Learn About the Epigenomics Shared Facility
Learn About the Epigenomics Shared Facility
On Thursday, January 27, 2022, at noon, learn how Einstein’s Epigenomics Shared Facility can aid your research during the bimonthly Pathways to Success at Einstein Cores seminar series, accessible via Zoom. Core director Shahina Maqbool, Ph.D., will provide an overview of the resources and services of the facility, then Amit Verma, M.B.B.S., and Ulrich Steidl, M.D., Ph.D., will share how the core has enhanced their respective research efforts.
About the Epigenomics Shared Facility (ESF)
The ESF provides support for a wide array of cutting-edge genomic and epigenomic massively parallel sequencing (MPS) assays. The dedicated core facility space offers an isolated positive-pressure sample preparation room as well as several high-throughput molecular technological resources, including the Oxford Nanopore MinION and multiple Illumina services. The ESF also provides a number of services in support of SARS-CoV-2 research to address the ongoing COVID-19 global pandemic.
Long read sequencing (Oxford Nanopore 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 2Mb)
- Amplicons sequencing
- Single-cell RNA sequencing combining 10x Chromium and Nanopore technology for longer reads
Short read sequencing
- 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 (Roche SeqCap Epi – human/mouse)
- Genome-wide hydroxymethylation analysis (5-hmC)
- Massively-parallel sequencing-based (HELP-GT)
- Oxidative bisulfite sequencing (oxBS-Seq)
- RNA sequencing assays
- Directional RNA-Seq
- Targeted RNA-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
HLA Genotyping (AlloSeq Tx17)
- Rapid high-throughput human leukocyte antigen (HLA) typing
It’s Been Said
“The Epigenomics Shared Facility is a part of Einstein’s Center for Epigenomics and an Illumina certified service provider laboratory. The ESF was established in 2008; it became the center’s core facility and has evolved to offer all assays based on massively-parallel sequencing. These assays are not only those that overtly study the epigenome but also include those studying different types of transcription, such as directional RNA-seq and small RNA-seq, and re-sequencing looking for DNA variants that includes whole genome sequencing and exome-seq. Our core personnel have deep experience in a wide range of sequencing-based assays.”
John Greally, M.B., Ph.D.
“The Epigenomics Shared Facility supports diverse assays for massively parallel sequencing analysis and strives to bring cutting-edge technologies to benefit the programs of Einstein researchers. Quality control and assurance is a critical component of the functions of our facility. The services include library preparation and sequencing, plus data storage, primary data return, and analysis and visualization through WASP.”
Shahina Maqbool, Ph.D.
Research Associate Professor, Genetics
“The ESF core does an outstanding job in getting us quality RNA-seq at very rapid turnaround to enable us to finish manuscripts in time. The addition of the long read nanopore sequencer will enable Einstein investigators to conduct studies on RNA modification [and] splicing using the latest tools.”
Amit Verma, M.B.B.S.
Professor, Medicine (Oncology)
Director of the Division of Hemato-Oncology, Montefiore Department of Oncology
“The ESF generated quality data for us with a really fast turnaround - it really helped propel our project forward."
Ulrich Steidl, M.D., Ph.D.
Professor, Cell Biology; Medicine
Posted on: Monday, January 24, 2022