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SPRING view of ICGS clusters

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UMAP view of ICGS clusters

BM_DONOR

File description

Mean gene expression for all 35 cell-populations for each donor (counts per 10,000 normalized).

CD34+ population specific markers and profiles. This document contains: (Tab-1) Marker genes and (Tab-2) gene expression centroids for markers.

Global population specific markers and profiles. This document contains: (Tab-1) Marker genes, (Tab-2) gene expression centroids for markers and (Tab-3) cell-associations per cluster.

Webportal Description

Citation

Introduction

The HCA Bone Marrow Viewer provides navigable results from the first large-scale release from the HCA bone marrow tissue project. These results were derived from the HCA Data Portal (https://preview.data.humancellatlas.org) and processed using the software ICGS (http://altanalyze.org) in combination with the tool cellHarmony. This analysis resolved common, rare and potential transitional cell populations from over 100,000 immune cells, spanning 35 transcriptionally coherent groups across eight healthy donors. Cell population identifies were predicted from a large compendium of prior bulk and single-cell transcriptome datasets.

Interfaces

This web data portal is organized into three hierarchical views: 1) Global cell population heterogeneity view (Global View), 2) combined donor pseudo-bulk profiles for all cell populations (Combined Donors View), and 3) individual donor-cell gene expression navigation (Individual Donors View and Cluster Comparison View). In addition, users can download associated markers and gene expression signatures.

Global View

This interface provides an interactive SPRING (https://github.com/AllonKleinLab/SPRING) graph to query the expression of any gene across the spectrum of identified progenitor and differentiated cell populations. Genes with expression restricted to each cell population can be quickly obtained using the built-in table sort function of this view, which reports MarkerFinder specificity (Pearson correlation) scores (values close to 1 indicate highly restricted cell population expression) for all of the cell populations.

Combined Donor View

To explore common donor gene expression variation for any of the 35-defined cell populations, the user can switch to the Combined Donor View, which plots the variation in expression among the 8-donors for pseudo-bulk expression values. The interface allows for selection of 5 gene symbols. By default, the boxplot view is displayed. Mouse-over of any data point indicates the sample meta-data. Users can switch between both boxplot and frequency barchart views of these data using the Plot Options tab a the top of browser.

Individual Donor View

To independently explore and visualize the frequency, distribution and amplitude of gene expression in individual donors, the user can switch to the Individual Donor View. This plot allows the user to assess whether a particular donor has more or less cells than other donors, which genes are expressed by those donors and in which cell populations. As an example, users can compare the distribution of expression of individual cells within the HSC in young versus middle aged donors to assess consistency in expression.

Cluster Comparison View

To directly compare the expression and frequency of cells for different donors for a single-cell populations, select the Cluster Comparison tab. In this interface, the user selects specific cell types to compare the expression level of a queried gene across all 8 donors.

Cincinnati Children's Hospital Medical Center ---- 2018