News & Events

New release: Gene expression patterns of the developing face at single cell resolution (20 January 2026)

The 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 (11 December 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 (10 November 2025)

Thank 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.

Data release: Identification of lymphatic vessels in skull periosteum but not bone marrow reveals skull channel heterogeneity (18 September 2025)

This 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.

Data release: OPT imaging of the craniofacial morphology of control and Shroom3 null embryos (15 September 2025)

Through integrating Kids First whole genome sequencing with eQTL analyses and supporting 3D imaging data from Shroom3 mouse models, Timothy Cox’s lab has identified SHROOM3 as a bona fide craniofacial microsomia gene. The mouse embryo imaging data from this study is now openly available through FaceBase.

FaceBase Dataset:

Optical Projection Tomography imaging of the craniofacial morphology of control and Shroom3 null embryos
Principal Investigator: Timothy Cox (University of Missouri-Kansas City)
DOI: https://doi.org/10.25550/7E-Y876

Related Publication:

Zhu H, et al. Common cis-regulatory variation modifies the penetrance of pathogenic SHROOM3 variants in craniofacial microsomia. Genome Res. 2025 May 2;35(5):1065-1079. doi: 10.1101/gr.280047.124. PMID: 40234029; PMCID: PMC12047249.

Description:

This study followed up on a prior GWAS conducted a large cohort of Chinese patients with craniofacial microsomia (CFM) in which multiple associated genomic loci were identified. Using whole genome sequencing data from 2009 patients with CFM, including data from the Gabriella Miller Kids First program, and 2625 population controls, we analyzed candidate CFM genes within these GWAS peaks and found a significant enrichment of rare variants in one candidate gene, SHROOM3. Subsequent analysis of public expression QTL (eQTL) data revealed numerous eQTLs within the SHROOM3 GWAS peak, prompting us to consider whether eQTLs in combination with the rare variants might determine the presentation of CFM. Allelic phasing identified specific haplotypes in CFM patients, but not in controls, that contained multiple eQTLs in cis with the rare SHROOM3 coding variants. Subsequent luciferase assays confirmed the functional impact of many of these eQTL SNPs. Our findings support the notion that the penetrance of rare variants, that might otherwise be ignored in bioinformatic pipelines because they are seen in unaffected individuals, is influenced by combinations of in cis eQTLs - that is, the expression level of the mutant heterozygous allele may determine the penetrance. Under this premise, we conducted 3D imaging of embryos from two separate Shroom3 mutant lines of mice and performed a morphometric analysis of facial and auricular tissues of wild-type as well as Shroom3 heterozygous and homozygous embryos. These analyses in both models showed Shroom3 gene dosage-dependent effects on both external ear size and maxillary and mandibular growth and, importantly facial asymmetry, providing validation of SHROOM3 as a bona fide CFM gene.

All new sequencing data has been submitted to the National Genomics Data Center (https://ngdc.cncb.ac.cn/gsa-human) under accession numbers HRA005132, HRA004333, HRA003925, and HRA003924. Raw, reconstructed, and rendered optical projection tomography (OPT) data for all mouse embryos of the Shroom3gt strain used for the morphometric analyses is available now on FaceBase (https://doi.org/10.25550/7E-Y876). MicroCT datasets of the Shroom3 null allele strain are available through the IMPC website with IDs 157760 (wildtype) and 612303 (homozygous) (https://www.mousephenotype.org/embryoviewer/?mgi=MGI%3A1351655).