Data and R Scripts for: "Transcriptome network analysis implicates CX3CR1-positive type 3 dendritic cells in non-infectious uveitis"

This dataset contains the processed RNA sequencing data of purified CD1c-positive conventional type 2 dendritic cells (CD1c+ cDC2s), functional enrichment analysis, manual and automatic gating data of (i.e., flowSOM) flow cytometry, and multiplex cytokine analyses as outlined in <i>Hiddingh et al. 2022 "Transcriptome network analysis implicates CX3CR1-positive type 3 dendritic cells in non-infectious uveitis </i> <dl>see preprint on <a href="https://www.biorxiv.org/content/10.1101/2021.11.16.468816v4"><i>BioRxiv</i></a>
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Data are from two cohorts (cohort I, n=36, and cohort II, n=42) of in total 51 patients with non-infectious uveitis (<i>HLA-B27-positive acute anterior uveitis</i>, <i>idiopathic intermediate uveitis</i>, <i>HLA-A29-positive Birdshot Uveitis (Birdshot chorioretinopathy)</i>, and 27 sex/age-matched healthy controls without ocular inflammatory disease). <br></br>
All raw sequencing data are available at NCBI SRA under the accession number: <dl>

<li> <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE195501"><i>GSE195501</i></a> (FACS-sorted cohort I). </li>
<li><a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE194060"><i>GSE194060</i></a> (MACS-sorted cohort II).</li>
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This dataverseNL dataset contains additional raw, processed, and metadata (see <a href="https://dataverse.nl/api/access/datafile/299114">readme</a> file and reproducible R notebooks (R script and Image) used for the analysis in the manuscript: <br></br>
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<dt>R scripts (markdown + R image) with <i>step-by-step</i> analyses </dt>
<ul><li><dd> Figure_1.rmd (see <a href="https://dataverse.nl/api/access/datafile/320666">"Figure_1.html"</a>)</dd></li>
<li><dd>Figure_2.rmd (see <a href="https://dataverse.nl/api/access/datafile/320651">"Figure_2.html"</a>)</dd></li>
<li><dd>Figure_3.rmd (see <a href="https://dataverse.nl/api/access/datafile/320723">"Figure_3.html"</a>)</dd>
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<li><dd>Figure_4.rmd (see <a href="https://dataverse.nl/api/access/datafile/320726">"Figure_4.html"</a>)</dd>
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<li><dd>Figure_5.rmd(see <a href="https://dataverse.nl/api/access/datafile/320692">"Figure_5.html"</a>)</dd></li>
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<li><dd>Processed RNA seq data (including WGCNA) (see folder <b>Uveitis_mDC</b> in files)</dd></li></ul>

<dt>Experimental data</dt>
<ul><li><dd>Manual gating data of MACS-sorted fractions cohort I (see <a href="https://dataverse.nl/api/access/datafile/320648">here</a>)</dd></li>
<li><dd>Manual gating data for CD1c+ cDC2 subsets in PBMCs (see <a href="https://dataverse.nl/api/access/datafile/320646">here</a>)</dd></li>
<li><dd>Manual gating CD14+ and CD14- CD1c+ cDC2 fractions from Buffy (see <a href="https://dataverse.nl/api/access/datafile/320697">here</a>)</dd></li>
<li><dd>qPCR data for <i>CX3CR1</i>,<i>CCR5</i>,<i>CCR2</i>,<i>IRF8</i>,<i>TLR7</i>,<i>RUNX3</i> and <i>CD36</i> in sorted CD14+ and CD14- CD1c+ DCs (see <a href="https://dataverse.nl/api/access/datafile/320682">here</a>)</dd></li>
<li><dd>qPCR data (fold change compared to medium) for <i>RUNX3</i> and <i>CD36</i> in overnight stimulated cDC2 cultures (see <a href="https://dataverse.nl/api/access/datafile/320652">here</a>)</dd></li>
<li><dd>Cell phenotypes identified by flowSOM (7x7 grid) using the cDC2-subset flow cytometry panel (see <a href="https://dataverse.nl/api/access/datafile/320674">here</a>)</dd></li>
<li><dd>IL-23 ELISA concentration in supernatant of overnight LTA-stimulated cDC2 subset cultures (see <a href="https://dataverse.nl/api/access/datafile/320658">here</a>)</dd></li>
<li><dd>Luminex Multiplex Cytokine analysis of supernatant of overnight LTA-stimulated cDC2 subset cultures (see <a href="https://dataverse.nl/api/access/datafile/320644">here</a>)</dd></li></ul>

<dt>Other transcriptomic data used in the R scripts (above)</dt>
<ul><li><dd> WT Untreated cDC2 versus cDC2 from <i>Runx3</i>-11cKO mice<a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE48590">GSE48590</i> </a> generated by <a href="https://pubmed.ncbi.nlm.nih.gov/24204843/"><i> Dicken et al., PLoS One
2013</i> </a></li>
<li><dd>WT Untreated cDC2 versus cDC2 from <i>Notch2</i>-11cKO mice<a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE119242">GSE119242</i> </a> generated by <a href="https://pubmed.ncbi.nlm.nih.gov/30279176/"><i> Briseño et al., Proc Natl Acad Sci U S A 2018</i> </a></li>

<li><dd>Sorted CD14+CD5-CD163+ and CD14-CD5-CD163+ cDC2s from SLE and Scleroderma patients <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE136731">GSE136731</i> </a> generated by <a href="https://www.cell.com/immunity/fulltext/S1074-7613(19)30334-6?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS1074761319303346%3Fshowall%3Dtrue"><i> Dutertre et al., Immunity 2019</i> </a></li>

<li><dd>Single-cell RNA-seq of aqueous humor from 4 HLA-B27-positive uveitis patients and control <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE178833">GSE178833</i> </a> generated by <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8594918/"><i> Kasper et al., Elife 2021</i> </a></li>

<li><dd>Inflammatory [inf-]cDC2s<a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE149619">GSE149619</i> </a> generated by <a href="https://pubmed.ncbi.nlm.nih.gov/32392463/"><i> Bosteels et al., Immunity 2020</i> </a></li>

<li><dd>RNA-seq data from cDC2s generated from murine bone marrow cells in co-culture with stromal OP-9 cell line transduced with or without expression of the Notch ligand Delta-like 1<a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE110577">GSE110577</i> </a> generated by <a href="https://pubmed.ncbi.nlm.nih.gov/29925006/"><i> Kirkling et al., Cell Rep 2018 </i> </a></li>
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