Dovetail™ Epigenetics Services
Dovetail™ Micro-C Library & Project Services
Description
Take advantage of having experienced Dovetail™ scientists produce Micro-C libraries for you in our lab. You provide the sample, Dovetail Genomics ships you the final library ready for you to sequence. Choose between a small or large library, or let us take your entire Micro-C project from sample to analysis-ready data.
The Dovetail Micro-C Kit offers the following key benefits:
- Sequence independent chromatin fragmentation enables even genome-wide detection of chromatin contacts (up to 20% of the genome lacks coverage using restriction enzyme based Hi-C approaches)
- Ultra-high nucleosome-level resolution of chromatin contacts
- Highest signal-to-noise data with both enrichment of long-range informative reads and nucleosome protected fragments
Dovetail™ Micro-C Libraries Are Enriched For Desirable Hi-C Properties
MNase enzyme possesses both sequence-independent endonuclease and exonuclease activities so generated fragments are nucleosome length (146 bp). The proximity ligation portion of the protocol is optimized to maximize long-range interactions. The resulting highly uniform, short fragments enable nucleosome-level resolution of chromatin contacts, a theoretical resolution maximum.
Improved calling of topological features
The ability to detect higher-order features, such as chromatin loops, in proximity ligation data is dependent on enriching long-range informative reads to capture chromatin interaction frequency. The increased chromosome conformation informative reads combined with ultra-high-resolution improves loop calling compared to RE-based methods.
Dovetail Micro-C uniquely captures nucleosome positioning
Chromatin digested with MNase reveals a genome-wide nucleosome map that is visible in the Dovetail Micro-C libraries. The map consists of sequence read peaks correlating to DNA that is protected by the nucleosome and troughs representing intervening DNA that is accessible to MNase digestion. This oscillation occurs at a frequency of ~146 bp (the length of DNA wrapped around a mono-nucleosome). This feature is unique to Micro-C data as it is absent from RE-based approaches. Dovetail Micro-C facilitates mapping nucleosome-to-nucleosome chromatin contacts.
Library Construction
SPECIFICATIONS |
OPTION 1 |
OPTION 2 |
Library Size: |
Large |
Small |
Sample Requirements: |
5 M cells (human, mouse, or rat) |
5 M cells (human, mouse, or rat) |
Sequence Read-Pairs (min): |
2 M |
2 M |
Delivery Time: |
6 weeks |
6 weeks |
Deliverables: |
QC report, Sufficient library material for up to 1200 M read-pairs |
QC report, Sufficient library material for up to 400 M read-pairs |
Sample-to-Sequence Project
SPECIFICATIONS |
OPTION 1 |
OPTION 2 |
Resolution: |
A/B compartments & TADs |
A/B compartments, TADs & Chromatin Loops |
Sample Requirements: |
5 M cells (human, mouse, or rat) |
5 M cells (human, mouse, or rat) |
Sequence Read-Pairs (min): |
330 M (30X coverage) |
990 M (90X coverage) |
Delivery Time: |
10 weeks |
10 weeks |
Deliverables: |
QC report, Sequence files, Contact matrix to 10 Kb resolution |
QC report, Sequence files, Contact matrix to 1 Kb resolution |
Dovetail™ HiChIP MNase Project Service
Description
Dovetail HiChIP combines ChIP-seq with Hi-C , a proximity ligation method that captures long-range interactions using standard Illumina paired-end sequencing. Let Dovetail™ scientists take on your HiCHIP project from sample to sequence data and contact matrices ready for downstream analysis and interpretation. For human cells only, choose from one of our three antibodies – CTCF, H3K4me3 and H3K27 – to map protein-directed chromatin conformation. You provide samples, Dovetail Genomics delivers sequence data (200M read-pairs per sample) and contact matrices ready for downstream analysis and interpretation.
The Dovetail HiChIP MNase Kit offers the following key benefits:
- Capture ChIP-seq and Hi-C data together in a single library
- Choose one of three chromatin related antibodies
- Map chromatin interactions at nucleosome level resolution
Map protein binding sites and long-range protein-directed interactions
The Dovetail HiChIP Kit enables study of protein-directed 3-D chromatin interactions. Akin to ChIP-seq, the Dovetail HiChIP data captures sequences directly bound by the protein of interest. However, additional long-range interactions mediated by the protein of interest are also captured. The use of MNase in the assay results in nucleosome resolution data.
Produce high-resolution contact maps with less sequencing
Enrichment of protein-directed chromatin features enables high-resolution contact map generation with less read depth. Compared to a high resolution restriction enzyme-based Hi-C, Dovetail HiChIP data enables visualization of higher-order chromatin features, such as loops and chromatin interactions, at a fraction of the read depth resulting in significant sequencing costs savings.
Project Specifications
Antibodies |
CTCF, H3K4me3, or H3K27ac |
Sample Requirements |
20 M cells (human only) |
Sequence Read-Pairs (min) |
200 M |
Delivery Time |
10 weeks |
Deliverables |
QC report, Sequence files, Contact matrix to 10 Kb resolution |