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3.3 KiB

Datasets

The data files are used for the primary analysis.

Individual_attributes

"SampleID","Phenotype","Time_to_diagnosis","Age","Gender","ELISA","Location","New.phenotype"
"16Kxxx","Slow growth",21,21,"M",6465.14,"Kilifi South","Slow growth"

Cytokines

SampleID,phenotype,Timepoint,IFNa,IFNg,IL.1b,IL.2,IL.4,IL.17,TNFa,TGFb,IL10
    17K0xxx,Highly Immune,C-1,7.8125,7.8125,1.1719,3.9063,1.5625,3.9063,3.9063,9417.62,10.092

Outcome 2020

excluded_for_drug_levels,negative_for_lumefantrine,subjectid,dihydroartemisinin_lvls_day_7,artemether_lvls_day_7,Chloroquine,Sulfadoxine,Pyrimethamine,location,schizont,age_at_screen,gender,thal_genotype,sickle,g6pd_genotype,time_to_diagnosis_last_PCR,mean_PCR,max_PCR,phenotypes_all,proportion_days_growing,median_day_of_growing,maximum_days_conseq_growing,gradient,innoculum,variability,proportion_days_declining,phenotype_1_treated_0_not,log_10_lumefantrine_day_7
,0,18K0xxx,0,0,0,0.0291,0,Kilifi South,1.005166,27,Male,Het,AA,,22,-2.602,-2.602,PCR -ve,0,,0,0,-2.602,,0,0,1.584331

PCR

Multiple lines per subject

subjectid,day,lPCR,year,location
16K0xxx,7.5,-0.275155365467072,16,Kilifi South
16K0xxx,8,0.199723362922668,16,Kilifi South
16K0xxx,8.5,-1.25866937637329,16,Kilifi South

Supernatent

SampleID,New phenotype,Timepoint,PfSE_prolif_%,A4.IL-4,A5.IL-2,A6.CXCL10,A7.IL-1b,A8.TNF-a,A10.CCL2,B2.IL-17a,B3.IL-6,B4.IL-10,B5.IFNy,B7.CXCL8,B9.TGF-B1
18A0xxx,Slow Growth,C-1,1.22,4.29,1,5362.09,1,1,43106.93,1,1,26.12,29.03,1,1

Transcription

SampleID,Timepoint,Cell type,CCR4,CD40LG,EGR2,GZMA,IFNGR1,IL1RL1,IL9,LAG3,NRP1,SOCS1,TIGIT,CCR5,CD69,ENTPD1,GZMB,IKZF2,IL2,IRF1,LAMP1,NT5E,SOCS3,TNF,BCL2,CCR6,CTLA4,FAS,HLA-DRA,IL10,IL21,IRF4,LCK,PAK2,SOCS5,TNFRSF18,CCL4,CCR7,CXCL13,FASLG,HLA-DRB1,IL10RA,IL21R,ITGB2,LRRC32,PDCD1,STAT5A,TNFRSF1B,CCL5,CD27,CXCR3,FOXP3,HPRT1,IL13,IL23R,ITK,MAF,PRDM1,STAT5B,TNFRSF4,CCR1,CD274,CXCR5,ICOS,IL17A,IL27RA,JAK3,MKI67,PRF1,TBP,TNFRSF9,CCR2,CD28,CXCR6,GATA3,IFNAR1,IL17F,IL2RA,KLRB1,NFATC2,RORC,TBX21,TNFSF10,CCR3,CD3G,DPP4,GFI1,IFNG,IL18R1,IL2RB,KLRG1,NFKB1,SELL,TGFB1,UBC,ACTB,GAPDH,B2M,Ref Mean
17Kxxx,C+9,Treg,5.725169477,16.0385686,30,18.48678262,15.49162182,30,15.70789301,30,14.36242315,18.05369551,12.9327269,30,13.56376227,30,18.09096578,14.31862564,19.20779524,15.12394995,14.79410618,17.25961972,17.39867246,19.21765892,13.72998002,16.16924943,12.86992642,14.68960828,16.85157059,30,30,30,14.56747294,13.75323888,15.9727563,30,17.63867345,12.22899225,30,21.0469146,10.95577439,12.14963933,15.8543272,14.60838771,17.43057694,19.51843968,16.07531569,10.20905636,30,14.02605586,16.76893203,13.32256541,16.54104187,30,30,11.86509117,15.33621417,15.60260208,13.80896926,17.26590272,23.72804334,18.57670836,17.06464556,15.6398031,30,15.43586838,14.62832081,15.5416587,17.37859754,15.36310371,12.20113477,16.64026291,13.81903244,17.07810347,15.79263145,15.59701822,18.575935,13.46395809,14.17970282,15.00442306,18.64595231,30,17.84707259,16.8252925,12.59536264,17.90646725,16.04699168,30,16.9437908,14.28275828,16.72353456,15.44115641,11.13219188,12.58570596,30,11.28527822,12.23308738,8.146090272,10.55481862

Treg phenotypes

"SampleID","Timepoint","Treg_frequency","Treg_CD137.","Treg_CD154.","Treg_Ki.67.","Treg_45RA.","Teff_CD137.","Teff_CD154.","Teff_Ki.67.","Teff_45RA."
"18A0xxx","C-1",5.8,0.041,0.32,3.687,13.727,0.013,0.15,0.1353,31.1053