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

Variants in non-coding DNA contribute to inherited autism risk

April 19, 2018
In recent years, researchers have firmly established that gene mutations appearing for the first time, called de novo mutations, contribute to approximately one-third of cases of autism spectrum disorder (ASD). In a new study, ...

Researchers discover link between gene variation and language

April 18, 2018
What shapes the basic features of a language?

Natural selection still at work in humans

April 18, 2018
Evolution has shaped the human race, with University of Queensland researchers finding signatures of natural selection in the genome that influence traits associated with fertility and heart function.

Gene therapy for beta-thalassemia safe, effective in people

April 18, 2018
In a powerful example of bench-to-bedside science showing how observations made in the lab can spark life-altering therapies in clinic, an international team of clinician-investigators has announced that gene therapy for ...

Potential lines of attack against prostate cancer

April 17, 2018
Researchers from The University of East Anglia (UEA) have contributed to the world's largest study into genes that drive prostate cancer – identifying 80 molecular weaknesses that could be targeted by drugs to treat the ...

Epstein-Barr virus linked to seven serious diseases

April 16, 2018
A far-reaching study conducted by scientists at Cincinnati Children's reports that the Epstein-Barr virus (EBV)—best known for causing mononucleosis—also increases the risks for some people of developing seven other major ...

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.