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
1BPD027H00_BC554DBC554DD27BP BPD027H00_BC554D.fcs 379,216
2BPD027H00_BT145BT145D27BP BPD027H00_BT145.fcs 542,145
3BPD027H00_CBL004CBL004D27BP BPD027H00_CBL004.fcs 426,000
4BPD027H00_CC840CC840D27BP BPD027H00_CC840.fcs 835,039
5BPD027H00_CCB116CCB116D27BP BPD027H00_CCB116.fcs 453,826
6BPD019H00_BC554DBC554DD19BP BPD019H00_BC554D.fcs 572,958
7BPD019H00_BT145BT145D19BP BPD019H00_BT145.fcs 514,273
8BPD019H00_CBL004CBL004D19BP BPD019H00_CBL004.fcs 649,982
9BPD019H00_CC840CC840D19BP BPD019H00_CC840.fcs 516,674
10BPD019H00_CCB116CCB116D19BP BPD019H00_CCB116.fcs 240,091
11PPD000H00_BC554DBC554DH00PP PPD000H00_BC554D.fcs 485,631
12PPD000H00_BT145BT145H00PP PPD000H000_BT145.fcs 549,104
13PPD000H00_CBL004CBL004H00PP PPD000H00_CBL004.fcs 387,036
14PPD000H00_CC840CC840H00PP PPD000H00_CC840.fcs 830,053
15PPD000H00_CCB116CCB116H00PP PPD000H00_CCB116.fcs 620,959
16PPD000H06_BC554DBC554DH00PPPPD000H06_BC554D.fcs 470,642
17PPD000H06_BT145BT145H00PPPPD000H06_BT145.fcs 670,857
18PPD000H06_CBL004CBL004H00PPPPD000H06_CBL004.fcs 568,345
19PPD000H06_CC840CC840H00PPPPD000H06_CC840.fcs 772,846
20PPD000H06_CCB116CCB116H00PPPPD000H06_CCB116.fcs 621,498
21PPD001H00_BC554DBC554DD01PP PPD001H00_BC554D.fcs 632,618
22PPD001H00_BT145BT145D01PP PPD001H00_BT145.fcs 653,277
23PPD001H00_CBL004CBL004D01PP PPD001H00_CBL004.fcs 469,087
24PPD001H00_CC840CC840D01PP PPD001H00_CC840.fcs 838,483
25PPD001H00_CCB116CCB116D01PP PPD001H00_CCB116.fcs 752,279
26PPD003H00_BC554DBC554DD03PP PPD003H00_BC554D.fcs 796,397
27PPD003H00_BT145BT145D03PP PPD003H00_BT145.fcs 363,416
28PPD003H00_CBL004CBL004D03PP PPD003H00_CCB116.fcs 762,792
29PPD003H00_CC840CC840D03PP PPD003H00_CC840.fcs 677,265
30PPD003H00_CCB116CCB116D03PP PPD003H00_CCB116.fcs 587,500
31PPD008H00_BC554DBC554DD08PP PPD008H00_BC554D.fcs 822,189
32PPD008H00_BT145BT145D08PP PPD008H00_BT145.fcs 659,918
33PPD008H00_CBL004CBL004D08PP PPD003H00_CCB116.fcs 495,605
34PPD008H00_CC840CC840D08PP PPD008H00_CC840.fcs 759,876
35PPD008H00_CCB116CCB116D08PP PPD008H00_CCB116.fcs 459,273
36PBD000H00_BC554DBC554DH00PB PBD000H00_BC554D.fcs 860,727
37PBD000H00_BT145BT145H00PB PBD000H00_BT145.fcs 778,709
38PBD000H00_CBL004CBL004H00PB PBD000H00_CBL004.fcs 642,882
39PBD000H00_CC840CC840H00PB PBD000H00_CC840.fcs 657,108
40PBD000H00_CCB116CCB116H00PB PBD000H00_CCB116.fcs 545,693
41PBD000H06_BC554DBC554DH06PB PBD000H06_BC554D.fcs 697,280
42PBD000H06_BT145BT145H06PB PBD000H06_BT145.fcs 759,853
43PBD000H06_CBL004CBL004H06PB PBD000H06_CBL004.fcs 821,341
44PBD000H06_CC840CC840H06PB PBD000H06_CC840.fcs 676,713
45PBD000H06_CCB116CCB116H06PB PBD000H06_CCB116.fcs 767,993
46PBD001H00_BC554DBC554DD01PB PBD001H00_BC554D.fcs 667,939
47PBD001H00_BT145BT145D01PB PBD001H00_BT145.fcs 598,244
48PBD001H00_CBL004CBL004D01PB PBD001H00_CBL004.fcs 861,405
49PBD001H00_CC840CC840D01PB PBD001H00_CC840.fcs 670,555
50PBD001H00_CCB116CCB116D01PB PBD001H00_CCB116.fcs 452,805
51PBD003H00_BC554DBC554DD03PB PBD003H00_BC554D.fcs 447,317
52PBD003H00_BT145BT145D03PB PBD003H00_BT145.fcs 736,728
53PBD003H00_CBL004CBL004D03PB PBD003H00_CBL004.fcs 96,283
54PBD003H00_CC840CC840D03PB PBD003H00_CC840.fcs 674,066
55PBD003H00_CCB116CCB116D03PB PBD003H00_CCB116.fcs 718,784
56PBD008H00_BC554DBC554DD08PB PBD008H00_BC554D.fcs 242,058
57PBD008H00_BT145BT145D08PB PBD008H00_BC554D.fcs 327,046
58PBD008H00_CBL004CBL004D08PB PBD008H00_CBL004.fcs 593,431
59PBD008H00_CC840CC840D08PB PBD008H00_CC840.fcs 291,948
60PBD008H00_CCB116CCB116D08PB PBD008H00_CCB116.fcs 519,604
61PBD014H00_BC554DBC554DD14PB PBD014H00_BC554D.fcs 536,453
62PBD014H00_BT145BT145D14PB PBD014H00_BT145.fcs 172,437
63PBD014H00_CBL004CBL004D14PB PBD014H00_CBL004.fcs 321,208
64PBD014H00_CC840CC840D14PB PBD014H00_CC840.fcs 499,992
65PBD014H00_CCB116CCB116D14PB PBD014H00_CCB116.fcs 474,893
66PBD028H00_BC554DBC554DD28PB PBD028H00_BC554D.fcs 564,540
67PBD028H00_BT145BT145D28PB PBD028H00_BT145.fcs 396,758
68PBD028H00_CBL004CBL004D28PB PBD028H00_CBL004.fcs 554,592
69PBD028H00_CC840CC840D28PB PBD028H00_CC840.fcs 1,035,383
70PBD028H00_CCB116CCB116D28PB PBD028H00_CCB116.fcs 623,748
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. 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.