Study: Cumulus HCA Demo 3018 cells

HCA DCP Project Title: Dissecting the human liver cellular landscape by single cell RNA-seq reveals novel intrahepatic monocyte/ macrophage populations

HCA DCP Project Page (go here for original data): https://data.humancellatlas.org/explore/projects/4d6f6c96-2a83-43d8-8fe1-0f53bffd4674

Organ, Developmental Stage, Technology: Liver, Adult, 10x

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

Publication Link: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6197289/

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

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

 

Study overview

This study presents an example analysis of a liver dataset from the Human Cell Atlas (HCA) Data Coordination Platform (DCP) Project entitled "Dissecting the human liver cellular landscape by single cell RNA-seq reveals novel intrahepatic monocyte/ macrophage populations". It is part of the HCA March 2020 Release (INSERT Link to the DCP page) 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 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. 

 

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 "Dissecting the human liver cellular landscape by single cell RNA-seq reveals novel intrahepatic monocyte/ macrophage populations", 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/4d6f6c96-2a83-43d8-8fe1-0f53bffd4674).  

 

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 (SingleCellLiverLandscape.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 SingleCellLiveLandscape.loom (see Download tab) to perform additional filtering, clustering, differential expression analyses and plotting. The HCA Release Methods documentation (INSERT LINK) details the Cumulus workflow parameters and outputs, including those available for download on this Single Cell Portal page. 

Annotation:

Cell annotations were obtained from MacParland et al., 2018. 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 (“INSERT FILE NAME”) and h5ad (“INSERT FILE NAME) 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

 

Contributions 

Researchers: 

Xue-Zhong Ma (Clinician), Elizabeth Lee (Administrator), Agata M Bartczak (Experimental Scientist), Zigong Shao (Clinician), Gordon Keller (Co-investigator), Blair K Gage (Experimental Scientist), Nazia Selzner (Clinician), Michael L Cheng (Experimental Scientist), Rebecca K Seliga (Experimental Scientist), Justin Manuel (Clinician), Nicholas Khuu (Experimental Scientist), Jeff C Liu (Clinician), Jason E Fish (Co-investigator), Sai W Chung (Experimental Scientist), Oyedele Adeyi (Pathologist), Michael D Wilson (Co-investigator), Neil Winegarden (Co-investigator), Ivan Linares (Clinician), Markus Selzner (Clinician), Mina Ogawa (Experimental Scientist), Shinichiro Ogawa (Experimental Scientist), Lewis Y Liu (Experimental Scientist), David Grant (Clinician), Brendan T Innes (Clinician), Gonzalo Sapisochin (Clinician), Rahul Gupta (Experimental Scientist), Damra Camat (Experimental Scientist), Anand Ghanekar (Clinician), Paul Greig (Clinician), Juan Echeverri (Clinician)

Project curators:

William G Sullivan

HCA DCP curators:

Zinaida A Perova

 

Acknowledgements

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

 

Contacts for HCA data are: 

Elo Madissoon (em17@sanger.ac.uk), Tracey Andrew (ta11@sanger.ac.uk), Oliver Stegle (stegle@ebi.ac.uk), Kerstin B Meyer (km16@sanger.ac.uk), Anna Wilbrey-Clark (aw24@sanger.ac.uk)

 

Questions

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

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