New release: Gene expression patterns of the developing face at single cell resolution
January 20th, 2026The following datasets have been released to FaceBase by Dr. Justin Cotney’s lab of the Children’s Hospital of Philadelphia. A related manuscript has been accepted but not yet released; in the meantime, these data are available for the community.
Description:
Justin Cotney’s lab generated a single-nucleus RNA sequencing (snRNA-seq) atlas of critical time points during human and mouse craniofacial development. Their analysis identified multiple subtypes of mesenchyme, epithelium, and cranial neural crest, among other functionally distinct cell types. Through cross-species comparisons, Cotney’s team identified functionally conserved cell types as well as anatomically distinct cell subtypes. Finally, following integration with data from the Gabriella Miller Kids First program, the Cotney lab revealed enrichment of de novo protein-altering variants from orofacial clefting trios in specific cell subtypes. The human and mouse snRNA-seq data from this study is now openly available through FaceBase.
FaceBase Datasets:
Alexandra Manchel, Justin Cotney. Gene expression patterns of the developing human face at single cell resolution (snRNA-seq). FaceBase Consortium https://doi.org/10.25550/8D-2JQ0 (2026).
Alexandra Manchel, Justin Cotney. Gene expression patterns of the developing mouse face at single cell resolution (snRNA-seq). FaceBase Consortium https://doi.org/10.25550/7N-54BY (2026).
Save the Date: 2026 FaceBase Community Forum – May 4–5 in Arlington, VA
December 11th, 2025
We’re excited to announce that the 2026 FaceBase Community Forum will take place May 4–5, 2026, at the University of Southern California/Information Sciences Institute East Office in Arlington, VA. This two-day, in-person event will bring together researchers, clinicians, data scientists, contributors, and trainees from across dental, oral, and craniofacial (DOC) science as well as related areas such as the ear, eye, and other craniofacial-associated systems.
This year’s annual meeting will highlight new tools, datasets, and research supported by FaceBase, with expanded discussions on AI-ready biomedical data and how structured metadata, packaging, and standards within the platform enable machine learning, multimodal integration, and new scientific insights.
Sessions will include invited talks, panel discussions, demonstrations, poster presentations, and community-driven conversations with the FaceBase team. It’s an opportunity to learn, collaborate, and help shape the future of the FaceBase resource.
An agenda, registration information, and the call for posters will be available early 2026.
For more details and updates, visit the event page: https://www.facebase.org/community/annual-meeting/2026-facebase-annual/
Materials Now Available: November 2025 FaceBase Bootcamp
November 10th, 2025Thank you to everyone who joined our November 2025 FaceBase Bootcamp for Users and Data Contributors!
Recordings, slides, and other materials from the session are now available on the event page.
The bootcamp covered:
- How to find, filter, and download data from FaceBase
- Requesting controlled-access human datasets
- Preparing and contributing data using FaceBase tools
- Guidance for NIH Data Management and Sharing (DMS) plans
- And more!
Watch individual segments or the full playlist on our YouTube channel, and download the presentation slides directly from the event page.
We’d love your feedback!
If you took the training (either live or later via video) please take our short, anonymous 3-minute survey to help shape future FaceBase trainings.
November 2025 FaceBase Bootcamp
October 1st, 2025Our next virtual bootcamp, tailored for both users and data contributors, is coming up on:
🗓 Date: Wednesday, November 5 (Register here!)
Whether you’re a seasoned user of FaceBase or looking to contribute data for the first time, this event is for you!
This bootcamp is designed for investigators, clinicians, and trainees in dental, oral, and craniofacial (DOC) research, as well as anatomically and biologically relevant diseases and conditions. It’s an excellent opportunity for anyone interested in accessing DOC biomedical data, understanding updated platform functionalities, or contributing data in compliance with NIH data-sharing requirements.
Event Page: For more details, including the full agenda, visit the event page.
Register: Registration via Zoom is required. A confirmation email will be sent upon registration that includes your Zoom link for the event.
Questions? Please direct any questions to help@facebase.org.
Data release: Identification of lymphatic vessels in skull periosteum but not bone marrow reveals skull channel heterogeneity
September 18th, 2025This dataset has been released to FaceBase by Dr. Jian-Fu Chen’s group of the University of Southern California. A related manuscript is in preparation; in the meantime, these data are available for the community.
FaceBase Dataset:
Identification of lymphatic vessels in skull periosteum but not bone marrow reveals skull channel heterogeneity
Principal Investigator: Jianfu Chen (University of Southern California)
DOI: https://doi.org/10.25550/8R-NM0R
Description:
We identified lymphatic vessels at the skull periosteum and found no evidence of lymphatic vessels in the cortical bones or skull bone marrow, where the lymphatic marker VEGFR3 labels blood vessels. Skull periosteum channels to the upper skin are found to occur more frequently in parietal bone than interparietal bone, whereas bone marrow is found more often in interparietal bone than parietal bone. Despite skull bone marrow expansion during aging, skull channels are significantly reduced, suggesting of aging-dependent uncoupling between skull channels and bone marrow. Together, our findings show lymphatic vessels are present in the skull periosteum but absent in bone marrow, with channel and bone marrow heterogeneity varying by skull region and age.