Spatial ATAC-seq

Mapping Open chromatin: A deeper dive into spatial ATAC-seq at the cellular level

Spatial ATAC-seq

A scientific image of a cross-section of a human brain with color-coded regions, labeled with 'Nature' at the top and 'Deng 2021' at the bottom.

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

Diagram showing processes of Tn5 transposition, barcode A ligation, and barcode B ligation in genetic editing, illustrating DNA structures, enzymes, and ligation steps.

Spatial ATAC-seq protocol

Detecting potential transcription factors/ regulatory elements

Graph showing NFR fragments density and mononucleosome peaks with labels for gene, transcription factor, nucleosome, transposase Tn5, peak, and footprint.

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

Microscopic image showing a germinal center and follicle with labeled regions: follicle, germinal center, marginal zone, and three smaller sections.

Match omics with morphology

A computer screen with a pixelated image of a butterfly, overlaid with colored dots representing data points, and three marked areas outlined in white.

Identify cell neighborhoods by gene activity score

Abstract pattern of vertical blue, yellow, and green stripes.

Annotate Clusters

Diagram of the genetic variation of COVID-19 Delta variant across South America, with a focus on the T-cell response and zone classifications, showing clusters of different mutations associated with lineages C1 to C8.

Exploring regulatory elements with spatial ATAC-seq

Map gene accessibility

A weather radar image showing weather patterns over a landmass with clusters of precipitation represented in red, orange, yellow, and blue on a gray background.

Motif analysis for transcription binding sites

A microscopic view of cells with various shapes and colors, mainly white, with red and orange areas indicating different cell types or states.
A dot matrix visualization of South America with a color gradient from white to red, indicating data density or intensity.

Identify unique cis regulator elements (potential enhancer, promoter elements)

A chromosomal visualization showing gene expression data across multiple samples, with a highlighted promoter region and gene locus, including labels for specific genes like MIR4540, MIR4476, MIR4475, PAX5, EBLN3P, and ZCCHC7.
Bar chart showing the distribution of three categories, Distal, Exonic, and Intronic, across eight groups labeled C1 to C8, with each bar divided into colored segments representing each category.