Childhood Cancer Data Lab

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.

📣 Join the Data Lab team! We are #hiring a part-time Operations Manager.

We are expanding the Single-cell Pediatric Cancer Atlas (ScPCA) Portal with data contributed by the pediatric cancer research community! In our latest blog post, read about: -Our first community-contributed datasets! These projects have added 15 high grade glioma and glioblastoma samples and 4 neuroblastoma cell lines to the ScPCA Portal.  -How to contribute your own data to the Portal. We are currently accepting submissions! Openly sharing your data on the Portal can enhance the visibility of your work. Over 300 users have downloaded data from the Portal since it launched, and thousands more have browsed the available projects. Researchers that submit data may also be eligible to receive a small one-time grant of unrestricted funds to be used for childhood cancer research. Get started! First, read the full guidelines to learn more about the requirements and the type of data we can accept. >> https://lnkd.in/e97RFBYt Then, fill out an intake form to determine the eligibility of your dataset. >> https://lnkd.in/d753VcfE Contact us at [email protected] with any questions.

The preprint for the Single-cell Pediatric Cancer Atlas (ScPCA) is now available! Read about this data resource, which holds uniformly processed single-cell and single-nuclei RNA-sequencing data and de-identified metadata from pediatric tumor samples. Originally comprised of data from 10 projects funded by Alex's Lemonade Stand Foundation, the ScPCA Portal currently has more than 500 samples from over 50 types of cancer from ALSF-funded and community-contributed datasets. More ScPCA news: -We have just launched the OpenScPCA project! This project aims to collaboratively analyze the ScPCA data and is designed to allow experts worldwide to contribute. Learn more at openscpca.readthedocs.io. -If you're interested in OpenScPCA, check out our upcoming workshop! This 2-day course will cover reproducible research practices and how to contribute to the project. Join us on May 14-15 in Philadelphia. Learn more! >> https://lnkd.in/e8fAnEFM

We are #hiring! The Alex's Lemonade Stand Foundation Childhood Cancer Data Lab and the UC Santa Cruz Genomics Institute Treehouse Childhood Cancer Initiative are jointly seeking a #PostdoctoralResearcher! The #Postdoc will: -Use large collections of bulk and single-cell RNA-seq data to characterize developmental subtypes of pediatric tumors -Build generalizable scientific software -Be appointed as a postdoctoral scholar at UCSC -Work alongside highly experienced data scientists Qualified candidates must have: -A PhD in computational or biological sciences with a strong background in #bioinformatics or a closely related field -Programming experience with attributable contributions to source code -Strong background in cancer biology preferred Learn more and apply here! https://lnkd.in/eCugBgsC