A Theorem on Matroid Homomorphism

This note generalizes a result contained in a previous paper [ J. Sanders, Circuit preserving edge maps II, J. Combin. Theory Ser. B 42 (1987), 146-155].Comment: 5 pages, 0 figure

Differentially expressed genes between clonally derived samples.

Differentially expressed genes between clonally derived samples.</p

Sample and log₂ CPM (counts per median) matrix with gene annotations.

(CSV)</p

Raw gel images.

(TIF)</p

Filtering reduces host RNA.

T25 flasks with HFFs (human foreskin fibroblasts) were infected with tachyzoites or left uninfected. Contents of a flask were scraped, passed through a 27 g needle three times, and half was then passed through a 5 μm filter to remove host material, the other half being kept for comparison. RNA was extracted from all samples using TRIzol and analyzed by agarose gel electrophoresis with visualization using ethidium bromide staining. Bands corresponding to the human and Toxoplasma large and small subunit rRNAs are indicated.</p

DESeq2 results for differentially expressed genes between samples.

(CSV)</p

Sample and read count matrix.

(CSV)</p

SRS expression among clonally derived tachyzoites.

To account for differences in read depth between the samples, the reads for each sample were randomly down-sampled 5 times (r1, r2, etc). The SRS genes were selected from these and then the distances between the samples as regards expression levels for each of these SRS genes were then calculated. The heatmap shows the relative expression level for each detected SRS in all samples, ordered by relatedness between genes (top dendrogram) and samples (right dendogram). The heatmap is log2 CPM values for the detected SRS genes. Black numbers indicate the groupings of the SRS genes.</p

<i>Toxoplasma</i> subcloning schematic.

A population of mCherry+ (mChr+) RH parasites was passed at least 90 times in human foreskin fibroblasts (HFFs) after thawing. Independent clones (indicated by colors and given the names C1, C2, C3, and C4) from the population were isolated by a first limiting dilution into 96-well plates with an HFF monolayer. After thirty hours, three wells with a single vacuole were identified and individual parasites were isolated by a second limiting dilution into new 96-well plates. Seventy-two hours after the second limiting dilution, subclones samples (designed by the lowercase letters) were harvested from wells for RNA sequencing (filled circles). A clone, C4, from the original population was also collected seventy-two hours after the first limiting dilution to mimic the collection of the subclones (same time from isolation of a single parasite in a well to harvest). For subclone C3c, the extracted RNA was divided prior to the reverse transcriptase reaction to yield C3ci and C3cii, and in some analyses these two datasets were aggregated to yield the “C3c” sample.</p

<i>Toxoplasma</i> transcript detection and read depth.

For each sample, the total number of Toxoplasma genes “detected” in that sample is plotted against the total number of reads that uniquely aligned to the Toxoplasma genome in that sample (top panel). A gene was considered “detected” if it was above 4 counts per median (CPM; see Materials and Methods). C3ci and C3cii represent the results from the RNA sample that was split prior to cDNA synthesis. C3c represents the aggregation of the C3ci and C3cii data. Bottom panel is the same analysis as the top panel except only reads mapping to the 111 annotated SRS genes were counted for plotting on the y-axis.</p