Epigenomics Core

Overview

The Epigenomics Shared Facility (ESF) is a part of Einstein’s Center for Epigenomics and an Illumina CSPro (certified service provider) laboratory. The high-throughput molecular technological resources in the ESF include massively parallel sequencing (MPS) platforms: the Oxford Nanopore MinION,  Illumina NEXTSeq500, Illumina HiSeq2500 and Illumina MiSeq; supported by TECAN freedom Evo® 200 Robotics.  The core facility space is dedicated and customized, with MPS library preparation performed in a positive-pressure room isolated from the post prep and sequencing room. The MPS machines are connected by high-bandwidth networking to dedicated computing equipment located in a server room.

Sample submission is coordinated through a laboratory information management system (LIMS) component of the WASP (an integrated LIMS and batch processing system). WASP allow users for electronic submission of their samples, real-time follow-up of the pipeline and access to the data once available. The facility has a turnaround of 2 to 3 weeks per library/job/project. The data is backed-up and available for at least 6 months on the WASP server from the Albert Einstein College of Medicine.

The ESF supports diverse assays for MPS analysis and strives to bring cutting-edge technologies to benefit the programs of Einstein researchers. Recently, with the current COVID-19 pandemic, ESF is ready to facilitate and support your research into the SARS-CoV-2 and the search for effective diagnostics and therapies to cure COVID-19. Please check Epigenomics Shared Facility -COVID-19 for details.

Services

Support for diverse assays to study the epigenome include:

1. The ESF is now providing support and services for long read sequencing utilizing Oxford Nanopore’s MinION platform. 
• Direct RNA sequencing: transcriptome and epitranscriptome (RNA modifications) analysis using the MinION platform.
• Direct cDNA Sequencing (For Low Input samples)
• Genomic DNA sequencing (Ultra-long reads - up to 2 Mb)
• Amplicons sequencing
• Single-cell RNA sequencing combining 10x Chromium  and  Nanopore technology for longer reads.
2. Support for diverse assays for short read sequencing to study the epigenome include:
• Epigenomic profiling of open chromatin (ATAC-Seq)
• Chromatin profiling assays
• Cleavage Under Targets and Release using Nuclease (CUT&RUN-Seq)
• Chromatin immunoprecipitation assays
• Massively-parallel sequencing-based (ChIP-Seq)
• Methylated DNA immunoprecipitation sequencing (MeDIP/hMeDIP-Seq)
• Genome-wide Cytosine methylation assay- (5-mC)
• Massively-parallel sequencing-based HELP-Tagging
• Whole genome Bisulphite sequencing (MethylC-Seq-WGSBS)
• Enzymatic Methyl-seq (EM-Seq)
• Reduced Representation Bisulfite Sequencing (ERRBS-Seq)
• Targeted bisulfite sequencing (SeqCap Epi -Roche - Human/Mouse)
• Genome-wide hydroxymethylation analysis (5-hmC)
• Massively-parallel sequencing-based (HELP-GT)
• Oxidative bisulfite sequencing (oxBS-Seq)
• Directional RNA-Seq, Targeted RNA-Seq, miRNA-Seq
• Ultra-Low RNA-Seq
• Single Cell DNA/RNA-Seq
• Single Cell ATAC-Seq
• Exome Capture Enrichment Sequencing (Human/Mouse) and Targeted Resequencing
• Whole-genome de novo or Resequencing and Amplicon-Resequencing 
3. Support for AlloSeq Tx17 (HLA genotyping):
• The ESF is now providing support and services for rapid high-throughput human leukocyte antigen (HLA) typing using innovative hybrid capture and massively Parallel sequencing-Please enquire.

The services include library preparation and sequencing plus Data Storage, primary data return, analysis and visualization through WASP. DNA/RNA isolation services are also provided through Molecular Cytogenetic Facility. We are available on Science Exchange as well as on iLab. 

Secondary analysis is also provided on request through our Computational and Statistical Genomics/Epigenomics Groups. Pricing information is also available through WASP. 

Fees

Please visit our available assays page for pricing or contact the core director.

Location

Price Center Room 159

Personnel

Faculty Advisor
John Greally, M.B., PhD
718.678.1234
john.greally@einsteinmed.org 

Director
Shahina Maqbool, Ph.D.
718.678.1163
shahina.maqbool@einsteinmed.org 

Selected Publications

• Li W, Zimmerman SE, Peregrina K, Houston M, Mayoral J, Zhang J, Maqbool S, Zhang Z, Cai Y, Ye K, Augenlicht LH. The nutritional environment determines which and how intestinal stem cells contribute to homeostasis and tumorigenesis. Carcinogenesis 40(8):937-946 (2019).
• Bowler TG, Pradhan K, Kong Y, Bartenstein M, Morrone KA, Sridharan A, Kessel RM, Shastri A, Giricz O, Bhagat TD, Gordon-Mitchell S, Rohanizadegan M, Hooda L, Datt I, Przychodzen BP, Parmar S, Maqbool S, Maciejewski JP, Steidl U, Greally JM, Verma A. Misidentification of MLL3 and other mutations in cancer due to highly homologous genomic regions. Leuk Lymphoma, 60(13):3132-3137 (2019). 
• Barris DM, Weiner SB, Dubin RA, Fremed M, Zhang X, Piperdi S, Zhang W, Maqbool S, Gill J, Roth M, Hoang B, Geller D, Gorlick R, Weiser DA. Detection of circulating tumor DNA in patients with osteosarcoma. Oncotarget, 9(16):12695-12704 (2018). 
• Kong Y, Berko ER, Marckette A, Maqbool SB, Simões-Pires CA, Kronn DF, Ye QK, Suzuki M, Auton A, Greally JM: Detecting, quantifying and discriminating the mechanism of mosaic chromosomal aneuploidies using MADseq. Genome Res, 28(7):1039–1052 (2018). 
• Wijetunga NA, Johnston AD, Maekawa R, Delahaye F et al. SMITE: an R/Bioconductor package that identifies network modules by integrating genomic and epigenomic information. BMC Bioinformatics, 18(1):41 (2017). 
• Ulahannan N, Suzuki M, Simoes-Pires CA, Wicik Z, Wijetunga NA, Croken MM, Bhattacharyya S, Johnston AD, Kong Y, Maqbool SB, Verma A, Greally JM: Intragenomic redistribution of host transcription factor binding with Toxoplasma gondii infection. bioRxiv 132076; doi: https://doi.org/10.1101/132076 (2017). 
• Kong Y, Berko ER, Marckette A, Maqbool SB, Simões-Pires CA, Kronn DF, Ye QK, Suzuki M, Auton A, Greally JM: Detecting, quantifying and discriminating the mechanism of mosaic chromosomal aneuploidies using MADseq. Genome, 226282 (2017). 
• Carvallo L, Lopez L, Fajardo JE, ry-Bravo MJ, Fiser A, Berman JW: HIV-Tat regulates macrophage gene expression in the context of neuroAIDS. PLoSONE 12(6): e0179882. (2017). 
• Cai Y, Nogales-Cadenas R, Zhang Q, Lin JR, Zhang W, Brien KO, Montagna C, Zhang ZD: Transcriptomic dynamics of breast cancer progression in the MMTV-PyMT mouse model. BMC Genomics, 18:185 (2017). 
• Barnicle A, Seoighe C, Golden A, Greally JM, Egan LJ: Differential DNA methylation patterns of homeobox genes in proximal and distal colon epithelial cells. Epigenetics and Epigenomics. 48(4): 257-273 (2016). 
• van Esterik JCJ, Vitins AP, Hodemaekers HM, Kamstra JH, Legler J, Pennings JLA, Steegenga WT, Lute C, Jelinek J, Issa JPJ, Dollé ME, van der Ven LTM: Liver DNA methylation analysis in adult female C57BL/6JxFVB mice following perinatal exposure to bisphenol A. Toxicology Letters, 232(1):293-300 (2015). 
• Ulahannan N, Greally JM: Genome-wide assays that identify and quantify modified cytosines in human disease studies. Epigenetics & Chromatin, 8:5 (2015). 
• Tufariello JM, Kerantzas CA, Vilchèze C, Calder RB, Nordberg EK, Fischer JA, Hartman TE, Yang E, Driscoll T, Cole LE, Sebra R, Maqbool SB, Wattam AR, Jacobs Jr WR: The Complete Genome Sequence of the Emerging Pathogen Mycobacterium haemophilum Explains Its Unique Culture Requirements. MBio.6(6). pii: e01313-15. PMID 26578674 (2015). 
• Ramos MP, Wijetunga NA, McLellan AS, Suzuki M, Greally JM: DNA demethylation by 5-aza-2′-deoxycytidine is imprinted, targeted to euchromatin, and has limited transcriptional consequences. Epigenetics & Chromatin, 8:11 (2015). 
• Parmalee NL, Maqbool SB, Ye B, Calder B, Bowman AB, Aschner M: RNASeq in C. elegans following manganese exposure. Current protocols in toxicology / editorial board, Mahin D Maines (editor-in-chief. [et al].65:11.20.1-11.20.17 (2015). 
• Nadel J, Athanasiadou R, Lemetre C, Wijetunga NA, Broin PO, Sato H, Zhang ZD, Jeddeloh J, Montagna C, Golden A, Seoighe C, Greally JM: RNA:DNA hybrids in the human genome have distinctive nucleotide characteristics, chromatin composition, and transcriptional relationships. Epigenetics Chromatin, 8:46 (2015).