The first single-cell sequencing datasets from the Human Cell Atlas are now available to the research community.
Profiling of immunocytes by single cell RNA-seq for understanding human health and disease.
Assessment of ischaemic sensitivity of human spleen tissue by single cell RNA-seq.
Single cell RNA-seq of CD45+ and CD45- cells isolated from tumour and lymph nodes of a mouse model of melanoma.
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.
Click on the download dataset button to save a shell script that will download data.
After saving the script, run it in your terminal as follows:
Replace FILENAME with the name of the shell script for the dataset you’d like to download.
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 email@example.com.
The mosaic circle is a trademark of the Human Cell Atlas consortium, registered by Broad Institute and used with permission.