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High-Throughput Approaches to Pinpoint Function within the Noncoding Genome

Antonino Montalbano, Matthew C. Canver, Neville E. Sanjana
2017 Molecular Cell  
Other approaches to identify functional regions have included a hidden Markov model (HMM) (Canver et al., 2015 (Canver et al., , 2017a .  ...  Although most studies have focused on class 2 effectors, recent work on type I-E CRISPR-Cas (Cascade) and Cas3 nuclease revealed a PAM specificity of NNNAAG (Xiao et al., 2017) .  ...  (E-G) The CRISPR system can also be used to introduce epigenetic modifications.  ... 
doi:10.1016/j.molcel.2017.09.017 pmid:28985510 pmcid:PMC5701515 fatcat:56x3md6v7za23oxgg4xftqtz6a

CRISPResso: sequencing analysis toolbox for CRISPR genome editing [article]

Luca Pinello, Matthew C Canver, Megan D Hoban, Stuart H Orkin, Donald B Kohn, Daniel E Bauer, Guo-Cheng Yuan
2015 bioRxiv   pre-print
mutations include any mutations that partially or fully overlap coding sequences as input by the user, with any non-overlapping mutations classified as noncoding (see also Supplementary Fig. 11 ). e-f  ...  Reference amplicon position (bp) Mutation position distribution of NHEJ Reference amplicon position (bp) Mutation position distribution of HDR Reference amplicon position (bp) 4.3% d c b a f e  ... 
doi:10.1101/031203 fatcat:k4dfyvy26bbklbkzmisv4tbtk4

Analysis and comparison of genome editing using CRISPResso2 [article]

Kendell Clement, Holly Rees, Matthew Canver, Jason Gehrke, Rick Farouni, Jonathan Hsu, Mitchel Cole, David R Liu, J. Keith Joung, Daniel E. Bauer, Luca Pinello
2018 bioRxiv   pre-print
Genome editing technologies are rapidly evolving, and analysis of deep sequencing data from target or off-target regions is necessary for measuring editing efficiency and evaluating safety. However, no software exists to analyze base editors, perform allele-specific quantification or that incorporates biologically-informed and scalable alignment approaches. Here, we present CRISPResso2 to fill this gap and illustrate its functionality by experimentally measuring and analyzing the editing properties of six genome editing agents.
doi:10.1101/392217 fatcat:yhfgd25v55hd3dgwkvp24go3pa

Generation of Genomic Deletions in Mammalian Cell Lines via CRISPR/Cas9

Daniel E. Bauer, Matthew C. Canver, Stuart H. Orkin
2014 Journal of Visualized Experiments  
Transform the plasmid into DH5α E. coli cells and plate onto LB agar plates with the relevant antibiotic.  ... 
doi:10.3791/52118 pmid:25549070 pmcid:PMC4279820 fatcat:toxosee575auxotjynxfeoyfaa

Embryonic stem cells as sources of donor-independent platelets

Matthew C. Canver, Daniel E. Bauer, Stuart H. Orkin
2015 Journal of Clinical Investigation  
C o m m e n t a r y 2 2 6 1  ...  Canver, 1 Daniel E. Bauer, 1, 2, 3 and Stuart H.  ... 
doi:10.1172/jci82348 pmid:25961451 pmcid:PMC4497771 fatcat:tqrktjxko5gjhkv67asunr4l3a

EHMT1 and EHMT2 inhibition induces fetal hemoglobin expression

A. Renneville, P. Van Galen, M. C. Canver, M. McConkey, J. M. Krill-Burger, D. M. Dorfman, E. B. Holson, B. E. Bernstein, S. H. Orkin, D. E. Bauer, B. L. Ebert
2015 Blood  
Ebert, 1 Blackfan Circle, Karp 5.210, Boston, MA 02115; e-mail: Benjamin_Ebert@dfci.harvard.edu.  ...  (E) Representative HPLC chromatograms showing HbF abundance.  ...  As expected, UNC0638 treatment caused a dose-dependent reduction in H3K9Me2 ( Figure 4D-E) .  ... 
doi:10.1182/blood-2015-06-649087 pmid:26320100 pmcid:PMC4608240 fatcat:xdzwxsebxzbehen4jcxqzp5osu

Analyzing CRISPR genome-editing experiments with CRISPResso

Luca Pinello, Matthew C Canver, Megan D Hoban, Stuart H Orkin, Donald B Kohn, Daniel E Bauer, Guo-Cheng Yuan
2016 Nature Biotechnology  
, An example of HDR-mediated recombination of an extrachromosomal donor sequence resulting in four substitutions relative to the reference amplicon (experiment 2). e, When an expected HDR amplicon is provided  ...  in-frame mutations include any mutations that partially or fully overlap coding sequences as input by the user, with any non-overlapping mutations classified as noncoding (see also Supplementary Fig. 11 ). e-f  ... 
doi:10.1038/nbt.3583 pmid:27404874 pmcid:PMC5242601 fatcat:5jblno25rjb2jcz6iiec7zdb44

Formal Development of Object-Based Systems in a Temporal Logic Setting [chapter]

E. Canver, F. W. Henke
1999 Formal Methods for Open Object-Based Distributed Systems  
as => as can be verified by proving • E /\ (/\j=lC(Mj)) => E; for all i = 1, ... , n • E /\ (/\j=lC(Mj)) => C(M) • E /\ (/\j=lMj) => M where C(M) denotes a formula defining just the safety aspects that  ...  If the visible variables of the open system specifications can be partitioned into input variables e and output variables m such that changes to input and output variables do not occur simultaneously then  ... 
doi:10.1007/978-0-387-35562-7_33 fatcat:eqtnm2keejfyllz3hhz7c6yuvq

Integrated design, execution, and analysis of arrayed and pooled CRISPR genome editing experiments [article]

Matthew C. Canver, Maximilian Haeussler, Daniel E. Bauer, Stuart H. Orkin, Neville E. Sanjana, Ophir Shalem, Guo-Cheng Yuan, Feng Zhang, Jean-Paul Concordet, Luca Pinello
2017 bioRxiv   pre-print
, Casdatabase 18 , Cas-OFFinder 19 , CasOT 20 , CCTop 21 , COSMID 22 , CHOPCHOP 23, 24 , CRISPRdirect 25 , CRISPR-DO 26 , CRISPR-ERA 27 , CRISPR-P 28 , CROP-IT 29 , DNA Striker 14 , E-CRISP  ...  To enable the frameshift analysis, it is necessary to add the option -e to the command line with the (sub)sequence of the amplicon corresponding to the exon (see Box 2) 79 The enrichment score is not  ...  O n -ta r g e t a n a ly s is O ffta r g e t a n a ly s is Any other customized library of sgRNA for a pooled experiment (Step 1; Box 1) 1.  ... 
doi:10.1101/125245 fatcat:leolxtqpyreyrffo4ukpjootfi

Integrated design, execution, and analysis of arrayed and pooled CRISPR genome-editing experiments

Matthew C Canver, Maximilian Haeussler, Daniel E Bauer, Stuart H Orkin, Neville E Sanjana, Ophir Shalem, Guo-Cheng Yuan, Feng Zhang, Jean-Paul Concordet, Luca Pinello
2018 Nature Protocols  
, Casdatabase 18 , Cas-OFFinder 19 , CasOT 20 , CCTop 21 , COSMID 22 , CHOPCHOP 23, 24 , CRISPRdirect 25 , CRISPR-DO 26 , CRISPR-ERA 27 , CRISPR-P 28 , CROP-IT 29 , DNA Striker 14 , E-CRISP  ...  To enable the frameshift analysis, it is necessary to add the option -e to the command line with the (sub)sequence of the amplicon corresponding to the exon (see Box 2) 79 The enrichment score is not  ...  O n -ta r g e t a n a ly s is O ffta r g e t a n a ly s is Any other customized library of sgRNA for a pooled experiment (Step 1; Box 1) 1.  ... 
doi:10.1038/nprot.2018.005 pmid:29651054 fatcat:n5qyu732lvgszmggogs3t7kgmu

CRISPRO Identifies Functional Protein Coding Sequences Based on Genome Editing Dense Mutagenesis [article]

Vivien A. C. Schoonenberg, Mitchel Alfonza Cole, Qiuming Yao, Claudio Macias-Treviño, Falak Sher, Patrick G. Schupp, Matthew C. Canver, Takahiro Maeda, Luca Pinello, Daniel E. Bauer
2018 bioRxiv   pre-print
C R I S P R O i d e n t i f i e s f u n c t i o n a l p r o t e i n c o d i n g s e q u e n c e s b a s e d o n g e n o m e e d i t i  ...  H o w e v e r , i n t h i s c e l l l i n e t h e r e i s a g r e e m e n t b e t w e e n t h e m o s t n e g a t i v e p h e n o t y p i c C R I S P R s c o r e s a n d c o n s e r v a t i o n , d i s  ... 
doi:10.1101/326504 fatcat:zcxacyvir5bs7fcygsokkqbwzu

CRISPResso2 provides accurate and rapid genome editing sequence analysis

Kendell Clement, Holly Rees, Matthew C. Canver, Jason M. Gehrke, Rick Farouni, Jonathan Y. Hsu, Mitchel A. Cole, David R. Liu, J. Keith Joung, Daniel E. Bauer, Luca Pinello
2019 Nature Biotechnology  
doi:10.1038/s41587-019-0032-3 pmid:30809026 pmcid:PMC6533916 fatcat:y4hhwlu7xffbnfnjrii3enmfmq

CRISPRO: identification of functional protein coding sequences based on genome editing dense mutagenesis

Vivien A. C. Schoonenberg, Mitchel A. Cole, Qiuming Yao, Claudio Macias-Treviño, Falak Sher, Patrick G. Schupp, Matthew C. Canver, Takahiro Maeda, Luca Pinello, Daniel E. Bauer
2018 Genome Biology  
charged (D, E), aliphatic (A, G, I, L, P, V), aromatic (F, W, Y), acidic (D, E), basic (R, H, K), hydroxilic (See figure on previous page.)  ...  (Additional file 1: Figure S1 , S9D-E, Additional file 2: Table S1 ).  ... 
doi:10.1186/s13059-018-1563-5 pmid:30340514 pmcid:PMC6195731 fatcat:5mv6tfirdva65cn47pz4p5esa4

CRISPR-SURF: Discovering regulatory elements by deconvolution of CRISPR tiling screen data [article]

Jonathan Y Hsu, Charles P Fulco, Mitchel A Cole, Matthew C Canver, Danilo Pellin, Falak Sher, Rick Farouni, Kendell Clement, James A Guo, Luca Biasco, Stuart H Orkin, Jesse M Engreitz (+4 others)
2018 bioRxiv   pre-print
Tiling screens using CRISPR-Cas technologies provide a powerful approach to map regulatory elements to phenotypes of interest, but computational methods that effectively model these experimental approaches for different CRISPR technologies are not readily available. Here we present CRISPR-SURF, a deconvolution framework to identify functional regulatory regions in the genome from data generated by CRISPR-Cas nuclease, CRISPR interference (CRISPRi), or CRISPR activation (CRISPRa) tiling screens.
more » ... We validated CRISPR-SURF on previously published and new data, identifying both experimentally validated and new potential regulatory elements. With CRISPR tiling screens now being increasingly used to elucidate the regulatory architecture of the non-coding genome, CRISPR-SURF provides a generalizable and accessible solution for the discovery of regulatory elements.
doi:10.1101/345850 fatcat:ffn7ac4u3re4bbz3wk6z3gh5ie

Transcription factors LRF and BCL11A independently repress expression of fetal hemoglobin

T. Masuda, X. Wang, M. Maeda, M. C. Canver, F. Sher, A. P. W. Funnell, C. Fisher, M. Suciu, G. E. Martyn, L. J. Norton, C. Zhu, R. Kurita (+8 others)
2016 Science  
Schupp for technical support and assistance; E. Lamar for critical reading of the manuscript; and S-U. Lee  ...  S12, E and F) . The HbF levels of DKO cells were at 91 to 94% of total Hb (Fig. 4, C and D) .  ...  (E) Representative HPLC profiles of control and ZBTB7A Δ/Δ HUDEP-2 clones. Author manuscript; available in PMC 2016 July 15.  ... 
doi:10.1126/science.aad3312 pmid:26816381 pmcid:PMC4778394 fatcat:m6akwas3inbdxga5pybbidl7na
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