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            <a:FirstGiven>Maximilian Julius</a:FirstGiven>
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        <r:String xml:lang="sv">Longitudinell proteomik och enkelcells-transkriptomdata från P. falciparum-malaria-infekterade resenärer</r:String>
        <r:String xml:lang="en">Longitudinal proteomics and single-cell transcriptomic data of P. falciparum malaria-infected travellers</r:String>
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          <r:String xml:lang="sv">Karolinska Institutet</r:String>
          <r:String xml:lang="en">Karolinska Institutet</r:String>
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          <r:String xml:lang="sv">Karolinska Institutet</r:String>
          <r:String xml:lang="en">Karolinska Institutet</r:String>
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        <r:SimpleDate>2026-02-16</r:SimpleDate>
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      <r:Content xml:lang="sv">Omfattande plasmaproteomik och riktad single‑cell multi‑omics genererades från en longitudinell kohort av återvändande resenärer behandlade för Plasmodium falciparum-malaria. Plasma och perifera mononukleära blodceller (PBMC) samlades in från symtomatiska patienter vid Karolinska Universitetssjukhuset efter informerat samtycke och följdes med upprepade provtagningar från akut sjukdom upp till ett år efter avslutad behandling i frånvaro av reinfektion. Plasmaproteinprofilering utfördes i samarbete med Human Protein Atlas med hjälp av nästa generations affinitetsproteomik baserad på Proximity Extension Assay med NGS‑avläsning (Olink Explore 1536). Proteinmängder rapporterades som Normalized Protein eXpression (NPX, log2‑skala) efter bryggnormalisering mellan batcher. Proteiner under detektionsgränsen i mer än 70 % av proverna exkluderades, vilket resulterade i ett slutligt dataset med 1 427 plasmaproteiner.
För att identifiera potentiella cellulära källor och mål för cirkulerande proteiner utfördes riktad single‑cell multi‑omics‑profilering på PBMC från ett urval av donatorer med överlappande tidpunkter. Genuttryck av 399 immunrelaterade gener samt 29 cellyteproteiner analyserades med BD Rhapsody och AbSeq. Bibliotek sekvenserades på en NovaSeq 6000‑plattform och bearbetades med BD Targeted Analysis Pipeline, och nedströmsanalyser genomfördes i R med Seurat. Dessutom återanalyserades ett publikt tillgängligt scRNA‑seq‑dataset från en oberoende malariakohort för att validera och utvidga resultaten. Integrerade analyser av proteomik‑ och single‑cell‑data användes för att stratifiera patienter i undergrupper associerade med sjukdomens svårighetsgrad.
Datasetet består av två datamodaliteter:

Plasmaproteomik: Olink‑NPX‑värden för 132 prover över 1 427 proteiner
PBMC single‑cell multi‑omics: riktade genuttrycks‑ och AbSeq‑proteindata från 12 prover

Delar av plasmaproteomikdatan finns tillgängliga i aggregerad form via Human Protein Atlas (Disease Atlas). En interaktiv Shiny‑applikation åtföljer den tillhörande publikationen (Lautenbach et al., Immunity, 2025) och möjliggör utforskande dataanalys.

Datasetet består av 2 filer:
Del1: Plasma proteomics (Olink PEA with NGS readout - Explore 1536) 
Fil: Plasma_proteomics/Explore1536_tidy_long.rds (709 kB)

Del 2: Targeted single-cell transcriptomics data (BD Rhapsody scRNA‑seq + AbSeq)
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Fil: MalariaTraveler_RhapsodyAbSeq_Cell_Calling_qc_cca_wnn_clustering_annotated_clean.rds (507.2 MB)</r:Content>
      <r:Content xml:lang="en">Comprehensive plasma proteomics and targeted single‑cell multi‑omics were generated from a longitudinal cohort of returning travelers treated for Plasmodium falciparum malaria. Plasma and peripheral blood mononuclear cells (PBMCs) were collected from symptomatic patients at Karolinska University Hospital after informed consent and followed with repeated sampling from acute disease up to one year post‑treatment in the absence of reinfection. Plasma protein profiling was performed in collaboration with the Human Protein Atlas using next‑generation affinity proteomics based on Proximity Extension Assay with NGS readout (Olink Explore 1536). Protein abundance was reported as Normalized Protein eXpression (NPX, log2 scale) after bridge normalization across batches. Proteins below the limit of detection in more than 70% of samples were excluded, resulting in a final dataset of 1,427 plasma proteins.
To infer potential cellular sources and targets of circulating proteins, targeted single‑cell multi‑omics profiling was performed on PBMCs from a subset of donors with overlapping time points. Gene expression of 399 immune‑related genes and 29 cell‑surface proteins was assessed using BD Rhapsody with AbSeq. Libraries were sequenced on a NovaSeq 6000 platform and processed using the BD Targeted Analysis Pipeline, and downstream analyses were conducted in R using Seurat. In addition, a publicly available scRNA‑seq dataset from an independent malaria cohort was reanalyzed to validate and extend the findings. Integrated proteomic and single‑cell analyses were used to stratify patients into subgroups associated with malaria disease severity.
The dataset consists of two data modalities:

Plasma proteomics: Olink NPX values for 132 samples across 1,427 proteins
PBMC single‑cell multi‑omics: targeted gene expression and AbSeq protein data from 12 samples

Parts of the plasma proteomics data are available in aggregated form through the Human Protein Atlas Disease Atlas. An interactive Shiny application accompanies the associated publication (Lautenbach et al., Immunity, 2025) to enable exploratory data analysis.

The dataset consists of 2 files:
Part1: Plasma proteomics (Olink PEA with NGS readout - Explore 1536) 
File: Plasma_proteomics/Explore1536_tidy_long.rds (709 kB)

Part2: Targeted single-cell transcriptomics data (BD Rhapsody scRNA‑seq + AbSeq)
- Seurat object
File: MalariaTraveler_RhapsodyAbSeq_Cell_Calling_qc_cca_wnn_clustering_annotated_clean.rds (507.2 MB)</r:Content>
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