Lunenfeld-Tanenbaum Research Institute

Contact Info:

Kin Chan

600 University Avenue

Mount Sinai Hospital, Sinai Health

Toronto, ON M5G 1X5

https://nbcc.lunenfeld.ca

Grants and Identifiers:

RRID: RRID:SCR_025385

Instrumentation:

Services Provided:

10x Genomics

ATAC-Seq

ChIP-Seq

CRISPR

Genomics

Long Read Amplicon Sequencing

Long Read Sequencing

Metatranscriptomics

RNAseq

SARS-CoV-2 Strain Sequencing

Sequencing - DNA Sequencing

Sequencing - Next Generation Sequencing (NGS)

Single-cell Sequencing

Spatial Transcriptomics

Targeted Amplicon Sequencing

Whole Exome Sequencing

Whole Genome Sequencing

Relevant Publications:

1.) Cho T, Hoeg L, Setiaputra D, Durocher D (2024 Apr 17). NFATC2IP is a mediator of SUMO-dependent genome integrity. Genes & development, 38(5), 233-252. . ID: 38503515.

2.) Lü Y, Cho T, Mukherjee S, Suarez CF, Gonzalez-Foutel NS, Malik A, Martinez S, Dervovic D, Oh RH, Langille E, Al-Zahrani KN, Hoeg L, Lin ZY, Tsai R, Mbamalu G, Rotter V, Ashton-Prolla P, Moffat J, Chemes LB, Gingras AC, Oren M, Durocher D, Schramek D (2024 Apr 5). Genome-wide CRISPR screens identify novel regulators of wild-type and mutant p53 stability. Molecular systems biology, (), . doi: 10.1038/s44320-024-00032-x. ID: 38580884.

3.) Yang A, Chidiac R, Russo E, Steenland H, Pauli Q, Bonin R, Blazer LL, Adams JJ, Sidhu SS, Goeva A, Salahpour A, Angers S (2024 Mar 1). Exploiting spatiotemporal regulation of FZD5 during neural patterning for efficient ventral midbrain specification. Development (Cambridge, England), 151(5), . . ID: 38358799.

4.) O (2023 Dec 21). FBXW7-loss Sensitizes Cells to ATR Inhibition Through Induced Mitotic Catastrophe. Cancer research communications, 3(12), 2596-2607. . ID: 38032106.

5.) Collignon E, Cho B, Furlan G, Fothergill-Robinson J, Martin SB, McClymont SA, Ross RL, Limbach PA, Ramalho-Santos M (2023 Sep). m(6)A RNA methylation orchestrates transcriptional dormancy during paused pluripotency. Nature cell biology, 25(9), 1279-1289. doi: 10.1038/s41556-023-01212-x. ID: 37696947.

6.) Zhao Y, Tabet D, Rubio Contreras D, Lao L, Kousholt AN, Weile J, Melo H, Hoeg L, Feng S, Coté AG, Lin ZY, Setiaputra D, Jonkers J, Gingras AC, Gómez Herreros F, Roth FP, Durocher D (2023 Aug 3). Genome-scale mapping of DNA damage suppressors through phenotypic CRISPR-Cas9 screens. Molecular cell, 83(15), 2792-2809.e9. . ID: 37478847.

7.) Dervovic D, Malik AA, Chen ELY, Narimatsu M, Adler N, Afiuni-Zadeh S, Krenbek D, Martinez S, Tsai R, Boucher J, Berman JM, Teng K, Ayyaz A, Lü Y, Mbamalu G, Loganathan SK, Lee J, Zhang L, Guidos C, Wrana J, Valipour A, Roux PP, Reimand J, Jackson HW, Schramek D (2023 May 31). In vivo CRISPR screens reveal Serpinb9 and Adam2 as regulators of immune therapy response in lung cancer. Nature communications, 14(1), 3150. . ID: 37258521.

8.) Kim YK, Cho B, Cook DP, Trcka D, Wrana JL, Ramalho-Santos M (2023 Jan 31). Absolute scaling of single-cell transcriptomes identifies pervasive hypertranscription in adult stem and progenitor cells. Cell reports, 42(1), 111978. doi: 10.1016/j.celrep.2022.111978. ID: 36640358.

9.) Yan Y, Gauthier MA, Malik A, Fotiadou I, Ostrovski M, Dervovic D, Ghadban L, Tsai R, Gish G, Loganathan SK, Schramek D (2023 Jan 25). The NOTCH-RIPK4-IRF6-ELOVL4 Axis Suppresses Squamous Cell Carcinoma. Cancers, 15(3), . . ID: 36765696.

10.) Langille E, Al-Zahrani KN, Ma Z, Liang M, Uuskula-Reimand L, Espin R, Teng K, Malik A, Bergholtz H, Ghamrasni SE, Afiuni-Zadeh S, Tsai R, Alvi S, Elia A, Lü Y, Oh RH, Kozma KJ, Trcka D, Narimatsu M, Liu JC, Nguyen T, Barutcu S, Loganathan SK, Bremner R, Bader GD, Egan SE, Cescon DW, Sørlie T, Wrana JL, Jackson HW, Wilson MD, Witkiewicz AK, Knudsen ES, Pujana MA, Wahl GM, Schramek D (2022 Dec 2). Loss of Epigenetic Regulation Disrupts Lineage Integrity, Induces Aberrant Alveogenesis, and Promotes Breast Cancer. Cancer discovery, 12(12), 2930-2953. . ID: 36108220.

11.) Yanchus C, Drucker KL, Kollmeyer TM, Tsai R, Winick-Ng W, Liang M, Malik A, Pawling J, De Lorenzo SB, Ali A, Decker PA, Kosel ML, Panda A, Al-Zahrani KN, Jiang L, Browning JWL, Lowden C, Geuenich M, Hernandez JJ, Gosio JT, Ahmed M, Loganathan SK, Berman J, Trcka D, Michealraj KA, Fortin J, Carson B, Hollingsworth EW, Jacinto S, Mazrooei P, Zhou L, Elia A, Lupien M, He HH, Murphy DJ, Wang L, Abyzov A, Dennis JW, Maass PG, Campbell K, Wilson MD, Lachance DH, Wrensch M, Wiencke J, Mak T, Pennacchio (2022 Oct 7). A noncoding single-nucleotide polymorphism at 8q24 drives IDH1-mutant glioma formation. Science (New York, N.Y.), 378(6615), 68-78. . ID: 36201590.

12.) Gallo D, Young JTF, Fourtounis J, Martino G, Álvarez-Quilón A, Bernier C, Duffy NM, Papp R, Roulston A, Stocco R, Szychowski J, Veloso A, Alam H, Baruah PS, Fortin AB, Bowlan J, Chaudhary N, Desjardins J, Dietrich E, Fournier S, Fugère-Desjardins C, Goullet de Rugy T, Leclaire ME, Liu B, Bhaskaran V, Mamane Y, Melo H, Nicolas O, Singhania A, Szilard RK, Tkáč J, Yin SY, Morris SJ, Zinda M, Marshall CG, Durocher D (2022 Apr). CCNE1 amplification is synthetic lethal with PKMYT1 kinase inhibition. Nature, 604(7907), 749-756. . ID: 35444283.

13.) Adam S, Rossi SE, Moatti N, De Marco Zompit M, Xue Y, Ng TF, Álvarez-Quilón A, Desjardins J, Bhaskaran V, Martino G, Setiaputra D, Noordermeer SM, Ohsumi TK, Hustedt N, Szilard RK, Chaudhary N, Munro M, Veloso A, Melo H, Yin SY, Papp R, Young JTF, Zinda M, Stucki M, Durocher D (2021 Dec). The CIP2A-TOPBP1 axis safeguards chromosome stability and is a synthetic lethal target for BRCA-mutated cancer. Nature cancer, 2(12), 1357-1371. doi: 10.1038/s43018-021-00266-w. ID: 35121901.

14.) Macrae TA, Ramalho-Santos M (2021 Mar 25). The deubiquitinase Usp9x regulates PRC2-mediated chromatin reprogramming during mouse development. Nature communications, 12(1), 1865. . ID: 33767158.

15.) Olivieri M, Durocher D (2021 Mar 19). Genome-scale chemogenomic CRISPR screens in human cells using the TKOv3 library. STAR protocols, 2(1), 100321. . ID: 33598657.

Description:

The next-generation sequencing facility of the Network Biology Collaborative Centre (NBCC) provides both short and long read sequencing capabilities for the analysis of gene function and expression. Directed by Dr. Jeff Wrana, this facility specializes in functional genomics and single cell biology. Our full-service offerings include consultation, sample preparation (especially for spatial and single cell applications), quality control, sequencing analysis, bioinformatics support, and assistance with grant and publication writing related to the services we offer. Applications include: - gene function analysis - pooled CRISPR screening, multiplexed barcode screens - whole genome sequencing - both short- and long-read sequencing - bulk gene expression profiling - single cell biology (single cells and single nuclei) - spatial profiling - pathogen detection and profiling