Study: 2020-Mar-Atlas-Adult-Retina-10x 19694 cells

An adult eye (retina) dataset from the Human Cell Atlas March 2020 Release, a collection of 23 human single-cell datasets.                                                                                                                                                                                                                                                                                                                     

Summary

HCA DCP Project Title: A single-cell transcriptome atlas of the adult human retina                                                                                                                        

HCA DCP Project Page (go here for original data): https://data.humancellatlas.org/explore/projects/8185730f-4113-40d3-9cc3-929271784c2b                     

Organ, Developmental Stage, Technology: Eye (retina), Adult, 10x

Publication Link: https://www.ncbi.nlm.nih.gov/pubmed/31436334                                                                                                                                                 

Links to Related Single Cell Portal Study Pages (if applicable): N/A     

March 2020 Release Site: data.humancellatlas.org/explore/releases/2020-mar                                                

Search genes across DCP Release projects on the Single Cell Portal HCA Release Page

 

Study overview

This study presents an example analysis of an eye (retina) dataset from the Human Cell Atlas (HCA) Data Coordination Platform (DCP) Project entitled "A single-cell transcriptome atlas of the adult human retina". It is part of the HCA March 2020 Release and showcases HCA single-cell data that were processed with standardized DCP pipelines, further analyzed by Cumulus, and annotated using published annotations. In this study, you can explore the biological and technical attributes of the analyzed HCA DCP data. Additionally, you can view all HCA Release study pages and search genes across all projects by visiting the Single Cell Portal HCA Release Page. Please note that Release data is not corrected for batch-effects, but is stratified by organ and (in some cases) developmental stage as described below. 

 

How do I view the annotated cells?

Go to the Explore tab above to interactively view annotated cells. In the View Options, click the "Select Annotations" drop-down menu. For annotated cell types, you can choose either "annotated_cell_identity.text" (unharmonized cell type annotations from the project contributor) or the "annotated_cell_identity.ontology_label" (cell type annotations harmonized with ontology services).

 

Please note that cells labelled “unannotated” correspond to the cells that have been filtered out by the author’s processing but are present after HCA DCP standardized processing.

 

You can also view annotated cells on other HCA DCP partner portals! See the March 2020 Release site for available portals.

 

Project stratification details

For the March 2020 Release, all DCP projects were stratified by organ (when projects included more than one organ), and when applicable, by additional parameters such as developmental stage (age) or sample processing technology (i.e. 10x or Smart-seq2). Each dataset stratification has a dedicated Single Cell Portal study page. If a project consisted of only one organ type (with consistent age and technology), no stratification was performed. For projects that were stratified into multiple datasets, you can find links to the related dataset study pages at the top of this summary page.

For the project "A single-cell transcriptome atlas of the adult human retina", no stratification was performed. This study page represents all available project-specific sample data. Detailed specifications for the Project samples are outlined on the Project page (https://data.humancellatlas.org/explore/projects/8185730f-4113-40d3-9cc3-929271784c2b).  

 

Analysis methods

Library Construction: 10x v2 sequencing

Count Matrix Construction: optimus_v1.3.5

The Optimus workflow processes 3' scRNA-seq (10x 3’ v2 and v3) data to produce quality metrics and raw count matrices. The workflow combines these outputs into Zarr and CSV files which are used by the HCA DCP Matrix Service for downstream processing, such as metadata addition and minimal count filtering. The finalized matrix files, including the Loom file used for this study (2020-Mar-Atlas-Adult-Retina-10x.loom) are available on the DCP Data Portal. You can also download the Matrix Service loom file from the Download tab on this study. The Matrix Service loom file is the starting input for the Cumulus pipeline detailed below. 

Clustering and Differential Expression Analyses: Cumulus v0.13.0 (Snapshot 14)

The Cumulus workflow uses the file 2020-Mar-Atlas-Adult-Retina-10x.loom (see Download tab) to perform additional filtering, clustering, differential expression analyses and plotting. The HCA Release Methods documentation details the Cumulus workflow parameters and outputs, including those available for download on this Single Cell Portal page. 

Annotation:

Cell annotations were obtained from Lukowksi et al., 2019. The nomenclature for annotations was harmonized across all DCP Release projects using the Ontology Lookup Service and the mapping tool Zooma. The resulting harmonized annotations were mapped to the Cumulus output loom (2020-Mar-Atlas-Adult-Retina-10x_annotated_v1.loom) and h5ad (2020-Mar-Atlas-Adult-Retina-10x_annotated_v1.seurat.h5ad) matrix files using cell barcodes. 

We encourage the scientific community to explore and expand on these annotations. To get started making new or additional annotations in Single Cell Portal, please see this Annotation Guide

 

Contributors

Raymond CB Wong (wongcb@unimelb.edu.au), Lyujie Fang (Experimental Scientist), Quan Nguyen (Computational Scientist), Emily Welby (Experimental Scientist), Camden Y Lo (Computational Scientist), Ulrike Grünert (Experimental Scientist), Sandy SC Hung (Experimental Scientist), Peng-Yuna Wang (Principal Investigator), Anne Senabouth (Experimental Scientist), Tu Nguyen (Experimental Scientist), Alex W Hewitt (Principal Investigator), Graeme Pollock (Biomaterial Provider), Hayley S Nguyen (Biomaterial Provider), Ting Zhang (Experimental Scientist), Samuel W Lukowski (Computational Scientist), Trevor D Lamb (Principal Investigator), Jane C Sowden (Principal Investigator), Jafar S Jabbari (Experimental Scientist), Joseph E Powell (Principal Investigator), Adrienne Mackey (Biomaterial Provider), Ling Zhu (Experimental Scientist), Mark C Gillies (Principal Investigator), Alexei A Sharov (Computational Scientist)

Data curators:

Marion F Shadbolt, Zinaida A Perova

 

Acknowledgements

HCA data release policy can be found here. When using this data, please cite the individuals listed under the above "Contributors" section. 

 

Questions

Single Cell Portal-related questions, please email: scp-support@broadinstitute.zendesk.com.

HCA DCP-related questions, please email: data-help@humancellatlas.org

 

Last Date Updated: (YYYY-MM-DD): 2020-01-31