About
EpiCore Workflow
After initial discussions with the core directors to identify project needs and sample requirements, the investigator submits the samples to EpiCore. To ensure high-quality results, the core conducts thorough sample quality checks before proceeding with the requested assay. Once the samples pass the quality assessment, EpiCore processes them for the specified assay. If the project involves sequencing, EpiCore coordinates with the investigators to transfer sequencing-ready libraries to their preferred Next Generation Sequencing (NGS) core facility. The NGS core facility then sends the data to the investigator or a suggested bioinformatician for analysis. EpiCore directors are available, upon request, to assist investigators in interpreting the data, providing valuable insights, and offering guidance throughout the process. They are often included as co-authors in manuscripts.
We are committed to ensuring the success of your epigenetic studies by not only providing fee-based assays but also engaging in project-specific collaborations to support manuscripts and grant proposals. Please feel free to contact us for any further inquiries.
DNA Methylation Analysis Services
DNA methylation is essential for normal development and modulates key regulatory processes, such as transcription, genomic imprinting, and X-chromosome inactivation. In cancer, abnormal DNA methylation can result in inactivation of tumor suppressor genes and potentiate chromosome instability. Furthermore, DNA methylation patterns are tissue-type and tumor-type specific, and such characteristic has been exploited for molecular classification of cancer and early detection in circulating cell-free DNA. The MDACC Epigenomics Profiling Core (EpiCore) provides investigators access to both global and gene-specific DNA methylation analysis through a wide array of methods.
Our services include:
- Consultation with investigators to select the best method of analysis for their research
- Single-locus assay design and optimization for Pyrosequencing-Methylation Analysis (PMA)
- Assessment of global DNA methylation by pyrosequencing for analysis of repetitive elements (LINE-1 and Alu repeats)
- Genome-wide methods to study DNA methylation (RRBS and MeDIP-Seq)
- Whole-genome study of DNA methylation
The choice of an appropriate DNA methylation analysis method depends on whether the investigation is still in the discovery stage or whether a set of targets has already been selected. Further, special considerations regarding assay design and detection methods must be addressed when dealing with minimal amounts of DNA or when applying DNA methylation as a molecular marker. The EpiCore will work with investigators to design assays and conduct experiments. To arrange a consultation, please contact Marcos Estécio, Ph.D., at mestecio@mdanderson.org.
Chromatin Analysis by Chromatin Immunoprecipitation (ChIP), CUT&RUN and ATAC-Seq
One of the major questions for researchers interested in understanding chromatin dynamics is how protein-DNA interactions and chromatin states alter the epigenetic landscape. Many features that control chromatin structure play a critical role in regulating gene expression. Thus, genome-wide mapping of TFs, chromatin-associated proteins and chromatin states, including histone post-translational modifications (PTMs), have become a major focus of research. The EpiCore offers a range of assays to accurately identify and examine alterations in chromatin:
Chromatin Immunoprecipitation (ChIP) Services
The Epicore offers Chromatin Immunoprecipitation followed by high-throughput sequencing (ChIP-Seq) to determine regions enriched for chromatin-bound proteins across the genome. Our full-service protocols encompass everything starting from cells or tissues to prepare chromatin, conduct protein-bound DNA pull-down, and generating ChIP DNA libraries ready for Next Generation Sequencing (NGS). Furthermore, we provide the capability to detect enrichment of a protein of interest at a specific genomic locus through ChIP-qPCR. Our services cover a wide range of ChIP offerings, and detailed information can be found on our services page, including specific sample requirements tailored to your project and assay needs.
CUT&RUN Services
The EpiCore has introduced the cutting-edge CUT&RUN assay, a revolutionary method for profiling protein-DNA interactions across the genome using small sample quantities. Unlike traditional approaches, CUT&RUN substantially reduces the number of final sequencing reads required. Our CUT&RUN services encompass the entire process, from start to finish, which involves performing the CUT&RUN reaction, including efficient pull-down of protein-bound DNA and library preparation suitable for NGS. For more information about our comprehensive CUT&RUN services and the specific sample requirements, please visit our services page.
ATAC-Seq Services
ATAC-seq (Assay for Transposase Accessible Chromatin with high-throughput sequencing) is widely used to map chromatin accessibility, transcription factor binding and nucleosome positioning across the genome. Our full-service ATAC-seq protocol begins with harvesting nuclei from cells and tissues, followed by the transposition step to prepare open chromatin. Subsequently, we perform library preparation to profile chromatin accessibility accurately. The resulting libraries are then submitted to the NGS core for sequencing, ensuring comprehensive and high-quality data generation. For more detailed information about our ATAC-seq services and specific sample requirements, please visit the services page.
To schedule an appointment, primary consultation, and inquire about project-specific sample requirements for ChIP-Seq, ChIP-qPCR, CUT&RUN, and ATAC-seq services, please reach out to Dr. Abhinav Jain at ajain@mdanderson.org. Dr. Abhinav Jain and the team look forward to assisting you with your chromatin dynamics and epigenetic studies.
For any additional scheduling needs, you can also utilize the iLab platform.