Log2 expression values of 517 protein-coding genes in whole blood during infection. Genes (rows) are ordered by hierarchical clustering whereas whole blood samples (columns) are ordered by volunteer …
An identical immune challenge leads to diverse outcomes in falciparum malaria.
Log2 fold-change of the 100 protein-coding genes with highest variance in whole blood during infection. Data are presented as deviation from median (within each volunteer). Genes (rows) are ordered by hierarchical clustering, whereas whole blood samples (columns) are ordered by time-point (pre-infection to diagnosis, left to right). Each volunteer was analysed independently and therefore every top 100 gene list is unique.
Log2 transformed expression values of the 517-gene superset in whole blood during infection.
Principal component analysis of the 517-gene superset in whole blood during infection. Each dot represents one time-point (pink is pre-infection) and every volunteer is centred around their own …
(A) Gene ontology network of 2028 genes differentially expressed at diagnosis in the inflammatory group. Each node represents a significantly enriched GO term (adj p<0.05) and node size is …
(A) Rlog expression values of the 117-gene superset in whole blood after mosquito challenge. Genes (rows) are ordered by hierarchical clustering, whereas whole blood samples (columns) are ordered by …
(A) Parasite growth curves colour-coded by host response; each line represents one volunteer. Blood samples were collected every 12 hr for qPCR analysis of circulating parasite density and the …
Data on symptoms were collected every 12 hr from day 2 post-infection either on diary cards (self-reporting) or during clinic visits. Adverse events were graded as mild (transient or mild discomfort …
(A) Proportion of mild, moderate and severe adverse events at diagnosis. For each volunteer, adverse events were recorded for 13 clinical categories and these were summed to give a clinical score at …
Volcano plot showing the 10 plasma metabolites that were differentially abundant during infection. We grouped unresponsive (v018 and v208), inflammatory (v016, v017 and v013), and suppressor (v022 …
(A and B) Rlog expression values of var (A) and rifin (B) genes in the inoculum and diagnosis parasite samples after blood challenge (blue study); parasites obtained from volunteers infected by …
Rlog expression values of var and rifin genes in parasites isolated from whole blood after controlled human malaria infection.
Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
---|---|---|---|---|
Strain, strain background (Plasmodium falciparum) | clone 3D7 | Cheng et al., 1997 | PMID:9347970 | |
Sequence-based reagent | TaqMan probe | Applied Biosystems | 5′ FAM AACAATTGGAGGGCAAG NFQ-MGB 3′ | |
Sequence-based reagent | ISPCR primer | biomers.net | 5’- AAG CAGTGGTATCAACGCAG AGT −3’ | |
Sequence-based reagent | LNA-modified TSO | exiqon.com | 5’- AAGCAGTGGTATCAACGCAGAGTACATrGrG+G −3’ | |
Sequence-based reagent | Oligo-dT30VN | biomers.net | 5’- AAGC AGTGGTATCAACGCAGAGT ACT30VN −3’ | |
Commercial assay or kit | Tempus spin RNA isolation | Applied Biosystems | cat. no. 4378926 | |
Commercial assay or kit | RNA clean and concentrator | Zymo Research | cat. no. R1016 | |
Commercial assay or kit | Globin-Zero Gold | Illumina | cat. no. GZG1224 | |
Commercial assay or kit | RNA 6000 pico chip | Agilent | cat. no. 5067–1513 | |
Commercial assay or kit | High sensitivity DNA kit bioanalyzer | Agilent | cat. no. 5067–4626 | |
Commercial assay or kit | TruSeq stranded mRNA library | Illumina | cat. no. RS-122–2101 | |
Commercial assay or kit | NEBNext Ultra DNA library prep kit | New England Biolabs | cat. no. E7370 | |
Software, algorithm | Kallisto v0.42.3 | Bray et al., 2016 | RRID:SCR_016582 | PMID:27043002 |
Software, algorithm | EdgeR | Robinson et al., 2010 | RRID:SCR_012802 | PMID:19910308 |
Software, algorithm | ClueGO v2.5.4 | Bindea et al., 2009 | RRID:SCR_005748 | PMID:19237447 |
Software, algorithm | IDEOM | Creek et al., 2012 | PMID:22308147 | |
Software, algorithm | mzCloud | RRID:SCR_014669 | ||
Software, algorithm | DESeq2 | Love et al., 2014 | RRID:SCR_015687 | PMID:25516281 |
Other | Saponin from quillaja bark | Sigma Aldrich | cat. no. S7900 | test each batch |
Other | Leucoflex LXT filters | Macopharma | macopharma.com/transfusion | |
Other | KAPA HiFi HotStart ReadyMix | Biosystems | cat. no. KK2601 | |
Other | AMPure XP beads | Beckman Coulter | cat. no. A63881 |
Demographics of volunteers infected by blood or mosquito challenge; includes genetic and non-genetic variables known to influence human immune variation in vitro.
Classification of volunteers by host response after blood challenge is described in the results and methods.
Three metrics that measure the magnitude of the human immune response to blood challenge.
[1] The mean variance of the top 50 most variable protein-coding genes in each volunteer. [2] The Euclidean distance travelled during principal component analysis of the 517-gene superset. [3] The number of differentially expressed genes at diagnosis in each group. Note that uninfected control volunteers set a threshold for baseline variation in gene expression through time; a Mann Whitney test was then used to support the observation that unresponsive volunteers were comparable to uninfected controls. Classification of volunteers by host response after blood challenge is described in the results and methods.
List of the 2028 differentially expressed genes identified in inflammatory volunteers at diagnosis (compared to pre-infection samples).
These data underpin the gene ontology network in Figure 2a.
List of the 217 significantly enriched GO terms identified in inflammatory volunteers at diagnosis.
GO terms are arranged into their functional groups and groups are ordered by size. The leading GO term in the top 12 functional groups is highlighted in red. On sheet 2, we highlight the top 20 GO terms as ordered by p value.
List of the 77 differentially expressed genes identified in suppressor volunteers at diagnosis (compared to pre-infection samples).
These data underpin the heatmap in Figure 2d.
List of the 893 genes that were differentially expressed between inflammatory and suppressor hosts at diagnosis.
There were no differentially expressed genes between these volunteers prior to infection (adj p<0.05).
Rlog expression values of the 117-gene superset in whole blood after mosquito challenge.
These data underpin the heatmap in Figure 2—figure supplement 1a. On sheet two we highlight the volunteers in which EdgeR identified these genes as differentially expressed. And on sheet three we look at the 21 genes that were most upregulated in inflammatory volunteers after blood challenge.
List of the 44 significantly enriched GO terms identified in the 117-gene superset.
GO terms are arranged into their functional groups and groups are ordered by size. On sheet two we highlight the top 20 GO terms as ordered by p value.