Magellan: COVID-19 Omics Explorer

Magellan is a web application for the display and analysis of next-generation sequencing data with a focus on COVID-19. The application runs on the de.NBI cloud infrastructure. We focus specifically on single-cell sequencing data, but other omics data, such as epigenetic data, will be integrated as well. The goal is to provide easy and open access to the highly relevant data of COVID-19 patients for the community.

We are constantly working on improving this app. If you have any comments, suggestions or critics please send us a note at: mail

Datasets

All sequencing data was produced at BIH/Charité and at locations of our cooperation partners. Integrated datasets are public available in open archives.

  • HBEC and lung cells: SARS ‐CoV‐2 receptor ACE 2 and TMPRSS 2 are primarily expressed in bronchial transient secretory cells. EMBO
  • COVID-19 patients: COVID-19 severity correlates with airway epithelium–immune cell interactions identified by single-cell analysis. Nature Biotechnology
  • COVID-19/cardio patients: Hypertension delays viral clearance and exacerbates airway hyperinflammation in COVID-19 patients. Nature Biotechnology
  • COVID-19/children Pre-activated antiviral innate immunity in the upper airways controls early SARS-CoV-2 infection in children. Nature Biotechnology

Updates

  • 2021/09/02: Integration of new data from SARS-CoV-2-positive children.
  • 2020/12/24: Added a new COVID-19 data set from patients with cardiovascular comorbidities.
  • 2020/11/10: Did some minor UI improvements.
  • 2020/06/16: Single-Cell-Map can visualize gene expression.
  • 2020/06/15: COVID-19 data is available for data analysis.
  • 2020/06/15: There is a major update of the user interface. Single-Cell-Map supports selection of subsets of cells to analyze cell-types and sample distribution.
  • 2020/06/11: Big news: first COVID-19 patients data integrated. The data is not public yet but it will be available next days.
  • 2020/04/05: HBEC and lunc cell data integrated.
  • 2020/04/01: Hello world!

de.NBI Cloud

Magellan is hosted at the de.NBI Cloud. The de.NBI cloud is a fully academic cloud funded by the BMBF (grant number(s): 031A537B, 031A533A, 031A538A, 031A533B, 031A535A, 031A537C, 031A534A, 031A532B), free of charge for academic users, which provides compute resources as well as storage capacity for large-scale scientific projects.

Tracking

We use Matomo to track access to Magellan in order to improve usability of the website. Thereby, we do not store any personal data.
Imprint

Description

Single-cell map displays cells in UMAP coordinates. Cell color indicate either cell type or gene expression level. Attaching and displaying gene expression is optional.
You can use your cursor to select an area of cells. Double-click on map to reset your selection.
The two central plots below the map indicate numbers of cells in samples or within cell-types either in total or in your selected area.
The two plots on the right side show gene expression within single samples or by cell-types either in total or in your selected area.

Dataset

Dataset 1: includes cells from lung tissue (12 donors, 39,778 cells) and cells derived from subsegmental bronchial branches (4 donors, 17,521 cells).
Dataset 2: includes data from 14 COVID-19 patients with multiple sampling times and sampling locations as well as cells from 5 control donors. Cells were derived from nasopharyngeal or pooled nasopharyngeal/pharyngeal swabs (NS), bronchiolar protected specimen brushes (PS), and bronchoalveolar lavages (BL).
Dataset 3: includes data from 32 COVID-19 patients including patients with hypertension and cardiovascular diseases as well as cells from 16 control donors. Cells were derived from nasopharyngeal epithelial swabs. Samples identifier code for: patients identifieres (e.g. BIH-Con-01), COVID-19 status (neg or pos), cardiovascular comorbidities (none, HT or CAD), antihypertensive medication (none, ACEi or ARB) and days after onset of symptoms (NA or number);
Dataset 4: includes data from overall 86 patients consisting of SARS-CoV-2-negative (n = 18), age-matched SARS-CoV-2-positive (n = 24) children and 44 adults. Cells were derived from the upper airways (nose). Samples identifier code for: patients identifieres (e.g. BIH-c-CoV-04), COVID-19 status within the group (child neg, child pos, adult neg or adult pso), severity of the disease, and days after onset of symptoms (negative, no symptoms or number);

Settings

Changing settings requires to reload data to have an effect.

Gene expression

Attach expression of a single gene to the cells to visualize its expression in selected cells, patients and cell types.

Samples

Visualization

You can choose to colorize cells by gene expression. Setting an expression threshold allows to highlight all cells with an expression value above the threshold.
The following options allow to set size and transparency of all cells.