Spatial ATAC-seq
Mapping Open chromatin: A deeper dive into spatial ATAC-seq at the cellular level
Spatial ATAC-seq
Spatial profiling of chromatin accessibility in mouse and human tissues
Yanxiang Deng1,2, Marek Bartosovic3, Sai Ma4, Di Zhang1, Petra Kukanja3, Yang Xiao5, Graham Su1,2, Yang Liu1,2, Xiaoyu Qin1,2, Gorazd B. Rosoklija6,7,8, Andrew J. Dwork6,7,8,9, J. John Mann6,7,10, Mina L. Xu11, Stephanie Halene2,12,13, Joseph E. Craft14, Kam W. Leong5,15, Maura Boldrini6,7, Gonçalo Castelo-Branco3,16 & Rong Fan1,2,11,17
Spatial ATAC-seq protocol
Detecting potential transcription factors/ regulatory elements
From reads to insight: a hitchhiker’s guide to ATAC-seq data analysis
Defining Cell types: General analysis of chromatin state
Analyze region of interest
Match omics with morphology
Identify cell neighborhoods by gene activity score
Annotate Clusters
Exploring regulatory elements with spatial ATAC-seq
Map gene accessibility
Motif analysis for transcription binding sites
Identify unique cis regulator elements (potential enhancer, promoter elements)
