Alignment and integration of spatial transcriptomics data.
Journal
Nature methods
ISSN: 1548-7105
Titre abrégé: Nat Methods
Pays: United States
ID NLM: 101215604
Informations de publication
Date de publication:
05 2022
05 2022
Historique:
received:
16
07
2021
accepted:
17
03
2022
pubmed:
17
5
2022
medline:
24
5
2022
entrez:
16
5
2022
Statut:
ppublish
Résumé
Spatial transcriptomics (ST) measures mRNA expression across thousands of spots from a tissue slice while recording the two-dimensional (2D) coordinates of each spot. We introduce probabilistic alignment of ST experiments (PASTE), a method to align and integrate ST data from multiple adjacent tissue slices. PASTE computes pairwise alignments of slices using an optimal transport formulation that models both transcriptional similarity and physical distances between spots. PASTE further combines pairwise alignments to construct a stacked 3D alignment of a tissue. Alternatively, PASTE can integrate multiple ST slices into a single consensus slice. We show that PASTE accurately aligns spots across adjacent slices in both simulated and real ST data, demonstrating the advantages of using both transcriptional similarity and spatial information. We further show that the PASTE integrated slice improves the identification of cell types and differentially expressed genes compared with existing approaches that either analyze single ST slices or ignore spatial information.
Identifiants
pubmed: 35577957
doi: 10.1038/s41592-022-01459-6
pii: 10.1038/s41592-022-01459-6
pmc: PMC9334025
mid: NIHMS1819659
doi:
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Langues
eng
Sous-ensembles de citation
IM
Pagination
567-575Subventions
Organisme : NHGRI NIH HHS
ID : T32 HG003284
Pays : United States
Organisme : NCI NIH HHS
ID : U24 CA211000
Pays : United States
Organisme : NCI NIH HHS
ID : U24 CA248453
Pays : United States
Commentaires et corrections
Type : CommentIn
Informations de copyright
© 2022. The Author(s), under exclusive licence to Springer Nature America, Inc.
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