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pciSeq files in csv format

dataset
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
<div>This figshare data set contains more easily accessible format of files included in figshare dataset https://doi.org/10.6084/m9.figshare.7150760</div><div><br><i></i></div><div>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)<br><div><div> </div> </div></div><div><br></div><div>* <b>spots_whole_section</b> files have three columns: genes, X and Y position</div><div><br></div><div>* <b>mask </b>files contain polygon coordinates of CA1 regions</div><div><br></div><div>* <b>cells </b>files have cell ID, X and Y position of cells in CA1, and sum of probabilities of all assigned reads. <br></div><div><br></div><div>* <b>spots_w_segmentation </b>files contain spot assignment results from pciSeq algorithm.</div><div><br></div><div>* <b>celltype </b>files contain cell type assignment results from pciSeq algorithm.<br></div><div><br></div>

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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.

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