Stockholm University
126 files

pciSeq files in csv format

posted on 2019-11-19, 09:51 authored by Xiaoyan QianXiaoyan Qian, Kenneth HarrisKenneth Harris, Thomas Hauling, Dimitris Nicoloutsopoulos, Ana B. Munoz-Manchado, Nathan Skene, Jens Hjerling-Leffler, Mats E. NilssonMats E. Nilsson
This figshare data set contains more easily accessible format of files included in figshare dataset

In situ sequencing (ISS) is a technology to sequence RNA directly inside tissue sections, and probabilistic cell typing by ISS (pciSeq) method is a method to spatially map single-cell RNA-sequencing defined cell types. (See Associated Publication)

* spots_whole_section files have three columns: genes, X and Y position

* mask files contain polygon coordinates of CA1 regions

* cells files have cell ID, X and Y position of cells in CA1, and sum of probabilities of all assigned reads.

* spots_w_segmentation files contain spot assignment results from pciSeq algorithm.

* celltype files contain cell type assignment results from pciSeq algorithm.


Associated Publication

Qian, X. et al. Probabilistic cell typing enables fine mapping of closely related cell types in situ. Nat Methods 1–6 (2019) doi:10.1038/s41592-019-0631-4.