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 PDF. See section 10 of the Guide for details on transferring metadata to the HIVE.

Donor

Donor Metadata Specification

Organ

• Specification

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• This Specification has been replaced by the individual Block, Section, and Suspension specifications below.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
  • Specification
• AF (Autofluorescence)
  • Specification
  • Contact: Jeffrey Spraggins
• Antibody-based MxIF (Multiplexed Immunofluorescence)
  • Specification
  • Contact: Jeffrey Spraggins
• ATACseq
  • scATACseq
    • Specification
  • bulkATACseq
    • Specification
  • Contacts: For bulk ATACseq, snATACseq or SNARE-ATACseq, contact Blue Lake. For sciATACseq, contact Dana Jackson
• Body CT
  • Specification
• CE-MS
  • Specification
• Cell DIVE
  • Specification
• CODEX
  • Specification
  • Contact: Vishal Venkataraaman
• Confocal
  • Specification
• CyCIF
  • Specification
• DESI
  • Specification
• Enhanced SRS
  • Specification
• GC-MS
  • Specification
• GeoMX
  • Specification
• HiFi
  • Specification
• Histology
  • Specification
• hrsTP-seq (DBiTSeq)
  • Specification
• IMC (Imaging Mass Cytometry)
  • 2D IMC
    • Specification
  • 3D IMC
    • Specification
  • Contact: Michelle Daniel
• LC-MS
  • Specification
  • Contact: Kevin Contrepois
• Light Sheet
  • Specification
• MALDI-IMS (neg and pos modes - Matrix Assisted Laser Desorption Ionization Imaging Mass Spectrometry)
  • Specification
  • Contact: Jeffrey Spraggins
• Molecular Cartography
  • Specification
• MERFISH
  • Specification
• MIBI
  • Specification
• Micro CT
  • Specification
• MRI
  • Specification
• NanoDESI
  • Specification
• OCT
  • Specification
• PAS (histological stain)
  • Specification
  • Contact: Jeffrey Spraggins
• PhenoCycler
  • Specification
• RNAseq
  • scRNAseq
    • Specification
  • bulkRNAseq
    • Specification
  • GeoMX
    • Specification
  • Visium
    • Specification
  • Contacts: For 10X RNAseq and snRNAseq, contact Stephanie Nevins. For SNARE-RNAseq, contact Blue Lake. For sciRNAseq, contact Dana Jackson.
• SeqFISH
  • Specification
  • Contact: Nico Pierson
• Second Harmonic Generation
  • Specification
• SIMS
  • Specification
• Slide-seq
  • Specification
• Thick Section Multiphoton MxIF
  • Specification
• Ultrasound
  • Specification
• Visium
  • Specification
• WGS
  • Specification
  • Contact: Aaron Horning
• Xenium
  • Specification