Single-Cell RNA-seq Data from Moauro et al 2023

<p>These experiments are described in the paper:&nbsp;</p> <p><strong>OCT4 is expressed in extraembryonic endoderm stem (XEN) cell progenitors during somatic cell reprogramming</strong></p> <p>Alexandra Moauro, Stephanie L. Hickey, Michael A. Halbisen, Anthony Parenti, and Amy Ralston*</p> <p>*Correspondence: aralston@msu.edu</p> <p>All code and results files can be found at <a href="https://github.com/slepphickey/scRNA_seq_Moauro_et_al_2023 ">https://github.com/slepphickey/scRNA_seq_Moauro_et_al_2023&nbsp;</a></p> <p><strong>Files:</strong></p> <ul> <li><strong>`matrix.tsv.gz`</strong>:&nbsp;Each element of the matrix is the number of UMIs associated with a feature (row) and a detected cell-associated barcode (column)&nbsp;from the cellranger output for the 17 day MEF reprogramming scRNA-seq data.</li> <li><strong>`barcodes.tsv.gz`</strong>: detected cell-associated barcodes from the cellranger output for the 17 day MEF reprogramming scRNA-seq data.&nbsp;</li> <li><strong>features.tsv.gz`</strong>: genes from the cellranger output for the 17 day MEF reprogramming scRNA-seq data.&nbsp;</li> <li><strong>`Day17_Reprogramming_scRNA_seq_QC_filtered_SeuratObject.Rdata`</strong>: a Seurat object containing the filtered UMI count data, normalized count data, and cluster assignments from all cells.</li> <li><strong>`Day17_Reprogramming_scRNA_seq_Pou5f1_expressing_QC_filtered_SeuratObject.Rdata`</strong>: a Seurat object containing the filtered UMI count data, normalized count data, and cluster assignments from Pou5f1 expressing cells.</li> <li><strong>`Day17_Reprogramming_scRNA_seq_Sox2_expressing_QC_filtered_SeuratObject.Rdata`</strong>:&nbsp;a Seurat object containing the filtered UMI count data, normalized count data, and cluster assignments from Sox2 expressing cells.</li> <li><strong>`Mohammed_seurat.rdata`:&nbsp;</strong>a Seurat object containing the filtered UMI count data, normalized count data, and cluster assignments from <a href="http://www.sciencedirect.com/science/article/pii/S2211124717309610"><em>Single-Cell Landscape of Transcriptional Heterogeneity and Cell Fate Decisions during Mouse Early Gastrulation, Mohammed et al. 201</em>7</a> (<a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE100597">GSE100597</a>).</li> <li><strong>`Mohammed2017_TabS1_set_table.Rdata` </strong>: Mohammed et al. cluster enriched genes&nbsp;copied from <a href="https://ars.els-cdn.com/content/image/1-s2.0-S2211124717309610-mmc2.xlsx">Table S1&nbsp;</a>-- tab: `SC3 Cluster specific genes` -- Columns: `Enriched genes by SC3 clustering for each lineage (All genes)`</li> <li><strong>`GSE69321_Non-normalized_data.txt.gz`:&nbsp;</strong>Raw Illumina beadarray data from&nbsp;Wamaitha et. al., 2015, <em><a href="https://genesdev.cshlp.org/content/29/12/1239.long#sec-9">Gata6 potently initiates reprograming of pluripotent and differentiated cells to extraembryonic endoderm stem cells</a>,</em>&nbsp;Genes &amp; Dev. 2015. 29: 1239-1255, doi:10.1101/gad.257071.11. (<a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE69323">GSE69321</a>).</li> <li><strong>`probe_raw.txt`</strong>: `GSE69321_Non-normalized_data.txt.gz` filtered for mESC and eXEN data.</li> </ul>