Supplemental Information
The ABC model
We model the cell dynamics as a stochastic Markov process which includes three
states, named state A, B and C. For sake of mathematical simplicity, we considered a
discrete time branching process, whose time step unit is named ∆t. We suppose that,
from a time step to the next, an A cell can die (rate Ad), stay the same (rate Ai), divide
giving rise to two type B cells (rate As), or produce an asymmetric division in an B
and a C cell (rate Aa). A B cell can die (rate Bd), stay the same (rate Bi), duplicate
(rate Bs), give rise to a type C cell (rate Bt), or divide asymmetrically in an B and a C
cell (rate Ba). Similarly, C cells can die, stay the same, divide (rates Cd, Ci, Cs). A
number of other state changes could be considered. For simplicity we only include the
above ones which are motivated on biological grounds. In our FACS data at day 3.5
the last populated subgroup is G6N, which points out that six division steps must have
occurred since day 0. From that we derive ∆t = 14h, a value compatible with the
known duration of the cell cycle.
The ABC model can be analytically fully solved. The recursive relations of the
average number of A, B and C cells, A(t), B(t) and C(t) can be derived from the
Master Equation of the Markov process:
A(t + 1)
α
(B(t + 1)) = (η
δ
C(t + 1)
0 0 A(t)
β 0) (B(t))
C(t)
σ γ
where
α = Ai ; β = 2Bs + Bi + Ba ; γ = 2Cs + Ci ; η = 2As + Aa ; σ = Bt + Ba ; δ = Aa .
The eigenvalues α, β, γ of the above matrix give the longer time scale growth rates of
the A, B and C populations respectively.
The number composition of the different subpopulations, G0N, G1N, …, G6N can be
analogously derived at any time, t, as a function of the microscopic parameters of the
model.
Fit of FACS data
The initial condition considered in our fit corresponds to have all cells in state A, i.e.,
B(0) = T(0) = 0. The number of cells in the A population at day 0, A(0), is taken from
the experiments. We refer here, for definiteness, to the case of the FACS data
collected at day 3.5, where A(0) = 3.1 × 104.
The model parameters are subject to the three normalization conditions of the
probability rates in each single state. In the general case where asymmetric transitions
are included, the ABC model has, thus, nine independent parameters. They are
obtained by a Least Squares fit from the 13 measured subpopulations at day 3.5. More
specifically, we find the minimum of the standard weighted squared distance:
6
2
5
GiN
GiP
D = ∑ ωiN ( ∗ − 1) + ∑ ωiP ( ∗ − 1)
GiN
GiP
i=0
2
i=0
∗
where GiN/P and GiN/P
are respectively, the predicted and observed number of IL13-
GFP± cells at day 3.5 having undergone i divisions. Finally, in the expression for D
the weights ωiN/P are the relative fractions of the different observed populations:
∗
∗
ωiN/P = GiN/P
/ ∑j GjN/P
.
Positive and Negative State specific gene
We call A Pos, B Pos and C Pos, those genes that were specifically expressed only in
state A, B and C respectively. We named A Neg, B Neg and C Neg those genes
whose expression was repressed only in state A, B and C respectively.
Genes were ranked with respect to the difference between the relative abundance in
the positive state and the maximum relative abundance of the other states.
The relative abundance of a given gene i in state j, si,j is:
𝑠𝑖,𝑗 =
𝑅𝑃𝐾𝑀𝑖,𝑗
⁄∑
𝑗=𝐸,𝐴,𝑇 𝑅𝑃𝐾𝑀𝑖,𝑗
where RPKMij is the RPKM value of gene i in state j.
In detail, we considered Positive only those genes whose expression is above their
average expression only in one state (i.e, say si,j>1 only in one state), while Negative
genes are those whose expression is below their average expression only in one state
(i.e, say si,j<1 only in on state).
Robustness of the fit with the ABC model
In the main text we focused, in particular, on our FACS data at day 3.5 as they
provide the broader and more precise measure of the different cell subpopulations.
However, to asses the quality of our fit, we also considered independent FACS data at
day 2 and day 3. Also in such cases the ABC model fits well the data. Importantly, the
values of the parameters from the day 3.5 fit are, within errors, fully consistent with
the values obtained by averaging the parameters of the fits across day 2, 3, 3.5. This is
illustrated in the Figure S4c. Moreover, the fit of day 3.5 well reproduces day 2 and
day 3 as shown in Figure S4b.
Asymmetric divisions
We also tested ABC model including asymmetric divisions. In particular, we
considered a model (As-ABC) where asymmetric division (Aa and Ba, see Figure S4h)
are added and a model (OA-ABC) where transitions Aa and Ba are take into account
instead of As and Bt.
The OA-ABC and A-ABC models do fit the day 3.5 and day 3 and day 2 FACS data,
but the state population growth curves obtained with the OA-ABC and As-ABC are
markedly different from the one obtained with the ABC Model (i.e., model with Aa =
Ba = 0), since the A population is predicted to dominate at all large time scales (see
Figure S4i and j). In facts, in all cases the OA-ABC fits give, for the longer time
scale, a growth rate for state B larger than for state C: β = 1.3 > γ = 0.2 (average).
More importantly, OA-ABC finds that transition from B to C are absent (Bt = Ba = 0).
The As-ABC gives in average β = 1.2 > γ = 0.9, but it results γ < β only in fit of day 2
and day 3 showing instability in model predictions. Moreover, the asymmetric models
give negligible asymmetric transition parameters in some cases suggesting that
asymmetric transitions are absent with respect to the symmetric one, in particular the
As-ABC finds the same parameters of those found by the ABC model at day 3.5 with
asymmetric transition completely absent (Aa = Ba = 0).
Statistical Model Selection: AIC and BIC
To compare the quality of the fit of FACS data at day 3.5 with different ABC models,
we computed the corresponding Akaike Information Criterion (AIC) and Bayesian
Information Criterion (BIC) model selection parameters. Let LM be the log-likelihood
of the parameter given the dataset, k the number of parameters and n the sample size.
In this way AIC and BIC, for a model, are calculated through their definitions:
AIC = 2k − 2LM
BIC = −2LM + kln(n)
In particular, we compared the AIC and BIC of the ABC model with As-ABC and
OA-ABC models. AIC and BIC were calculated for all three cases of day 2, day 3 and
day 3.5. In all cases the Symmetric ABC Model represents the minimum, while the
OA-ABC results to be always the maximum. This suggest that the ABC model shows
the best performances in terms of model fitting and complexity of the model
compared with As-ABC and OA-ABC as shown in Figure S4k, which is the case of
the fit of day 3.5.
ERCC total reads
The reduction in ERCC content from day 2 to days 3 and 4 can be ascribed to changes
in cell sizes and total mRNA content due to cell cycle activation (rather than ERCC
degradation, which is an alternative explanation). Cells at day 2 have a diameter of
roughly 6 μM, while at day 3 and 4 they can reach up to 10 μM of diameter. The
corresponding cell volume can then vary by up to a factor of 5 with the result of a
significant dilution of the ERCC molecules as in the plot below.
Supplementary Table 1 Single cell Read Statistic and capturing efficiency for
Nippostrongilus brasiliensis infection experiment
Cell Name Total
Reads
lung_3
1487939
lung_9
1928230
lung_19
2053091
lung_21
1610331
lung_27
930412
lung_43
1257027
lung_49
968646
lung_57
2184210
lung_58
2078589
lung_61
800147
lung_66
748231
lung_70
819601
lung_72
789447
lung_84
1748822
Mapped
(%)
80.5
88.3
79.3
83.5
67.8
73.4
68.1
86.7
82.4
73.5
76.4
87.7
87.2
81.4
Unmapped
(%)
19.0
12.0
21.0
17.0
32.0
27.0
32.0
13.0
18.0
27.0
24.0
12.0
13.0
19.0
Mapped to
ERCCs (%)
20.0
5.0
8.0
7.0
33.0
24.0
28.0
6.0
6.0
31.0
39.0
8.0
3.0
19.0
lung_94
lung_96
med_2
med_9
med_20
med_24
med_26
med_28
med_38
med_39
med_44
med_45
med_46
med_50
med_53
med_54
med_57
med_64
med_66
med_67
med_70
med_73
med_75
med_80
med_81
med_86
med_88
med_90
med_91
mes_4
mes_5
mes_11
mes_14
mes_15
mes_17
mes_19
mes_20
mes_21
mes_22
mes_26
mes_29
mes_31
mes_34
mes_35
mes_36
1018096
1446210
1504147
1645725
1063495
1358355
1372033
1491171
1805011
1283232
1110165
422249
674987
885442
1167662
961377
1656932
1361864
1133447
1065950
1515411
1603212
1570878
1613727
1605686
1087474
1674417
1377321
2129850
1969331
1894309
2018354
1590749
1340324
1228724
2014018
1491172
1469916
819325
1097654
1787702
1867026
1700704
1241742
2099841
84.1
78.7
69.3
80.9
82.7
83.5
82.6
83.2
85.0
85.3
80.8
80.1
87.2
81.0
85.2
78.7
81.6
84.4
74.8
85.1
83.3
84.8
83.2
83.4
83.6
68.0
59.7
75.4
81.5
86.9
83.7
84.2
89.1
83.5
83.8
88.8
81.5
76.6
77.5
89.9
88.1
87.5
88.5
81.4
82.3
16.0
21.0
31.0
19.0
17.0
16.0
17.0
17.0
15.0
15.0
19.0
20.0
13.0
19.0
15.0
21.0
18.0
16.0
25.0
15.0
17.0
15.0
17.0
17.0
16.0
32.0
40.0
25.0
18.0
13.0
16.0
16.0
11.0
17.0
16.0
11.0
18.0
23.0
23.0
10.0
12.0
12.0
11.0
19.0
18.0
11.0
18.0
17.0
12.0
10.0
4.0
10.0
12.0
9.0
10.0
12.0
16.0
7.0
16.0
9.0
5.0
9.0
12.0
15.0
11.0
10.0
3.0
5.0
3.0
8.0
25.0
19.0
17.0
9.0
8.0
7.0
9.0
8.0
13.0
21.0
7.0
11.0
9.0
25.0
11.0
10.0
12.0
10.0
22.0
8.0
mes_38
mes_44
mes_51
mes_53
mes_54
mes_56
mes_57
mes_62
mes_63
mes_64
mes_66
mes_68
mes_72
mes_79
mes_80
mes_84
mes_85
mes_88
mes_93
1001506
922259
1407907
755217
1075598
1632849
625455
956076
1135589
1020401
806268
1790649
1291221
1338069
858360
1883627
292537
1254618
1600476
22.0
19.0
11.0
32.0
22.0
18.0
14.0
15.0
13.0
19.0
18.0
14.0
21.0
25.0
16.0
27.0
17.0
28.0
10.0
78.2
81.1
89.2
68.5
78.1
82.5
86.4
85.3
87.4
81.1
82.1
85.9
79.1
74.8
83.7
72.9
82.7
72.3
83.1
19.0
16.0
11.0
38.0
26.0
12.0
7.0
11.0
17.0
20.0
30.0
12.0
18.0
21.0
13.0
13.0
13.0
18.0
10.0
Cell capturing efficiency
1 cell
0 cells
2+ cells
Mediastinal
LN
60
0
36
Mesenteric
LN
68
6
22
Lungs
Total (5)
75
3
18
71%
3%
26%
Supplementary Table 2 Number of sorted cells and purity (between brackets)
Replicate 1
Replicate 2
G0N
74140
41079
G2N
283389 (98%)
236661
G4N
665203 (97%)
382689
G4P
186135
93783
Supplementary Table 3 Read statistic
Total number of reads, mapped reads (with relative percentage) and unmapped reads
(with relative percentage). Spearman or correlations between biological replicates are
reported.
G0Na
G0Nb
G2Na
G2Nb
G4Na
G4Nb
G4Pa
G4Pb
Total
Mapp.
36389086
39659196
55740953
50481720
54573367
59346788
49367823
55327073
28801842
31818429
47164694
40256442
45166697
47739047
40873758
44434595
%
Unmapp.
%
79.15
80.23
84.61
79.74
82.76
80.44
82.79
80.31
7587244
7840767
8576259
10225278
9406670
11607741
8494065
10892478
20.85
19.77
15.39
20.26
17.24
19.56
17.21
19.69
Spear
man
Corr
Pearso
n Corr
0.949
0.989
0.959
0.991
0.959
0.993
0.962
0.993
Supplementary Table 4 Antibody list
Atibody
anti CD8
anti CD11b
anti CD11c
anti CD19
anti CD25
anti Ly6G
anti CD3e
anti CD28
anti GATA3
anti Tbx21
Conjugation
FITC
FITC
FITC
FITC
FITC
FITC
Alexa647
PE
Clone
Clone 536.7
Clone M1/70
Clone N418
Clone 1D3
Clone 7D4
Clone RB6 8C5
Clone 1452C11
Clone 37.51
eBioscience
clone eBio4B10
Company
eBioscience
eBioscience
eBioscience
BD Bioscience
BD Bioscience
eBioscience
eBioscience
eBioscience
eBioscience
eBioscience
Supplementary Table 5 Primer list
BATF3
BATF3
EPAS11
EPAS11
FOS
FOS
GAPDH
GAPDH
GATA3
GATA3
IFNGAMMA
IFNGAMMA
IL-10
IL-10
IL-17a
IL-17a
F
R
F
R
F
R
F
R
F
R
F
R
F
R
F
R
AGGACGATGACAGGAAAGTTCG
CTGCAACCCGGTTTTTCTCT
CTGAGGAAGGAGAAATCCCGT
TGTGTCCGAAGGAAGCTGATG
CGGGTTTCAACGCCGACTA
TGGCACTAGAGACGGACAGAT
AACATCAAATGGGGTGAGGCC
GTTGTCATGGATGACCTTGGC
CCCTCCGGCTTCATCCTCT
CTGCACCTGATACTTGAGGC
ATGAACGCTACACACTGCATC
CCATCCTTTTGCCAGTTCCTC
TGGGTGAGAAGCTGAAGACC
GCTCCACTGCCTTGCTCTTA
CTCCAGAAGGCCCTCAGACTAC
AGCTTTCCCTCCGCATTGACACAG
IL-4
IL-4
IL-5
IL-5
IL-22
IL-22
MYB
MYB
NFKBIA
NFKBIA
NR4A1
NR4A1
NR4A3
NR4A3
POU6F1
POU6F1
RBPJ
RBPJ
TCF7
TCF7
VDR
VDR
ZBTB16
ZBTB16
F
R
F
R
F
R
F
R
F
R
F
R
F
R
F
R
F
R
F
R
F
R
F
R
ACTTGAGAGAGATCATCGGCA
AGCTCCATGAGAACACTAGAGTT
CTCTGTTGACAAGCAATGAGACG
TCTTCAGTATGTCTAGCCCCTG
AGACAGGTTCCAGCCCTACA
CTGGATGTTCTGGTCGTCAC
GAACAGATGGGCAGAGATCG
AGCCTTCCTGTTCCACCTTG
ACGAGCAAATGGTGAAGGAG
GGCTTCTCTTCGTGGATGAT
GCAGTCTGTGGTGACAATGC
CTCTTGTCCACAGGGCAATC
ACTACGGAGTCCGCACCTG
CTTGTCCACTGGGCAGTTTT
GTCAGATCCTCACGAATGCTC
GAGTCACGGCTTGGACCTG
CAGCAGCTGAACTTGGAAGG
GGAGGGTTTGGAGATGACCT
AGCTTTCTCCACTCTACGAACA
AATCCAGAGAGATCGGGGGTC
ACCCTGGTGACTTTGACCG
GGCAATCTCCATTGAAGGGG
GTGCCCAGTTCTCAAAGGAG
CCCACACAGCAGACAGAAGA
Supplementary Table 6 Biomark Gene list
Informative Genes
Ahr
Asb22
Atf3
Atp5a1
Bcl2
Bcl2l11
Cd3e
Ptprc
Cdh17
Cxcr3
Cxcr5
Cxcr6
Cyp11a1
Ddit3
E2f8
Epas11
Foxp1
Gata3
Hlx
Ifng
Ifngr1
Il10
Il12rb2
Il21
Il4
Il4ra
Il5
Il6
Il7r
Jhdm1d
Mllt6
Myb
Mycn
Ncf1
Pou6f1
Pparg
Prdm1
Ptgir
Pth
Rora
Rorc
Smad7
Tbx21
Tcf7
Tg
Tgfb1
Txk
Zc3h12c
Zfp36
Housekeeping genes
Atp5a1
Ubc
polr2a
Elf2b
Hprt
Lowly expressed/Not consistent with RNA-seq data genes
Batf
Fgf18
Il2
Il9
Pde2a
Ccr8
Sell
Runx3
Il2ra
Msc
Ccr2
Ccr5
Cd4
Eif2b1
Gata2
Il13
Il13ra1
Il23r
Il27r
Il4r
Irf8
Phf1
Scml4
Vdr
Zbtb16
Negative Control Genes (other immune cell types/plant gene)
Arf1
Hbb-b2
Cd33
Cd19
Cd20
Cd8b1
Cd56
Cd11b
Cd11c
Cd44
Foxp3
Supplementary Table 7 Single cell Read Statistic for Plasmodium chabaudi
infection experiment
Day2-1
Day2-2
Day2-3
Day2-4
Day2-5
Day2-6
Day2-7
Day2-8
Day2-9
Day2-10
Day2-11
Day2-12
Day2-13
Day2-14
Day2-15
Day2-16
Day2-17
Day2-18
Day2-19
Day2-20
Day2-21
Total
Reads
4133223
3435415
3428253
3269806
2339041
4778547
3052057
4206871
3911806
4052925
4116936
3001127
4783089
4058289
3934260
3971835
3661468
4595352
2660478
3632743
3737703
Mapped
(%)
96.7
93.2
95.0
94.4
88.6
95.0
92.0
97.8
95.9
95.5
91.3
93.7
91.2
91.7
93.1
95.7
95.8
97.0
93.5
96.0
94.3
Unmapped
(%)
3.3
6.8
5.0
5.6
11.4
5.0
8.0
2.2
4.1
4.5
8.7
6.3
8.8
8.3
6.9
4.3
4.2
3.0
6.5
4.0
5.7
mapped to
ERCCs (%)
71.9
46.8
48.9
47.2
11.6
51.0
13.2
40.9
49.2
47.5
33.0
18.2
37.8
33.0
22.4
31.3
62.5
36.0
34.7
36.2
37.6
Day2-22
Day2-23
Day2-24
Day2-25
Day2-26
Day2-27
Day2-28
Day2-29
Day2-30
Day2-31
Day2-32
Day2-33
Day2-34
Day2-35
Day2-36
Day2-37
Day2-38
Day2-39
Day2-40
Day2-41
Day2-42
Day2-43
Day2-44
Day2-45
Day2-46
Day2-47
Day2-48
Day2-49
Day2-50
Day2-51
Day2-52
Day2-53
Day2-54
Day2-55
Day2-56
Day2-57
Day2-58
Day2-59
Day2-60
Day2-61
Day2-62
Day2-63
Day2-64
Day2-65
Day2-66
4391500
3144777
3524278
2966082
6310636
4047191
3889842
4391290
4757378
4341656
4055725
5140121
3389254
3200548
1874506
1795653
3039249
3631534
4008279
5300814
5055768
5247577
4195124
3203341
3856873
3992316
3293602
4073607
6795957
5682346
5657855
4675838
5226447
3945055
3277850
4485815
3534877
4314973
4135137
3204662
4604455
2266048
3146084
3680954
1814091
95.0
98.0
95.0
94.4
97.7
96.0
99.4
94.1
95.9
95.3
94.4
94.7
95.0
97.3
89.6
89.6
94.7
97.1
91.4
92.0
96.4
96.0
97.1
94.8
94.0
96.5
93.6
93.6
94.8
95.7
96.7
94.7
94.0
94.0
93.4
97.9
94.1
89.6
96.6
90.4
89.2
97.2
97.9
94.8
88.7
5.0
2.0
5.0
5.6
2.3
4.0
0.6
5.9
4.1
4.7
5.6
5.3
5.0
2.7
10.4
10.4
5.3
2.9
8.6
8.0
3.6
4.0
2.9
5.2
6.0
3.5
6.4
6.4
5.2
4.3
3.3
5.3
6.0
6.0
6.6
2.1
5.9
10.4
3.4
9.6
10.8
2.8
2.1
5.2
11.3
25.1
55.6
26.7
34.4
40.4
53.2
84.8
38.7
53.1
26.4
29.1
35.0
26.4
76.5
9.3
18.4
38.5
39.7
32.7
41.3
40.3
41.2
77.8
23.1
49.9
57.7
15.8
33.9
49.2
54.3
48.1
44.8
37.1
27.1
41.8
34.1
42.0
33.6
61.1
22.5
14.5
74.1
78.9
34.9
36.5
Day2-67
Day2-68
Day2-69
Day2-70
Day2-71
Day2-72
Day2-73
Day2-74
Day2-75
Day2-76
Day2-77
Day2-78
Day2-79
Day2-80
Day2-81
Day2-82
Day2-83
Day2-84
Day2-85
Day2-86
Day2-87
Day2-88
Day2-89
Day2-90
Day2-91
Day2-92
Day2-93
Day2-94
Day2-95
Day2-96
Day2-97
Day2-98
Day2-99
Day2-100
Day2-101
Day2-102
Day2-103
Day2-104
Day2-105
Day2-106
Day2-107
Day2-108
Day2-109
Day2-110
Day2-111
904345
2566002
1871331
1947833
1535703
1070463
1569117
1499146
2290535
913484
2234854
2675755
761920
2285398
1771452
1963853
1969632
873648
1555037
1361770
1965443
840884
2078510
2382656
2136037
1207217
1587915
1286158
1810082
168815
2166049
1437104
2573322
1607540
1071741
2368179
3203672
2317557
3076419
2601905
3393576
2148526
2840076
4569705
2149176
93.2
90.0
91.8
92.3
95.4
96.5
93.2
90.2
94.1
97.0
90.1
95.2
95.1
89.8
94.8
93.0
97.0
92.4
93.9
94.0
87.3
93.1
91.9
92.4
90.3
92.7
97.3
94.4
93.6
96.8
94.7
94.0
91.9
96.1
94.4
90.3
86.6
95.9
87.4
93.6
85.4
92.8
95.3
86.5
95.7
6.8
10.0
8.2
7.7
4.6
3.5
6.8
9.8
5.9
3.0
9.9
4.8
4.9
10.2
5.2
7.0
3.0
7.6
6.1
6.0
12.7
6.9
8.1
7.6
9.7
7.3
2.7
5.6
6.4
3.2
5.3
6.0
8.1
3.9
5.6
9.7
13.4
4.1
12.6
6.4
14.6
7.2
4.7
13.5
4.3
67.0
47.5
60.8
58.7
69.6
70.4
55.7
43.2
58.8
86.4
41.4
69.3
62.5
45.6
65.8
56.9
73.6
66.4
63.9
62.7
39.0
63.5
58.1
51.7
45.8
61.6
78.4
72.9
61.0
76.4
65.9
66.7
50.2
80.6
72.1
62.1
27.3
67.5
35.3
58.5
22.1
59.0
66.2
20.4
68.8
Day2-112
Day2-113
Day2-114
Day2-115
Day2-116
Day2-117
Day2-118
Day3-1
Day3-2
Day3-3
Day3-4
Day3-5
Day3-6
Day3-7
Day3-8
Day3-9
Day3-10
Day3-11
Day3-12
Day3-13
Day3-14
Day3-15
Day3-16
Day3-17
Day3-18
Day3-19
Day3-20
Day3-21
Day4-1
Day4-2
Day4-3
Day4-4
Day4-5
Day4-6
Day4-7
Day4-8
Day4-9
Day4-10
Day4-11
Day4-12
Day4-13
Day4-14
Day4-15
Day4-16
Day4-17
2410226
3554313
2462448
2807757
1547509
2365408
2096486
2909734
3293855
3796373
3014799
3208761
3205203
3612156
2538581
3097036
3109515
3657519
3598460
3857296
4380009
3508476
3007040
3538040
3471819
3418594
2776169
3386860
2512088
237349
2209597
2545036
2789708
3333524
2147804
3954984
3435188
4439136
4718270
3295232
2643263
5160664
4396294
5604739
4488570
97.1
90.0
93.2
93.8
88.4
92.5
95.5
86.7
85.3
86.5
86.2
86.0
84.3
86.0
83.1
84.3
85.2
85.4
85.6
86.8
87.2
86.4
85.4
86.3
85.7
85.3
85.5
83.9
91.0
88.9
88.7
90.1
89.2
92.0
88.6
91.7
90.4
87.4
91.8
88.3
91.1
93.0
89.4
94.7
89.6
2.9
10.0
6.8
6.2
11.6
7.5
4.5
13.3
14.7
13.5
13.8
14.0
15.7
14.0
16.9
15.7
14.8
14.6
14.4
13.2
12.8
13.6
14.6
13.7
14.3
14.7
14.5
16.1
9.0
11.1
11.3
9.9
10.8
8.0
11.4
8.3
9.6
12.6
8.2
11.7
8.9
7.0
10.6
5.3
10.4
73.6
36.9
57.0
58.5
33.1
57.3
68.8
17.2
8.6
10.6
10.7
10.2
6.3
11.7
7.1
7.0
7.5
6.8
9.4
11.4
13.8
22.1
5.6
7.0
12.2
6.5
4.6
5.6
3.3
2.9
3.4
3.7
6.6
8.1
3.4
8.0
7.3
8.5
21.0
3.1
10.4
14.6
6.4
31.7
6.1
Day4-18
Day4-19
Day4-20
Day4-21
Day4-22
Day4-23
Day4-24
Day4-25
Day4-26
Day4-27
Day4-28
Day4-29
Day4-30
Day4-31
Day4-32
Day4-33
Day4-34
Day4-35
Day4-36
Day4-37
Day4-38
Day4-39
Day4-40
Day4-41
Day4-42
Day4-43
Day4-44
Day4-45
Day4-46
Day4-47
Day4-48
Day4-49
Day4-50
Day4-51
Day4-52
Day4-53
Day4-54
Day4-55
Day4-56
Day4-57
Day4-58
Day4-59
Day4-60
Day4-61
Day4-62
4428250
5191296
4619674
5334058
3144079
3114956
6467589
3606348
5399174
3666688
4298976
5083878
4751914
3486362
2844116
2330343
2844014
1966120
2911691
3332447
2464554
4709950
4138274
3810021
5103061
3888809
4751964
4208059
4389228
4912179
5897013
4126511
5843328
5676481
6070802
3475745
5887451
5439110
5152065
5982702
4466965
4062662
3645661
215556
4150903
91.1
91.8
90.3
89.3
90.5
88.7
91.3
87.6
92.3
89.6
91.5
92.2
90.5
90.0
91.7
88.1
87.3
87.1
88.8
90.9
90.0
90.9
91.9
88.4
91.6
87.5
87.7
91.6
89.1
84.6
89.3
89.1
89.6
89.0
90.1
88.7
90.1
90.0
87.2
91.5
91.4
89.9
89.5
87.3
88.5
8.9
8.2
9.7
10.7
9.5
11.3
8.7
12.4
7.7
10.4
8.5
7.8
9.5
10.0
8.3
11.9
12.7
12.9
11.2
9.1
10.0
9.1
8.1
11.6
8.4
12.5
12.3
8.4
10.9
15.4
10.7
10.9
10.4
11.0
9.9
11.3
9.9
10.0
12.8
8.5
8.6
10.1
10.5
12.7
11.5
8.4
7.3
7.7
6.9
6.8
6.1
12.8
4.6
12.7
3.0
4.9
8.5
7.4
3.6
18.9
2.6
3.6
3.2
5.4
8.0
5.6
13.5
10.4
2.3
13.8
7.0
9.3
9.0
4.9
17.9
5.3
3.8
6.6
28.4
23.7
3.3
6.9
5.2
6.5
23.1
4.8
3.3
5.9
12.0
4.4
Day4-63
Day4-64
Day4-65
Day4-66
Day4-67
Day4-68
Day4-69
Day4-70
Day4-71
Day4-72
Day4-73
Day4-74
Day4-75
Day4-76
Day4-77
Day4-78
Day4-79
Day4-80
Day4-81
Day4-82
Day4-83
Day4-84
Day4-85
Day4-86
Day4-87
Day4-88
Day4-89
Day4-90
Day4-91
Day4-92
Day4-93
Day4-94
Day4-95
Day4-96
Day4-97
Day4-98
Day4-99
Day4-100
Day4-101
Day4-102
Day4-103
Day4-104
Day4-105
Day4-106
Day4-107
3821974
5572853
4981137
6195393
4421955
3521532
1064893
1404139
5390391
4102383
5280794
4056904
4372793
5086293
5387463
3705902
3906320
3334828
4543410
4838562
5524961
3219732
5791874
3093063
4297457
3755072
2865061
4510234
6164704
2674293
3662908
2731931
2373159
2492055
2640683
2482042
2514843
3271422
3770702
5057897
2871117
4383179
3486803
3992782
3950722
91.4
87.3
89.4
91.4
87.5
87.6
90.5
86.7
90.9
88.0
89.2
89.0
90.5
87.4
86.5
88.1
87.1
88.2
88.5
92.2
89.4
87.1
90.4
86.6
89.3
88.9
89.1
92.5
89.5
87.6
87.4
88.5
87.3
89.1
89.1
88.9
87.0
87.2
88.4
89.7
86.7
89.3
88.6
87.6
90.3
8.6
12.7
10.6
8.6
12.5
12.4
9.5
13.3
9.1
12.0
10.8
11.0
9.5
12.6
13.5
11.9
12.9
11.8
11.5
7.8
10.6
12.9
9.6
13.4
10.7
11.1
10.9
7.5
10.5
12.4
12.6
11.5
12.7
10.9
10.9
11.1
13.0
12.8
11.6
10.3
13.3
10.7
11.4
12.4
9.7
8.6
7.5
12.4
12.5
16.3
4.6
12.1
5.0
6.5
7.1
8.5
11.7
14.5
8.9
9.7
4.9
5.5
18.9
4.8
25.7
6.1
6.9
14.2
4.3
13.0
4.8
5.4
20.3
12.0
2.9
5.9
6.5
3.1
4.2
8.6
3.5
3.9
3.0
5.4
11.9
3.3
14.3
5.4
5.7
9.4
Day4-108
Day4-109
Day4-110
Day4-111
Day4-112
Day4-113
Day4-114
Day4-115
Day4-116
Day4-117
Day4-118
Day4-119
Day4-120
Day4-121
Day4-122
Day4-123
Day4-124
Day4-125
Day4-126
Day4-127
Day4-128
Day4-129
5153840
2922007
5623250
4644992
3853437
2293675
3674858
6050217
4057988
4399563
5867785
5695465
5025104
5470248
668514
3476134
3264661
5372286
4909627
2714678
4351069
5522563
93.7
88.6
92.1
92.0
87.9
85.1
93.1
87.3
88.4
88.5
90.9
88.8
89.0
88.6
88.9
85.9
86.8
86.8
86.7
90.4
86.6
86.9
6.3
11.4
7.9
8.0
12.1
14.9
6.9
12.7
11.6
11.5
9.1
11.2
11.0
11.4
11.1
14.1
13.2
13.2
13.3
9.6
13.4
13.1
32.0
3.5
13.5
22.3
7.2
6.5
48.1
9.4
7.5
8.5
14.4
9.5
8.6
8.7
10.1
4.1
3.6
10.4
7.7
24.6
4.3
7.3
Capturing efficiency P. chabaudi infection
Day 2
1 cell
0 cells
2+ cells
Day 3
139
49
4
Supplementary Table 8
Traditional academic point system:
Day 4
73
16
7
Total (%)
75%
143
20%
35
5%
14





.90-1 = excellent (A)
.80-.90 = good (B)
.70-.80 = fair (C)
.60-.70 = poor (D)
.50-.60 = fail (F)