DOI: 10.5061/dryad.t76hdr806
title: Spatial reconstruction of the early hepatic transcriptomic landscape after an acetaminophen overdose using single-cell RNA sequencing

description: We leveraged single-cell RNA sequencing to understand the early molecular
 events that define the hepatocyte response to acetaminophen exposure at a
 subpopulation level. We spatially assigned hepatocytes along the
 portol-central vein axis by using established landmark genes. By spatially
 assigning the hepatocytes were were able to account for innate differences
 in gene expression that existed along this gradient. The excel files
 herein provide the full list of differentially expressed genes between key
 subpopulations of interest. Additionally, we classified genes as either
 pericentral zonated, periportal zonated, or non-zonated, the full list of
 genes and their spatial assignments are included in the appropriate excel
 file. 
description: This is processed single-cell data from Genomics single cell
 3' end expression 10x chromium.  <strong>Additional File
 1</strong> Description: Table indicating
 number of hepatocytes, low confidence hepatocytes, endothelial and Kupffer
 cells identified within either the control or APAP dataset.
 <strong>Additional
 File 2</strong> Description: List of all sampled
 genes from control hepatocytes, ordered based on mean square error,
 assigned either as perivenous (PV, e.g. pericentral), periportal (PP) or
 no zonation. <strong>Additional File
 3</strong> Description: List of all sampled
 genes from APAP hepatocytes, ordered based on mean square error, assigned
 either as perivenous (PV, e.g. pericentral), periportal (PP) or no
 zonation. <strong>Additional File
 4</strong> Description: Pearson correlations
 comparing zonation profiles of landmark pericentral or periportal
 genes. <strong>Additional File
 5</strong> Description: Differential
 expression using Wilcoxon rank sum test in Seurat comparing all APAP
 hepatocytes to all control hepatocytes. <strong>Additional File
 6</strong> Description: Differential
 expression using Wilcoxon rank sum test in Seurat comparing layer 1 APAP
 hepatocytes vs layer 1 control hepatocytes. <strong>Additional File
 7</strong> Description: Differential
 expression using Wilcoxon rank sum test in Seurat comparing layer 9 APAP
 hepatocytes vs layer 9 control hepatocytes. <strong>Additional File
 8</strong> Description: Using the
 AverageExpression () function in Seurat giving gene expression for an
 ‘average’ cell among the 18 identity classes (e.g. layer 1 APAP, layer 1
 control, layer 2 APAP, layer 2 control etc.) <strong>Additional File
 9</strong> Description: Differential
 expression using Wilcoxon rank sum test in Seurat comparing the
 pericentral clusters that were predominately APAP hepatocytes.
 <strong>Additional
 File 10</strong> Description: Differential
 expression using Wilcoxon rank sum test in Seurat comparing
 the Glul<sup>+</sup>/Stress<sup>High</sup>
 subclusters. <strong>Additional File
 11</strong> Description: List of all sampled
 genes from human hepatocytes (GSE124395), ordered based on mean square
 error, assigned either as perivenous (PV, e.g. pericentral), periportal
 (PP) or no zonation. <strong>Additional File
 12</strong> Description: Count matrix of
 single-cell RNA seq data, column names are treatment condition, row names
 are genes.