Childhood Cancer Data Lab

The Data Lab team is hosting a workshop at the University of Minnesota this week! We’re introducing researchers to bulk RNA-Seq data analysis and techniques to achieve reproducible results in computational cancer research. Interested in attending a future workshop? Later this year, we will hold courses on reproducible research practices and advanced single-cell RNA-Seq. Join our mailing list to be alerted when registration opens! ✉ bit.ly/3eQZXGQ

The Open Single-cell Pediatric Cancer Atlas (OpenScPCA) is an open, collaborative project to explore, analyze, and synthesize data available on the Single-cell Pediatric Cancer Atlas (ScPCA) Portal. We're seeking collaborators who can help annotate and assign cell types to existing ScPCA datasets! Small one-time grants are available for eligible pediatric cancer researchers. OpenScPCA collaborators have started analyzing data from multiple pediatric cancer types. Check out the work that is currently being done and join the community on GitHub!

📣 Are you interested in sharing data on the #SingleCell #PediatricCancer Atlas (ScPCA) Portal? We have extended the deadlines for community contributions! What can you share? -10x Genomics single-cell or single-nuclei profiling of pediatric cancer data, broadly defined to include relevant animal models, patient-derived xenografts, or cell lines, as well as tumor data. Requirements for eligible researchers: -Generate summarized gene expression data using our production pipeline. -Submit the output, along with project, sample, and cell metadata. -Execute a Data Transfer Agreement between your institution and ALSF. 🌟 Up to five eligible researchers who share data on the Portal will receive a small one-time grant of unrestricted funds to be used for childhood cancer research! New deadlines: -Dataset submission deadline: October 15, 2024 -Application Submission Deadline (if eligible): November 1, 2024 View the full data contribution guidelines below!

More data is now available on the #SingleCell #PediatricCancer Atlas (ScPCA) Portal! -The Portal currently holds uniformly processed single-cell gene expression data from over 600 samples representing 55 cancer types. We have just released two new projects, adding 81 Osteosarcoma samples. Explore the available data! scpca.alexslemonade.org -Do you have pediatric cancer single-cell data you want to make openly available? We are currently accepting data submissions from the community. Up to five eligible researchers who share data will receive a small one-time grant of unrestricted funds to be used for childhood cancer research. Learn more! https://lnkd.in/e97RFBYt

In April 2024, we announced the Open Single-cell Pediatric Cancer Atlas (OpenScPCA) project. Since then, we've been working to build a supportive community while getting started on a few analysis ideas! We’re excited to see growing interest in the project, and we have some big news for prospective collaborators. Contribute your expertise to help us build a valuable pediatric cancer resource, and you may become eligible for a grant! We are seeking collaborators with experience analyzing single-cell RNA-seq datasets to help annotate and assign cell types to existing datasets on the Single-cell Pediatric Cancer Atlas (ScPCA) Portal. Small one-time grants are now available for eligible pediatric cancer researchers who annotate cell types for all samples in a given group. Read more about grant opportunities and what we've been working on!

We've had the opportunity to meet and train pediatric cancer researchers during two exciting workshops this year! In May, we taught our Reproducible Research Practices course with an additional module introducing attendees to our collaborative project, the Open Single-cell Pediatric Cancer Atlas (OpenScPCA). Earlier this month, we welcomed over 20 researchers to a virtual Introduction to Single-cell RNA-Sequencing workshop. We're looking forward to more Data Lab workshops in 2024! ✉ Sign up to be notified about future opportunities: bit.ly/3eQZXGQ

We're #hiring! Interested in childhood cancer, transcriptomics and data science? The Data Lab and UC Santa Cruz Genomics Institute Treehouse Childhood Cancer Initiative are jointly seeking a Postdoctoral Researcher to develop new analytical approaches and apply them to pediatric cancer. The Postdoctoral Researcher will work alongside a team of highly experienced data scientists with mentorship from the co-founder of the Treehouse Initiative and the director of the Data Lab. Learn more about this unique opportunity!👇 For full consideration, please apply and submit your materials by June 15.

📣 Do you have pediatric cancer single-cell data you want to make openly available on the #SingleCell #PediatricCancer Atlas (ScPCA) Portal? We are now accepting submissions from the community! What can you share?  -10x Genomics single-cell or single-nuclei profiling of pediatric cancer data, broadly defined to include relevant animal models, patient-derived xenografts, or cell lines, as well as tumor data. Requirements for eligible researchers: -Generate summarized gene expression data using our production pipeline. -Submit the output, along with project, sample, and cell metadata. -Execute a Data Transfer Agreement between your institution and ALSF. 🌟 Up to five eligible researchers who share data on the Portal will receive a small one-time grant of unrestricted funds to be used for childhood cancer research! Important dates: -Dataset submission deadline: September 1, 2024 -Application Submission Deadline (if eligible): September 15, 2024 View the full data contribution guidelines below!

We've added new features to the Single-cell Pediatric Cancer Atlas (ScPCA) Portal! -Download samples with added cell type annotations -Download data as one merged file, which contains combined information for all samples within a project We use two different methods for annotating cell types:  -SingleR, a reference-based cell type annotation method -CellAssign, a marker-gene-based cell type annotation method A cell type report is available with each sample you download from the Portal, and includes a comparison of the annotations obtained from both tools. We also implemented a new module for annotating cell types in scpca-nf, processed all datasets from the Portal through the updated pipeline and released them to the community! Read our blog about implementing this feature, which includes our tips for choosing and testing tools for specific analyses.

Going into the Open Single-cell Pediatric Cancer Atlas (OpenScPCA) project, we knew it would be important to have a clear sense of how collaborators will interact with the project and good documentation to help external researchers make contributions. To achieve this, we first had to understand more about who our collaborators might be! Check out our latest blog post on how we used journey mapping to prepare for the OpenScPCA project. We used this process to: -characterize our potential collaborators -identify challenges that we, and our collaborators, may encounter -develop strategies to mitigate those challenges -ensure our team members are in agreement Read our blog post for more on how we did it, what we learned, and how journey mapping might be useful for your own projects! Learn more about OpenScPCA at openscpca.readthedocs.io.