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 |
|
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 | |
► Chromatin Immunoprecipitation (17) | |||
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 | |
Histone-PTM antibody ChIPs |
These are the cost of antibodies available at the core/sample |
Inquire | |
Reagents for Histone ChIPs |
These are reagent cost per histone ChIP |
Inquire | |
Labor for Histone ChIPs (1-8 ChIPs) |
These are the labor costs for processing each histone ChIPs when total number of ChIPs is less than 8. |
Inquire | |
Labor for Histone ChIPs (>8 ChIPs) |
These are the labor costs for processing each histone ChIP when total number of ChIPs is more than 8. |
Inquire | |
Reagent to prepare Inputs |
These are reagent cost to make each Input |
Inquire | |
Labor to prepare Inputs (1-4 samples) |
These are the labor costs for preparing upto 4 Inputs from chromatin of cell pellets or frozen tissues |
Inquire | |
Negative control antibody ChIP |
IgG antibody will be used as negative control for non-histone ChIPs, as requested |
Inquire | |
Positive control antibody ChIP |
CTCF antibody will be used as positive control for non-histone ChIPs, as requested |
Inquire | |
Reagent for Custom (non-histone) ChIPs |
These are reagenet cost per non-histone custom ChIP |
Inquire | |
Labor for custom (non-Histone) ChIPs (1-8 ChIPs) |
These are the labor costs for processing each non-histone ChIPs when total number of ChIPs is less than 8. |
Inquire | |
Labor for custom (non-Histone) ChIPs (>8 ChIPs) |
These are the labor costs for processing each non-histone ChIP when total number of ChIPs is more than 8. |
Inquire | |
QC on ChIP DNA by qPCR |
Costs for running qPCR after histone or custom ChIPs from cell lines or tissues. |
Inquire | |
Library preparation from ChIP DNA |
Cost for preparing NGS ready library from each histone or custom ChIP DNA from cell lines or tissues. |
Inquire | |
QC on Library DNA by qPCR |
Costs for running qPCR after histone or custom ChIP DNA libraries. |
Inquire | |
Library Pooling |
These costs cover poling upto 8 libraries followed by QC (quantitation and fragment analysis) and delivery. |
Inquire | |
► Fragment Analysis (2) | |||
Name | Description | Price | |
Fragment Analysis by Agilent TapeStation 4200 | Inquire | ||
Fragment analysis in 2100 Bioanalyzer Instrument |
per Chip |
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 |