Albert Einstein College of Medicine

Contact Info:

Dr. Shahina Maqbool

1301 Morris Park Ave

Bronx, NY 10461

https://www.einsteinmed.edu/research/shared-facilities/cores/53/epigenomics/

Grants and Identifiers:

RRID: RRID:SCR_023284

Instrumentation:

Services Provided:

10x Genomics

AlloSeq Tx17 (HLA Genotyping)

ATAC-Seq

CDNA Synthesis

ChIP-Seq

CITE-seq

Computational - Bioinformatics

CUT&RUN-Seq

CUT&Tag-R-Loop-Seq

CUT&Tag-Seq

DNA Analysis

DNA Isolation

EM-Seq (Enzymatic Methyl-seq)

Genomics

Long Read Sequencing Utilizing Oxford Nanopore’s MinION Platform

Metabolomics

Metagenomics Analysis

Methylation Analysis

Ribosomal Reduction

RNA analysis

RNA Integrity

RNA Isolation

RNA Modification Analysis

RNAseq

Single-Cell Analysis

Single-cell Sequencing

Small/miRNA-Seq

Targeted RNA-Seq

Targeted-Seq

Ultra-Low RNA-Seq

WEM-Seq (whole Exome Sequencing)

Relevant Publications:

1.) Luchtel RA, Zhao Y, Aggarwal RK, Pradhan K, Maqbool SB (2022 Oct 25). ETS1 is a novel transcriptional regulator of adult T-cell leukemia/lymphoma of North American descent. Blood advances, 6(20), 5613-5624. . ID: 35675522.

2.) Ulahannan N, Cutler R, Doña-Termine R, Simões-Pires CA, Wijetunga NA, Croken MM, Johnston AD, Kong Y, Maqbool SB, Suzuki M, Greally JM (2022). Genomic insights into host and parasite interactions during intracellular infection by Toxoplasma gondii. PloS one, 17(9), e0275226. . ID: 36178892.

3.) Rahmani NE, Ramachandra N, Sahu S, Gitego N, Lopez A, Pradhan K, Bhagat TD, Gordon-Mitchell S, Pena BR, Kazemi M, Rao K, Giricz O, Maqbool SB, Olea R, Zhao Y, Zhang J, Dolatshad H, Tittrea V, Tatwavedi D, Singh S, Lee J, Sun T, Steidl U, Shastri A, Inoue D, Abdel-Wahab O, Pellagatti A, Gavathiotis E, Boultwood J, Verma A (2021 Sep 21). ASXL1 mutations are associated with distinct epigenomic alterations that lead to sensitivity to venetoclax and azacytidine. Blood cancer journal, 11(9), 157. . ID: 34548471.

4.) Johnston AD, Abdulrazak A, Sato H, Maqbool SB, Suzuki M, Greally JM, Simões-Pires CA (2020 Jun). A Cellular Stress Response Induced by the CRISPR-dCas9 Activation System Is Not Heritable Through Cell Divisions. The CRISPR journal, 3(3), 188-197. doi: 10.1089/crispr.2019.0077. ID: 33560917.

5.) Kong Y, Berko ER, Marcketta A, Maqbool SB, Simões-Pires CA, Kronn DF, Ye KQ, Suzuki M, Auton A, Greally JM (2018 Jul). Detecting, quantifying, and discriminating the mechanism of mosaic chromosomal aneuploidies using MAD-seq. Genome research, 28(7), 1039-1052. . ID: 29773658.

6.) 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 WR Jr (2015 Nov 17). The Complete Genome Sequence of the Emerging Pathogen Mycobacterium haemophilum Explains Its Unique Culture Requirements. mBio, 6(6), e01313-15. . ID: 26578674.

7.) Parmalee NL, Maqbool SB, Ye B, Calder B, Bowman AB, Aschner M (2015 Aug 6). RNASeq in C. elegans Following Manganese Exposure. Current protocols in toxicology, 65(), 11.20.1-11.20.17. . ID: 26250396.

8.) Berko ER, Suzuki M, Beren F, Lemetre C, Alaimo CM, Calder RB, Ballaban-Gil K, Gounder B, Kampf K, Kirschen J, Maqbool SB, Momin Z, Reynolds DM, Russo N, Shulman L, Stasiek E, Tozour J, Valicenti-McDermott M, Wang S, Abrahams BS, Hargitai J, Inbar D, Zhang Z, Buxbaum JD, Molholm S, Foxe JJ, Marion RW, Auton A, Greally JM (2014). Mosaic epigenetic dysregulation of ectodermal cells in autism spectrum disorder. PLoS genetics, 10(5), e1004402. . ID: 24875834.

9.) Gundry M, Li W, Maqbool SB, Vijg J (2012 Mar). Direct, genome-wide assessment of DNA mutations in single cells. Nucleic acids research, 40(5), 2032-40. . ID: 22086961.

10.) McLellan AS, Dubin RA, Jing Q, Maqbool SB, Olea R, Westby G, Broin PÓ, Fazzari MJ, Zheng D, Suzuki M, Greally JM (2009 Oct). The Einstein Center for Epigenomics: studying the role of epigenomic dysregulation in human disease. Epigenomics, 1(1), 33-8. doi: 10.2217/epi.09.9. ID: 22122636.

Description:

The Epigenomics Shared Facility (ESF), part of Einstein’s Center for Epigenomics and an Illumina CSPro (certified service provider) laboratory, offers massively-parallel sequencing (MPS) including fully-automated library preparation, quality control and assurance, and a number of assays to study the genome/epigenome. Data analytical services are provided by the Computational Genomics Facility. The ESF supports diverse assays for MPS analysis and strive to bring cutting-edge technologies. 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. Secondary analysis is also provided on request through our Computational and Statistical Genomics/Epigenomics Groups. Services include: • Directional RNA-Seq, Targeted RNA-Seq, miRNA-Seq • Ultra-Low RNA-Seq • Exome Capture Enrichment Sequencing (Human/Mouse) and Targeted Resequencing • Whole-genome de novo or Resequencing and Amplicon-Resequencing • Epigenomic profiling of open chromatin (ATAC-Seq) • Cleavage Under Targets and Release using Nuclease (CUT&RUN-Seq) • Enzymatic Methyl-seq (EM-Seq) long read sequencing utilizing Oxford Nanopore’s MinION platform.