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

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

Fastqs and jsons. 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

Fastqs and jsons. 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 Primary Data

To download the datasets, use the shell scripts provided above. There is one script for each dataset. The shell script will install the HCA command line client using the pip installer, then call the client to download the dataset to your local machine.

You will need a Unix environment (Linux, OS X, Windows WSL, or Windows Cygwin), as well as a Python installation (version 2.7+) with a functional pip installer.

Since downloads can take an hour or more for the larger datasets, we recommend you use a tool like nohup or screen to ensure your download is not interrupted. Additionally, we advise downloading these datasets one at a time. Some people have reported issues when downloading multiple in parallel.

1. Download the shell script for the dataset you are interested in

Click on the download dataset button to save a shell script that will download data.

2. Run the script in the terminal

After saving the script, run it in your terminal as follows:

chmod +x ~/Downloads/FILENAME

Next, run:

~/Downloads/FILENAME

Replace FILENAME with the name of the shell script for the dataset you’d like to download.

Dataset
Shell script file
Census of Immune Cells
Ischaemic Sensitivity of Human Tissue
Melanoma Infiltration of Stromal and Immune Cells

3. View the files

The script will download the dataset to your environment. For some of the datasets there will be multiple directories of data corresponding the number of samples in the dataset. Inside you will find both metadata files as well as fastq files.

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.