HTAN centers are generating both single cell and single nucleus RNA sequencing data (sc/snRNAseq). Single cell as the name implies targets single cells, whereas single nucleus targets nuclei. The latter is often used in cases where it is difficult to obtain the cell intact.


The set of metadata attributes is harmonized with the Human Cell Atlas metadata on sc/snRNA-seq, where possible. It also includes QC variables coordinated with individual HTAN centers & working groups, in consideration of downstream analysis use-cases.

Files organized by levels

The files are organized by Levels (a concept borrowed from the TCGA / GDC):

Level 1 – Raw primary data, e.g. FASTQs and unaligned BAMs

Level 2 – Aligned primary data, e.g. aligned BAMs

Level 3 – Derived biomolecular data, i.e. gene expression matrix file

Level 4 – Sample level summary, i.e. t-SNE plot coordinates

Level 5 – Cohort level summary, i.e. significantly mutated genes