyses using manual gating. We created gates for each phenotypic family and superfamily, so you can visualize our data (phenotype and cell number) at these two levels and decide which marker, animal, and time-points you want to display as histograms, including overlays, or biplots. Cytobank Premium and Enterprise allow additional multidimensional analyses using SPADE, but also viSNE and CITRUS, although without a random pre-downsampling step, which we believe is key to equalize the contribution of each sample and which was included in the current analysis.

#sample nameanimal IDtimepointFCSnumber of events
1BPD019H00_BB078BB078D19BP BPD019H00_BB078.fcs 114,244
2BPD019H00_BB231BB231D19BP BPD019H00_BB231.fcs 117,463
3BPD019H00_BC641BC641D19BP BPD019H00_BC641.fcs 147,515
4BPD019H00_BD619BD619D19BP BPD019H00_BD619.fcs 160,415
5BPD019H00_BD620BD620D19BP BPD019H00_BD620.fcs 137,862
6PPD000H00_BB078BB078H00PP PPD000H00_BB078.fcs 105,318
7PPD000H00_BB231BB231H00PP PPD000H000_BB231.fcs 62,451
8PPD000H00_BC641BC641H00PP PPD000H00_BC641.fcs 71,336
9PPD000H00_BD619BD619H00PP PPD000H00_BD619.fcs 131,117
10PPD000H00_BD620BD620H00PP PPD000H00_BD620.fcs 161,546
11PPD000H03_BB078BB078 H00PPPPD000H03_BB078.fcs 158,371
12PPD000H03_BB231BB231 H00PPPPD000H03_BB231.fcs 159,250
13PPD000H03_BC641BC641H00PP PPD000H03_BC641.fcs 190,509
14PPD000H03_BD619BD619H00PPPPD000H03_BD619.fcs 133,164
15PPD000H03_BD620BD620H00PPPPD000H03_BD620.fcs 194,991
16PPD000H06_BB078BB078H00PPPPD000H06_BB078.fcs 154,642
17PPD000H06_BB231BB231H00PPPPD000H06_BB231.fcs 197,605
18PPD000H06_BC641BC641H00PPPPD000H06_BC641.fcs 192,414
19PPD000H06_BD619BD619H00PPPPD000H06_BD619.fcs 186,113
20PPD000H06_BD620BD620H00PPPPD000H06_BD620.fcs 150,724
21PPD001H00_BB078BB078D01PP PPD001H00_BB078.fcs 146,185
22PPD001H00_BB231BB231D01PP PPD001H00_BB231.fcs 87,666
23PPD001H00_BC641BC641D01PP PPD001H00_BC641.fcs 153,658
24PPD001H00_BD619BD619D01PP PPD001H00_BD619.fcs 151,935
25PPD001H00_BD620BD620D01PP PPD001H00_BD620.fcs 185,683
26PPD003H00_BB078BB078D03PP PPD003H00_BB078.fcs 115,397
27PPD003H00_BB231BB231D03PP PPD003H00_BB231.fcs 93,663
28PPD003H00_BD619BD619D03PP PPD003H00_BD619.fcs 134,085
29PPD003H00_BD620BD620D03PP PPD003H00_BD620.fcs 132,034
30PPD008H00_BB078BB078D08PP PPD008H00_BB078.fcs 133,512
31PPD008H00_BB231BB231D08PP PPD008H00_BB231.fcs 124,869
32PPD008H00_BD619BD619D08PP PPD008H00_BD619.fcs 121,685
33PPD008H00_BD620BD620D08PP PPD008H00_BD620.fcs 97,003
34PPD014H00_BB078BB078D14PP PPD014H00_BB078.fcs 157,067
35PPD014H00_BB231BB231D14PP PPD014H00_BB231.fcs 146,843
36PPD014H00_BC641BC641D14PP PPD014H00_BC641.fcs 144,849
37PPD014H00_BD619BD619D14PP PPD014H00_BD619.fcs 116,936
38PPD014H00_BD620BD620D14PP PPD014H00_BD620.fcs 144,753
39PBD000H00_BB078BB078H00PB PBD000H00_BB078.fcs 173,286
40PBD000H00_BB231BB231H00PB PBD000H00_BB231.fcs 200,907
41PBD000H00_BC641BC641H00PB PBD000H00_BC641.fcs 68,326
42PBD000H00_BD619BD619H00PB PBD000H00_BD619.fcs 147,323
43PBD000H00_BD620BD620H00PB PBD000H00_BD620.fcs 139,075
44PBD000H03_BB078BB078H03PB PBD000H03_BB078.fcs 214,595
45PBD000H03_BB231BB231H03PB PBD000H03_BB231.fcs 164,924
46PBD000H03_BC641BC641H03PB PBD000H03_BC641.fcs 68,369
47PBD000H03_BD619BD619H03PB PBD000H03_BD619.fcs 64,272
48PBD000H03_BD620BD620H03PB PBD000H03_BD620.fcs 113,498
49PBD000H06_BB078BB078H06PB PBD000H06_BB078.fcs 225,773
50PBD000H06_BB231BB231H06PB PBD000H06_BB231.fcs 244,110
51PBD000H06_BC641BC641H06PB PBD000H06_BC641.fcs 270,132
52PBD000H06_BD619BD619H06PB PBD000H06_BD619.fcs 233,035
53PBD000H06_BD620BD620H06PB PBD000H06_BD620.fcs 233,264
54PBD001H00_BB078BB078D01PB PBD001H00_BB078.fcs 193,136
55PBD001H00_BB231BB231D01PB PBD001H00_BB231.fcs 128,369
56PBD001H00_BC641BC641D01PB PBD001H00_BC641.fcs 234,244
57PBD001H00_BD619BD619D01PB PBD001H00_BD619.fcs 159,883
58PBD001H00_BD620BD620D01PB PBD001H00_BD620.fcs 175,616
59PBD003H00_BB078BB078D03PB PBD003H00_BB078.fcs 108,404
60PBD003H00_BB231BB231D03PB PBD003H00_BB231.fcs 189,688
61PBD003H00_BC641BC641D03PB PBD003H00_BC641.fcs 95,487
62PBD003H00_BD619BD619D03PB PBD003H00_BD619.fcs 103,584
63PBD003H00_BD620BD620D03PB PBD003H00_BD620.fcs 164,337
64PBD008H00_BB078BB078D08PB PBD008H00_BB078.fcs 226,125
65PBD008H00_BC641BC641D08PB PBD008H00_BC641.fcs 239,341
66PBD008H00_BD619BD619D08PB PBD008H00_BD619.fcs 233,747
67PBD008H00_BD620BD620D08PB PBD008H00_BD620.fcs 318,350
68PBD014H00_BB078BB078D14PB PBD014H00_BB078.fcs 225,733
69PBD014H00_BB231BB231D14PB PBD014H00_BB231.fcs 230,585
70PBD014H00_BC641BC641D14PB PBD014H00_BC641.fcs 140,196
71PBD014H00_BD619BD619D14PB PBD014H00_BD619.fcs 150,390
72PBD014H00_BD620BD620D14PB PBD014H00_BD620.fcs 295,739
Cytometry data were processed as followed. They were normalized using Rachel Finck’s MATLAB normalizer. Replicates were concatenated using the FCS file concatenation tool from Cytobank. Using Cytobank, Four-Element Calibration Beads were excluded by manual gating. Singlets were selected on an Ir191 (DNA intercalator)/cell_length bivariate plot. Finally, cells were gated on a CD66/CD3 bivariate plot after exclusion of the contaminated double positive cells (likely eosinophils). The number of cells per sample analyzed after these pre-processing steps is indicated. Samples were given a name, which includes the timepoint of blood collection and specifies the number of days (D) and hours (H) before or after immunization, as well as the macaque ID. BP is for before prime; PP for post-prime and PB for post-boost. Samples from macaque BC641 at D3PP and D8PP and macaque BB231 at D8PB were excluded from the SPADE analysis due to the low number of acquired cells of interest (<50,000 live non CD3+ CD66+ singlets). They are not provided.