Single Cell ATAC-Seq

Overview

Single cell ATAC-Seq is a next-generation sequencing (NGS) application that identifies open chromatin states of individual subpopulations of cells within a sample. Open chromatin states are generally associated with sites bound by transcription factors or undergoing active transcription.

General Workflow

A typical single cell ATAC-Seq experimental workflow involves the isolation of single intact nuclei. After the nuclei are isolated, a modified Tn5 transposase enzyme inserts sequencing adapters directly onto double stranded DNA fragments. The DNA is purified, and PCR extension and amplification is performed to create an NGS library.

Data Analysis

SciDAP is a no-code bioinformatics platform that enables scientists to analyze NGS-based data without a bioinformatician. It has built-in pipelines based on open-source workflows to analyze data from single cell ATAC-Seq libraries. SciDAP starts from the FASTQ files provided by most DNA core facilities and commercial service providers. Starting from raw data allows SciDAP to ensure that all experiments have been processed in the same way and simplifies the deposition of data to GEO upon publication. The data can be uploaded from the end-users’ computer, downloaded directly from an FTP server of the core facility by providing a URL, or from GEO by providing SRA accession number.

Steps in the SciDAP Single Cell ATAC-Seq workflow

STEP 1
STEP 2
STEP 3
STEP 4
STEP 5
STEP 6
STEP 7

Start with raw data

SciDAP can start with fastq files or NCBI accession numbers for published data
slide 2

Quantitation

Identification of ATAC islands and initial clustering
CellRanger ARC output

Aggregate multiple experiments

Aggregate scATAC data
scMultiome CellRanger ARCAggr output

Filter out bad cells

Filter out bad cells
scRNA-Seq filtering

Dimensionality reduction and integration for both GEX and ATAC data

Integrate multiple samples with scTriangulate or Harmony
scATAC Integration

Clustering

Browse Signac clusters for ATAC data
scATAC clustering with Signac

Differential expression and accessibility analysis

Differential accessibility analysis for subsets of cells or between conditions using pseudobulk approach
Differential accessibility analysis for pseudobulks

Easy-to-use, no-code bioinformatics software for NGS data analysis