Human Cell Atlas Preview Datasets

The first single-cell sequencing datasets from the Human Cell Atlas are now available to the research community.

Census of Immune Cells1

Profiling of immunocytes by single cell RNA-seq for understanding human health and disease.

Species
Homo sapiens
Organ
Umbilical cord blood and bone marrow
Method
10x
Cell count
~530,000 cells
File size
1.3 TB
DOWNLOADS

TSV of project files (e.g. Fastqs and jsons) for downloading with the HCA CLI. Additional instructions below.

Ischaemic Sensitivity of Human Tissue2

Assessment of ischaemic sensitivity of human spleen tissue by single cell RNA-seq.

Species
Homo sapiens
Organ
Spleen
Method
10x
Cell count
~2,000 cells
File size
14 GB
DOWNLOADS

TSV of project files (e.g. Fastqs and jsons) for downloading with the HCA CLI. Additional instructions below.

Melanoma Infiltration of Stromal and Immune Cells3

Single cell RNA-seq of CD45+ and CD45- cells isolated from tumour and lymph nodes of a mouse model of melanoma.

Species
Mus musculus
Organ
Lymph node
Method
Smart-seq2
Cell count
6,639 cells
File size
380 GB
DOWNLOADS

TSV of project files (e.g. Fastqs and jsons) for downloading with the HCA CLI. Additional instructions below.

All Preview Datasets include primary data (fastq and metadata). Additional analysis of the Preview Datasets will be made available here as donated by the data generators.

Download Instructions for Project Data

1. Install the HCA Command Line Interface (HCA CLI)

The HCA CLI is used to download the data files listed in the project's file manifest. Install the HCA CLI by following the HCA CLI installation instructions.

2. Obtain the preview project's file manifest

Follow any of the "Project Data File Manifest" links above to select the desired project in the HCA Data Browser. In the Data Browser, select the "Request File Manifest" button, then select the desired file types and generate and download the project's file manifest.

3. Use the HCA CLI to download the files listed in the project's file manifest

With the HCA CLI installed, and the project's file manifest downloaded, use the HCA CLI to download the files listed in the project's file manifest.

If you have questions or issues to report please email data-help@humancellatlas.org.

  • Census of Immune Cells - Contributors: Bo Li, Monika S Kowalczyk, Danielle Dionne, Orr Ashenberg, Marcin Tabaka, Timothy Tickle, Jane Lee, Karthik Shekhar, Michal Slyper, Julia Waldman, Orit Rozenblatt-Rosen, Aviv Regev. Collaborating organisations: Broad Institute, Massachusetts Institute of Technology, Howard Hughes Medical Institute.
  • Ischaemic Sensitivity of Human Tissue - Contributors: Phillipa Harding, Anna Wilbrey-Clark, Krzysztof Polanski, Kevin Loudon, John R Ferdinand, Krishnaa Mahbubani, Nikitas Georgakopoulos, Kourosh Saeb-Parsy, Kerstin Meyer, Mike Stubbington. Collaborating organisations: Wellcome Trust Sanger Institute, University of Cambridge.
  • Melanoma Infiltration of Stromal and Immune Cells - Contributors: Mirjana Efremova, Sarah Davidson, Bidesh Mahata, Angela Riedel, Roser Vento-Tormo, Jhuma Pramanik, Gozde Kar, Jani Huuhtanen, Jacqueline D Shields, Sarah A Teichmann. Collaborating organisations: Wellcome Trust Sanger Institute, University of Cambridge, DKFZ German Cancer Research Center, EMBL-EBI, University of Helsinki.

The mosaic circle is a trademark of the Human Cell Atlas consortium, registered by Broad Institute and used with permission.