Single-cell transcriptome atlas of lamprey exploring Natterin induced white adipose tissue browning: Code and processed scRNA-seq data

This repository contains code and processed scRNA-seq data of lamprey, which constructed a comprehensive cell atlas comprising 604,460 cells/nuclei and 70 cell types from 14 tissues.

lamprey_atlas.raw.h5ad:

Python data set (.h5ad) containing raw counts matrix from all tissues and libraries.

lamprey_atlas.scanpy_merge.h5ad:

Python data set (.h5ad) containing scanpy processed matrix, used in projection of cells from all tissues into shared UMAP space. Only highly-variable genes calculated by scanpy are included.

immune.h5ad:

Python data set (.h5ad) containing scanpy processed matrix, used in re-clustering of immune cells. Only highly-variable genes calculated by scanpy are included.

pancreas.evo.rds:

R data set (.rds) containing integrated data of intestine, liver, pancreas from human and mouse, as well as intestine and liver from lamprey. 

lamprey-single-cell-atlas-1.0.0.zip:

Code used in processing of scRNA-seq data.