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Analysis of 10X Genomics basal cell carcinoma scRNA-seq and scATAC-seq dataset

CW Chenfei Wang
DS Dongqing Sun
XH Xin Huang
CW Changxin Wan
ZL Ziyi Li
YH Ya Han
QQ Qian Qin
JF Jingyu Fan
XQ Xintao Qiu
YX Yingtian Xie
CM Clifford A. Meyer
MB Myles Brown
MT Ming Tang
HL Henry Long
TL Tao Liu
XL X. Shirley Liu
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We downloaded the processed expression matrix of 53K scRNA-seq from BCC microenvironment from the GEO database (GSE123814). Then, we performed the clustering analysis using MAESTRO with default parameters. The cell types for the scRNA-seq clusters were annotated using the meta-information provided in the original study. The BCC 38K scATAC-seq fragments and peak files were downloaded from the GEO database (GSE129785). We then lifted over the fragments and peaks from hg19 to hg38 and calculated the binarized peak count matrix based on the fragments and peak files. The gene activity scores were calculated using TSS 10K “enhanced RP model” in MAESTRO. Before clustering, we first filtered out the peaks only present in less than 50 cells and cells with less than 500 peaks. After clustering, we performed differential analysis and annotated the cell types using the annotations from the original study [83]; we integrated the scATAC-seq with scRNA-seq using MAESTRO and transferred the cell-type labels from scRNA-seq to scATAC-seq.

Copyright and License information: The Author(s) ©2020
Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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