End-to-end Single Cell ATAC-seq Service, Chromatin Profiling

Intro to Diagenode’s and Bio-Rad’s scATAC-seq

Single cell sequencing provides you more in-depth insight of gene expression and gene regulation at individual cell resolution
ATAC-Seq identifies subpopulations

Chromatin accessibility is more cell type specific than mRNA expression in primary blood cells

RNA-seq: profile gene expression patterns
ATAC-seq: profile regulators of cell identity
Chromatin accessibility more adept than mRNA expression levels at classifying cell types.

Chromatin accessibility is more cell type specific than mRNA expression in primary blood cells

The technology and data of our scATAC-seq

Workflow of our scATAC-seq solution

Input: ~7,500 tagmented nuclei per well

Output: 5,000 nuclei analyzed

Bio-Rad’s Droplet Digital Technology

1.
1. Typically, cell data points are represented twice, “fractionated” which can cause inaccuracy
2. Bio-Rad’s Droplet Digital Technology merges bead barcodes to create a droplet barcode to resolve this issue
3. Unique “ATAC fingerpint” can be resolved using BAP: Bead-based scATAC-Seq Processing

2.

Since Tn5 cuts randomly, every cell has a unique set of cut fragments: an ATAC fingerprint!

If % unique fragments shared is high enough (compared to background), beads are inferred to have originated from the same droplet

3.

This bioinformatic process, BAP, works very well because there is a large difference in the similarity score between barcodes originating in the same droplet versus barcodes originating in different droplets. This is demonstrated by the very sharp knee on the plot.

Y-axis = “similarity score” or the Jaccard index
X-axis = bead pairs in rank order

4.

First PCR product fully adaptered

In the workflow, droplet reaction yields sequencing ready library. During droplet PCR, the tagmented nuclei are ligated with adaptors with beads barcode, sample index and P5 and P7, generating sufficient library that can be ready to sequence.

Performance data from a species mixing experiment of human and mouse cell lines.

Excellent cell utilization and enrichment

Mixed mouse 3T3 and human K562 cells

Cell Utilization up to 95%
TSS Enrichment score: >40*
> 40% Fraction of reads in peaks**
> 20,000 Unique Genomics Fragments/cell at a read depth of 50k reads/cell

*40x more reads at TSS than at sites 2kb away from the TSS. ** . FRIP should be as high as possible because reads outside peaks are not useful for analyzing chromatin accessibility.

Assay for Transposase-Accessible Chromatin with high-throughput sequencing

Highly complex libraries results in more biological meaningful data at less sequencing depth

Data generated from Bio-Rad’s ATAC-Seq kit

Encyclopedia of DNA Elements (ENCODE)

NIH’s resource of human epigenomics data to catalyze basic biology and disease oriented research.
ENCODE contains consensus regions of open chromatin in PBMCs

Data generated from Bio-Rad’s ATAC-Seq kit shows more consensus peaks across sequencing depth compared to competitor

Better classification of cell types with Bio-Rad’s ATAC-Seq than competing technology

PBMCs: Cell mis-classification

PBMC datasets from Bio-Rad’s and competitor’s ATAC-Seq were correlated with the bulk ATAC-Seq references and assigned a cell type to each barcode

Mis-classification rate of both datasets calculated by progressively down sampling the libraries by measuring number of cell types changed from non-downsampled cell types.

Data obtained from competing technology has ~2X greater rate of misclassifying cells.

Our service advantages, workflow, and requirements

Diagenode service advantages:

Design your project with a leader in epigenomics profiling services.

End to end service from nuclei isolation optimization to bioinformatic analyses, including 3 reports.

Bio-Rad’s powerful technology:

Up to 95% cell capture for your precious samples
Allows analysis of 400-10,000 single cells, i.e. more than 30,000 cells/kit
Higher number of unique reads per cell
Obtain highly complex library dataset from both cultured and primary tissue samples
More biologically meaningful data at less sequencing compared to competitor
Better classification of cell types, true resolution of cell clusters

Wide offering for bioinformatic analyses: Standard analyses, advanced analyses, integrative analyses, data mining.

Documents

Full Diagenode products brochure BROCHURE Need to know more about our products? Download the brochure.	Download
Epigenomics Profiling Services FLYER Chromatin analysis DNA methylation services RNA-seq analysis	Download

Publications

How to properly cite this product in your work

Diagenode strongly recommends using this: Single-Cell ATAC-seq Services (Diagenode Cat# G02110000). Click here to copy to clipboard.

Using our products in your publication? Let us know!

Droplet-based combinatorial indexing for massive-scale single-cell chromatin accessibility
Caleb A. Lareau, Fabiana M. Duarte, Jennifer G. Chew, Vinay K. Kartha, Zach D. Burkett, Andrew S. Kohlway, Dmitry Pokholok, Martin J. Aryee, Frank J. Steemers, Ronald Lebofsky, and Jason D. Buenrostro
Recent technical advancements have facilitated the mapping of epigenomes at single-cell resolution; however, the throughput and quality of these methods have limited their widespread adoption. Here we describe a high-quality (105 nuclear fragments per cell) droplet-microfluidics-based method for single-cell pro...

>>> Click for Diagenode’s approach to COVID-19

Single-Cell ATAC-seq Services

Single cell sequencing provides you more in-depth insight of gene expression and gene regulation at individual cell resolution

ATAC-Seq identifies subpopulations

Chromatin accessibility more adept than mRNA expression levels at classifying cell types.

Workflow of our scATAC-seq solution

Bio-Rad’s Droplet Digital Technology

1.

2.

3.

4.

First PCR product fully adaptered

Performance data from a species mixing experiment of human and mouse cell lines.

Excellent cell utilization and enrichment

Highly complex libraries results in more biological meaningful data at less sequencing depth

Encyclopedia of DNA Elements (ENCODE)

Better classification of cell types with Bio-Rad’s ATAC-Seq than competing technology

PBMCs: Cell mis-classification

Diagenode service advantages:

How to properly cite this product in your work

Events

News

>>> Click for Diagenode’s approach to COVID-19

Single-Cell ATAC-seq Services

Single cell sequencing provides you more in-depth insight of gene expression and gene regulation at individual cell resolution

ATAC-Seq identifies subpopulations

Chromatin accessibility more adept than mRNA expression levels at classifying cell types.

Workflow of our scATAC-seq solution

Bio-Rad’s Droplet Digital Technology

1.

2.

3.

4.

First PCR product fully adaptered

Performance data from a species mixing experiment of human and mouse cell lines.

Excellent cell utilization and enrichment

Highly complex libraries results in more biological meaningful data at less sequencing depth

Encyclopedia of DNA Elements (ENCODE)

Better classification of cell types with Bio-Rad’s ATAC-Seq than competing technology

PBMCs: Cell mis-classification

Diagenode service advantages:

How to properly cite this product in your work

Bioinformatics Data Mining Service

ATAC-seq service (Assay for Transposase-Accessi...

Events

News