Researchers post genetic profiles of a half-million human immune cells on Human Cell Atlas online portal

April 16, 2018 by Jenny Rood, Broad Institute of MIT and Harvard
Credit: CC0 Public Domain

A team of postdoctoral and research scientists at the Broad Institute has made a data set of half a million human immune cells openly accessible on a preview site that provides initial access to data for the Human Cell Atlas initiative.

The data set, one of the largest of its kind, includes primary data and associated metadata from nearly 530,000 immune cells from umbilical cord blood of newborns and bone marrow of adults. Additional data sets were also provided by Wellcome Sanger Institute and collaborators.

"This is a wonderful example of science at its most open and collaborative," said team co-leader Orit Rozenblatt-Rosen, an Institute Scientist at the Broad and director of the Klarman Cell Observatory (KCO).

This data lays the foundation for an immune cell atlas, an important first step in the Human Cell Atlas consortium's goal of an initial draft atlas of 30 million cells covering many tissues. "The immune system is deeply complex, involved in many diseases, and distributed throughout our body. This data set will be critical to help unlock its secrets," said Monika Kowalczyk, a hematologist who led the experimental team while a postdoctoral researcher in the lab of Broad Core Institute Member Aviv Regev.

By making the data openly accessible before drafting their manuscript for publication the researchers have provided the broader scientific community with a valuable resource. The data set can reveal basic biology, provide a reference for studying disease, and allow computational biologists to test new analysis tools on a large data set that would be hard for smaller labs to generate.

"Collecting and processing half a million immune cells was a Herculean feat, involving tightly coordinated teamwork across many areas of expertise," said team member Danielle Dionne of the KCO at the Broad.

First, Kowalczyk and her KCO colleagues Dionne, Michal Slyper, and Julia Waldman isolated single cells from human cord blood and bone marrow samples and prepared them for sequencing. This required meticulous advanced planning since the team was handling 224,000 cells from four patients in a 20-minute window—up to 100-fold more cells than in a typical experiment.

Computational biologists on the team then needed to determine how to assess quality and analyze a batch of data large enough that they couldn't be analyzed with existing computational tools. To handle the data, the trio of Orr Ashenberg of the KCO and Bo Li and Marcin Tabaka of the Regev lab built new computational methods, working from code that was either openly available (such as SCANPY) or provided by their colleague Karthik Shekhar. These tools identified for example cell types from the sequencing data, found signature genes that characterize them and showed how particular cell types developed from others.

Next, before releasing the massive data set, the team worked with other Broad colleagues—Jane Lee, who coordinated logistics for the entire project, Stacey Donnelly, and Andrea Saltzman—to ensure that each sample had appropriate patient consent for data release. In the process, they set up an approach applicable to future samples—including an additional set of 1.08 million cord blood, bone marrow, and white blood cells that the team, in collaboration with Broad Institute Member Nir Hacohen and Alexandra-Chloe Villani, has already processed and will release once all approvals are confirmed.

Explore further: New types of blood cells discovered

More information: The data is now available at preview.data.humancellatlas.org

Related Stories

New types of blood cells discovered

April 21, 2017
Scientists have identified new classes of cells in the human immune system.

Recommended for you

Scientists cut main heart disease risk locus out of DNA by genome editing

December 6, 2018
Over the past decade we've learned that billions of people carry a mysterious specter in their DNA that strongly increases their risk for life threatening cardiovascular diseases, such as heart attacks, aneurysms or strokes, ...

What can a snowflake teach us about how cancer spreads in the body?

December 6, 2018
What can seashells, lightning and the coastline of Britain teach us about new drugs for cancer?

New genetic insight could help treat rare debilitating heart and lung condition

December 6, 2018
The largest study of genetic variation in patients with pulmonary arterial hypertension has associated two important genes with the disease.

Are scientists studying the wrong kind of mice?

December 5, 2018
Mice represent well over half of the non-human subjects of biomedical research, and the vast majority of those mice are inbred. Formed by generation after generation of mating between brothers and sisters, inbred mice are ...

Researchers find evidence of prenatal environment tuning genomic imprinting

December 5, 2018
A team of researchers from the U.S., Australia and Denmark has found evidence of the prenatal environment tuning genomic imprinting. In their paper published in Proceedings of the National Academy of Sciences, the group describes ...

Gene that lets you eat as much as you want holds promise against obesity

December 4, 2018
It sounds too good to be true, but a novel approach that might allow you to eat as much food as you want without gaining weight could be a reality in the near future.

0 comments

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.