MD Anderson's core facilities are slowly returning to operations and will be at reduced capacity. Please contact core personnel for instructions prior to submitting a request and indicate if the sample is known to be COVID-19 positive.
(hide this warning on this page)The Epigenomics Profiling Core is funded jointly by the Center for Cancer Epigenetics and Department of Epigenetics and Molecular Carcinogenesis. The mission of Epigenomics Profiling core is to actively participate and contribute to the growing Epigenetics community at the University of Texas M.D. Anderson Cancer Center (UTMDACC) by providing services to analyze alterations to chromatin such as, DNA methylation and DNA-bound protein modifications (ChIP). The overall goal of this core is to facilitate researchers’ efforts to understand Epigenetic mechanisms that alter the chromatin state that regulate the transcription output in normal vs. disease conditions. This new core facility is an expansion of previously established DNA Methylation Core combined with now available High-throughput ChIP-Seq (HT ChIP-Seq) services. The core is located at the Basic Science Research Building of the MD Anderson Cancer Center and is fully equipped for molecular biology research.
DNA Methylation Analysis: Methylation that occur at specific sites of DNA is one of the earliest identified modifications to chromatin. DNA methylation is essential for normal development and is associated with a number of key processes, such as imprinting. DNA methylation, which is reversible if occurs at regulatory elements of the genome affects the transcription of neighboring genes. Thus, alterations in DNA methylation is one of the key components of Epigenetic modifications to chromatin. The core will provide investigators with access to global and gene-specific DNA methylation analysis. Services include: consultation with investigators to chose the best method of analysis; sample preparation, assay design and processing of the most used methods to study DNA methylation, both gene-specific and genome-wide (PyroMeth, RRBS and Methyl-Seq); and assessment of global DNA methylation by pyrosequencing methylation analysis of repetitive elements (LINE-1 and Alu repeats). Please contact Dr. Marcos Estecio to set up an appointment and primary consult for DNA methylation services.
Chromatin Immunoprecipitation (ChIP)-Seq: One of the major questions for researchers interested in understanding chromatin dynamics is to investigate how protein-DNA interactions alter Epigenetic profiles and subsequent gene expression. Chromatin immunoprecipitation (ChIP) is a technique to investigate protein-DNA interactions at a specific genomic-site. ChIP-Seq (ChIP followed by deep sequencing of DNA) is an extension of ChIP technology to determine the chromatin enrichment of a transcription factor on a genome-wide scale. In the past few years, ChIP-Seq has become a very useful technique to understand the chromatin states that regulate the transcription output. The overall goal of the core is to provide support to investigators interested in characterizing the interactions of post-translational modifications of histones (epigenetic marks that define a chromatin state or Epigenome) or transcription factors at specific genomic loci or genome-wide (Cistrome). This innovative platform provides ChIP services followed by library preparation in a cost effective high-throughput (HT) format from cell lines and tissues to assess the chromatin-enrichment of well-established histone marks or your protein of interest. The core has adapted a high-throughput method to perform multiple ChIPs (HT ChIP-seq) in a 96-well format, which not only saves time and costs but is doable with limited starting material and high reproducibility. The resource provides services including: processing of the samples (cells or tissues) to make high quality chromatin for ChIP, ChIP with a set of validated antibodies for histone marks (Promoter marks: H3K4me3 and H3K27me3, Enhancer marks: H3K4me1 and H3K27ac, Gene body marks for transcription activity: H3K36me3 and H3K79me2, and Heterochromatin mark: H3K9me3), ChIP with investigator preferred custom antibodies, and library preparation from ChIP DNA and multi-plexing for high-throughput DNA sequencing. These services are aimed to deliver high quality sequencing-ready libraries to map chromatin states (histone modifications), or profile binding of epigenetic modifiers (transcription co-regulators) or DNA binding proteins (transcription factors) on a genomic scale. Please contact Dr. Abhinav Jain to set up an appointment and primary consult for ChIP services.
DNA Methylation Services
Marcos Estecio, Ph.D., Co-Director
Associate Professor
mestecio@mdanderson.org
713-792-9108
Chromatin IP (ChIP-Seq) and ATAC-Seq Services
Abhinav Jain, Ph.D., Co-Director
Assistant Professor
ajain@mdanderson.org
713-834-6366
Hours | Location |
Monday - Friday 9 am - 5 pm |
6767 Bertner Ave BSRB, S9.8414 Houston, TX 77030 |
MDACC Epigenomics Profiling Core (EpiCore)
Name | Role | Phone | Location | |
---|---|---|---|---|
Marcos Estecio |
Co-director, DNA Methylation Analysis
|
713-792-9108
|
mestecio@mdanderson.org
|
S9.8136b
|
Abhinav Jain |
Co-director, Chromatin IP (ChIP-Seq) and ATAC-Seq Services
|
713-834-6366
|
ajain@mdanderson.org
|
S9.8136b
|
Kimie Kondo |
Research Investigator
|
832-751-9840
|
kkondo@mdanderson.org
|
S9.8414 (EpiCore lab)
|
Baozhen Ke |
Research Investigator
|
832-751-9840
|
bke@mdanderson.org
|
S9.8414 (EpiCore lab)
|
Service list |
► DNA Methylation Services (7) | |||
Name | Description | Price | |
---|---|---|---|
Bisulfite Treatment |
Conversion of DNA with NaHSO3 prior to methylation analysis |
Inquire | |
cfMeDIP-Seq library preparation |
Capture of methylated DNA and preparation of Illumina-captible libraries from small amounts of DNA samples, including FFPE and cell-free DNA samples. |
Inquire | |
Fragmentation of genomic DNA |
Fragmentation of genomic DNA in Covaris ultrasonicator |
Inquire | |
PMA Assay Design and Optimization |
Oligo design and optimization of PCR conditions |
Inquire | |
Pyrosequencing Methylation Analysis (PMA) |
PCR and pyrosequencing run |
Inquire | |
RRBS Library Preparation | Inquire | ||
WGBS Library Preparation |
Library preparation for whole-genome analysis of DNA methylation |
Inquire | |
► Chromatin Immunoprecipitation Services in High Throughput (HT-ChIP) (9) | |||
Name | Description | Price | |
Sample preparation: Chromatin preparation from cells |
Chromatin preparation and shearing from single frozen pellet of cells cross-linked with formaldehyde. |
Inquire | |
Sample preparation: Chromatin prepration from tissues |
Farmaldehyde crosslinking followed by chromatin preparation and shearing from single sample of frozen tissue. |
Inquire | |
ChIP: Chromatin Immunoprecipitation with Core antibodies |
Antibodies available at the core for histones (H3K4me1, H3K4me3, H4K9me3, H3K27me3, H3K27ac, H3K36me3, H3K79me2 and H3) and non-histone controls (IgG and CTCF) |
Inquire | |
ChIP: Chromatin Immunoprecipitation (tissues) with Core antibodies |
Antibodies available at the core for histones (H3K4me1, H3K4me3, H4K9me3, H3K27me3, H3K27ac, H3K36me3, H3K79me2 and H3) and non-histone controls (IgG and CTCF) |
Inquire | |
ChIP: Chromatin Immunoprecipitation for custom antibodies from cells. |
Cost per lane = 8 ChIPs Note: Antibodies provided by customer. |
Inquire | |
ChIP: Chromatin Immunoprecipitation for custom antibodies from tissue. |
Cost per lane = 8 ChIPs Note: Antibodies provided by customer. |
Inquire | |
QC on ChIP DNA from cells or tissues |
Cost per lane = 8 ChIPs |
Inquire | |
ChIP library preparation and QC |
Cost per lane = 8 ChIPs |
Inquire | |
Drosophila Spike-in |
Internal
$13.62
each
External in network $13.62 each |
||
► ATAC-Seq (6) | |||
Name | Description | Price | |
Tissue processing and nuclei isolation |
Prepare, harvest and count nuclei from frozen tissue for processing for ATAC-Seq |
Internal
$74.94
each
External in network $74.94 each External out of network $121.40 each UT-System $74.94 each User Group $0.00 each Texas Institutions $0.00 each |
|
Cell counting and collection |
EpiCore will harvest and count the cells required for ATAC-Seq protocol |
Internal
$20.87
each
External in network $20.87 each External out of network $33.80 each Non-academic $0.00 each UT-System $20.87 each |
|
ATAC-Seq module reagents |
Cost of reagent/sample for transposition reaction |
Inquire | |
ATAC-Seq module labor |
These are the labor costs for processing upto 6 samples |
Inquire | |
Library QC by TapeStation |
These costs are for library fragment analysis of upto 15 samples by Agilent TapeStation4200 |
Inquire | |
Library QC by qPCR |
QC of ATAC-seq library by qPCR (upto 6 samples) |
Inquire | |
► Bioanalyzer (2) | |||
Name | Description | Price | |
Fragment analysis in 2100 Bioanalyzer Instrument |
per Chip |
Inquire | |
Fragment QC by TapeStation | Inquire | ||
► Recombinant Antibody Service (1) | |||
Name | Description | Price | |
Recombinant Antibody Project Charge |
This service is currently only available internally to M.D. Anderson researchers. |
Inquire | |
► Special reagents and consumables (1) | |||
Name | Description | Price | |
Custom oligos |
These costs include the design and the cost of oligoes for this project. |
Inquire |