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High-Throughput Approaches to Pinpoint Function within the Noncoding Genome
2017
Molecular Cell
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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]
2015
bioRxiv
pre-print
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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]
2018
bioRxiv
pre-print
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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
2014
Journal of Visualized Experiments
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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
2015
Journal of Clinical Investigation
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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
2015
Blood
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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
2016
Nature Biotechnology
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, 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]
1999
Formal Methods for Open Object-Based Distributed Systems
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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]
2017
bioRxiv
pre-print
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, 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
2018
Nature Protocols
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, 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]
2018
bioRxiv
pre-print
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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
2019
Nature Biotechnology
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CRISPRO: identification of functional protein coding sequences based on genome editing dense mutagenesis
2018
Genome Biology
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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]
2018
bioRxiv
pre-print
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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.
doi:10.1101/345850
fatcat:ffn7ac4u3re4bbz3wk6z3gh5ie
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... 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.
Transcription factors LRF and BCL11A independently repress expression of fetal hemoglobin
2016
Science
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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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