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  1. 1
    A. Mouse transcriptome non-negative matrix factorization component weights across all time points and conditions. Larger weight values indicate components with upregulated genes dominating. B. Gene set enrichment plot for selected features from each component in panel A. Components 1, 4, and 5 did not exhibit enrichment in these broad terms. C. Number of genes in enriched gene ontology terms related to immunity, signaling, and transcription for each time point and condition. D. Time course transcriptional profiles for mouse genes characteristic to component 3. E. PARFA-seq validation by quantitative PCR and gene expression changes during immortalized bone marrow-derived macrophage infection by <i>T. gondii</i> assessed by quantitative PCR.

    A. Mouse transcriptome non-negative matrix factorization component weights across all time points and conditions. Larger weight values indicate components with upregulated genes do... von Dominykas Murza (22676289)

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  2. 2
    A. <i>T. gondii</i> gene group changes throughout the time course, expressed as log<sub>2</sub>(fold change) relative to pre-infection tachyzoites (t = 0). Grey area depicts the 95% confidence interval. n value refers to number of genes detected in each group. B. Gene set enrichment plot for most enriched terms from <i>T. gondii</i> transcriptome features at 15 min to 120 min. Five most significant terms are displayed for each database. C and D. Transcriptional profiles of top five upregulated and downregulated <i>T. gondii</i> transcription factors, respectively.

    A. <i>T. gondii</i> gene group changes throughout the time course, expressed as log<sub>2</sub>(fold change) relative to pre-infection tachyzoites (t = 0). Grey area depicts the 95... von Dominykas Murza (22676289)

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  3. 3
    Oligonucleotides used in this study.

    Oligonucleotides used in this study. von Dominykas Murza (22676289)

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  4. 4
    A. Library preparation strategy: poly-A(+) RNAs are captured by complementarity to reverse transcription primer, then second strand is synthesized using random hexamers and handles for sequencing are attached through two rounds of PCR. B. Mapped read distribution by species and by biotype. C and D. Principal component analysis of mouse and <i>T. gondii</i> transcriptomes, respectively. E and F. Volcano plots of Live <i>Toxoplasma</i>-infected mouse and <i>T. gondii</i> time points, respectively. To calculate Log<sub>2</sub>(Fold change), every timepoint is compared to corresponding samples (either macrophage or <i>Toxoplasma</i>) before infection (t = 0 min). Most significant and most upregulated transcripts are labelled. Number of significantly (p ≤ 0.05) downregulated and upregulated genes for each time point is given in blue and red, respectively. In F, 24-hour time point, red dots mark ROP

    A. Library preparation strategy: poly-A(+) RNAs are captured by complementarity to reverse transcription primer, then second strand is synthesized using random hexamers and handles... von Dominykas Murza (22676289)

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  5. 5
    A. Experimental scheme of infection time course and downstream workflow; B. Optimization of tachyzoite concentration to achieve adequate infection rates, with a threshold set at 50% infection efficiency. Error bars represent ± 1 standard deviation. Corresponding MOI values are given for each condition; C. Infection time course micrograph merged from brightfield and green channels. <i>T. gondii</i> exhibits green fluorescence due to stable GFP expression in the strain used. Percentage at the top left indicates infection efficiency (± 1 standard deviation) for each time point.

    A. Experimental scheme of infection time course and downstream workflow; B. Optimization of tachyzoite concentration to achieve adequate infection rates, with a threshold set at 50... von Dominykas Murza (22676289)

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  6. 6
    Summary of all significant gene enrichment terms for every condition (as combination of sample type and timepoint).

    Summary of all significant gene enrichment terms for every condition (as combination of sample type and timepoint). von Dominykas Murza (22676289)

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