Metadata
HuBMAP metadata documentation and submission specifications. Please refer to the HuBMAP Data Upload Guidelines for the latest assay metadata options and specifications. The Ingest Validation Tools repository is used to maintain the Data Upload Guidelines.
Link to the current version of the Data Submission Guide. See section 10 of the Guide for details on transferring metadata to the HIVE.
Donor
Sample
- This Specification has been replaced by the individual Block, Section, and Suspension specifications below. For more details please review this document.
Sample Block
- Specification
Sample Section
- Specification
Sample Suspension
- Specification
Assay
- 10x Multiome
- AF (Autofluorescence)
- Specification
- Contact: Jeffrey Spraggins
- ATACseq
- Specification
- scATACseq
- bulkATACseq
- Contacts: For bulk ATACseq, snATACseq or SNARE-ATACseq, contact Blue Lake. For sciATACseq, contact Dana Jackson
- Body CT
- CODEX (Not PhenoCycler)
- Specification
- Contact: Vishal Venkataraaman
- Confocal
- DESI
- Enhanced SRS
- GeoMx (NGS)
- HiFi
- Histology
- IMC (Imaging Mass Cytometry)
- 2D IMC
- 3D IMC
- Contact: Michelle Daniel
- LC-MS
- Specification
- Contact: Kevin Contrepois
- Light Sheet
- MALDI-IMS (neg and pos modes - Matrix Assisted Laser Desorption Ionization Imaging Mass Spectrometry)
- Specification
- Contact: Jeffrey Spraggins
- MERFISH
- Molecular Cartography
- MIBI
- Micro CT
- MRI
- MUSIC
- NanoDESI
- OCT
- PhenoCycler
- RNAseq
- Specification
- scRNAseq
- bulkRNAseq
- With Probes
- Contacts: For 10X RNAseq and snRNAseq, contact Stephanie Nevins. For sciRNAseq, contact Dana Jackson.
- SeqFISH
- Specification
- Contact: Nico Pierson
- Second Harmonic Generation
- SIMS
- Slide-seq
- SnareSeq2
- Thick Section Multiphoton MxIF
- Ultrasound
- Visium
- With Probes
- No Probes
- Xenium
EPICs
- Segmentation Mask
Other
- Antibodies
- Contributors