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Inhibition of inflammatory microglia by dietary fiber and short-chain fatty acids
Authors Caetano-Silva ME, Rund L, Hutchinson NT, Woods JA, Steelman AJ, Johnson RW
Journal Scientific Reports·2023PubMed10.1038/s41598-022-27086-x·PDF attached

Microglia play a vital role maintaining brain homeostasis but can also cause persistent neuroinflammation. Short-chain fatty acids (SCFAs) produced by the intestinal microbiota have been suggested to regulate microglia inflammation indirectly by signaling through the gut-brain axis or directly by reaching the brain. The present work evaluated the anti-inflammatory effects of SCFAs on lipopolysaccharide (LPS)-stimulated microglia from mice fed inulin, a soluble fiber that is fermented by intestinal microbiota to produce SCFAs in vivo, and SCFAs applied to primary microglia in vitro.

Host microbiota constantly control maturation and function of microglia in the CNS
Authors Erny D, Hrabě de Angelis AL, Jaitin D, et al.
Journal Nature Neuroscience·2015PubMed10.1038/nn.4030·PDF attached

Microglia in germ-free mice were immature and responded poorly to infection. Recolonizing the mice with a complex microbiota restored them, and short-chain fatty acids alone, given in drinking water, were enough to restore microglial maturation. Mice lacking the receptor FFAR2 showed similar microglial defects.

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Gut bacteria ferment dietary fibre into short-chain fatty acids, mainly acetate, propionate and butyrate. Short-chain fatty acids from the gut microbiota are needed for microglia to mature (Erny et al., 2015). Germ-free mice also have a leakier blood–brain barrier (Braniste et al., 2014) and an exaggerated stress response (Sudo et al., 2004), and these fatty acids may act on the brain directly (Dalile et al., 2019).

How they reach the brain remains debated. Proposed routes include the vagus nerve, immune signalling and transport across the blood–brain barrier.

References

Braniste, V., Al-Asmakh, M., Kowal, C., Anuar, F., Abbaspour, A., Tóth, M., … Pettersson, S. (2014). The gut microbiota influences blood-brain barrier permeability in mice. Science Translational Medicine.

Dalile, B., Van Oudenhove, L., Vervliet, B., & Verbeke, K. (2019). The role of short-chain fatty acids in microbiota–gut–brain communication. Nature Reviews Gastroenterology & Hepatology.

Erny, D., Hrabě de Angelis, A. L., Jaitin, D., Wieghofer, P., Staszewski, O., David, E., … Prinz, M. (2015). Host microbiota constantly control maturation and function of microglia in the CNS. Nature Neuroscience, 18(7), 965–977.

Sudo, N., Chida, Y., Aiba, Y., Sonoda, J., Oyama, N., Yu, X.-N., Kubo, C., & Koga, Y. (2004). Postnatal microbial colonization programs the hypothalamic–pituitary–adrenal system for stress response in mice. The Journal of Physiology.

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Short-chain fatty acids, products of bacterial fermentation, were enough to restore the maturation of microglia in germ-free mice.
Host microbiota constantly control maturation and function of microglia in the CNS
Erny, Hrabě de Angelis, Jaitin, et al. · Nat Neurosci · 2015
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Erny 2015 · Library
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Stain brain sections for Iba1-positive microgliaTo doSMOct 24
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Microbial metabolites and behaviour
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Four of the seven papers carry the fields you asked for. The other three are reviews, without a single model or measure to extract.

PaperModelDesignMeasureFinding vs control
Erny et al. (2015)
Microbiota and microglia
Germ-free miceRecolonization; SCFAs in waterMicroglial maturationSCFAs alone restore maturation
Braniste et al. (2014)
Microbiota and the blood–brain barrier
Germ-free miceRecolonization; butyrateBarrier permeabilityBarrier tightened
Sudo et al. (2004)
Colonization and the stress axis
Germ-free miceRestraint stressACTH and corticosteroneExaggerated stress response
Caetano-Silva et al. (2023)
Fibre, SCFAs and microglia
Mice; primary microgliaInulin diet; SCFAs in vitroTNF-α secretionAcetate, butyrate lower it
4 papers · every field found

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Compare the studies in my library: model, design, measure and finding
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Chain-of-thought prompting elicits reasoning in large language models
Authors Wei J, Wang X, Schuurmans D, Bosma M, Ichter B, Xia F, Chi E, Le Q, Zhou D
Journal NeurIPS·2022arXiv·PDF attached
Shows that prompting with a few worked examples that spell out intermediate steps markedly improves large models on arithmetic, commonsense and symbolic reasoning, with the gains appearing only at large scale.
OverviewOpen readerCite
Large language models are zero-shot reasoners
Authors Kojima T, Gu SS, Reid M, Matsuo Y, Iwasawa Y
Journal NeurIPS·2022arXiv·PDF attached
Shows that adding one instruction, to think step by step, lets large models work through arithmetic and logic problems without any worked examples.
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Language models often fail at multi-step arithmetic when asked for the answer directly. Writing out intermediate steps makes a model more accurate on reasoning tasks. Even one instruction to think step by step helps [2].
Best match
Generating a chain of thought, a series of intermediate reasoning steps, significantly improves the ability of large language models to perform complex reasoning.
Chain-of-thought prompting elicits reasoning in large language models
Wei, Wang, Schuurmans, et al. · NeurIPS · 2022
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4 references · IEEECopy all
[1]
J. Wei et al., “Chain-of-thought prompting elicits reasoning in large language models,” in Proc. NeurIPS, 2022, pp. 24824–24837.
[2]
T. Kojima, S. S. Gu, M. Reid, Y. Matsuo, and Y. Iwasawa, “Large language models are zero-shot reasoners,” in Proc. NeurIPS, 2022.
[3]
K. Cobbe et al., “Training verifiers to solve math word problems,” arXiv:2110.14168, 2021.
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Methods: We estimated the effects of air pollution on mortality, while controlling for individual risk factors, in a prospective cohort study of 8111 adults in six U.S. cities. Methods: The adjusted mortality-rate ratio for the most polluted of the cities as compared with the least polluted was 1.26 (95 percent confidence interval, 1.08 to 1.47). Air pollution was positively associated with death from lung cancer and cardiopulmonary disease.

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Species are moving toward the poles and uphill as the climate warms.
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Rapid range shifts of species associated with high levels of climate warming
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Genome editing once meant engineering a new protein for every target sequence. Cas9 can be pointed at a chosen DNA sequence by a single guide RNA (Jinek et al., 2012). Bacteria use the same system to remember and destroy viruses (Barrangou et al., 2007), and within a year it was editing human cells (Cong et al., 2013; Mali et al., 2013).

How precisely it cuts remains a concern. Off-target edits, delivery and immune responses all limit its use in patients.

References

Barrangou, R., Fremaux, C., Deveau, H., Richards, M., Boyaval, P., Moineau, S., Romero, D. A., & Horvath, P. (2007). CRISPR provides acquired resistance against viruses in prokaryotes. Science, 315(5819), 1709–1712.

Cong, L., Ran, F. A., Cox, D., Lin, S., Barretto, R., Habib, N., … Zhang, F. (2013). Multiplex genome engineering using CRISPR/Cas systems. Science, 339(6121), 819–823.

Jinek, M., Chylinski, K., Fonfara, I., Hauer, M., Doudna, J. A., & Charpentier, E. (2012). A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science, 337(6096), 816–821.

Mali, P., Yang, L., Esvelt, K. M., Aach, J., Guell, M., DiCarlo, J. E., … Church, G. M. (2013). RNA-guided human genome engineering via Cas9. Science, 339(6121), 823–826.

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The Cas9 endonuclease can be programmed with a single guide RNA to cleave a chosen site in double-stranded DNA.
A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity
Jinek, Chylinski, Fonfara, et al. · Science · 2012
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Precision and off-target effects in genome editing
CRISPR-Cas9 in vivo gene editing for transthyretin amyloidosis
Authors Gillmore JD, Gane E, Taubel J, et al.
Journal New England Journal of Medicine·2021PubMed

A first-in-human trial of editing inside the body, delivering Cas9 to the liver in lipid nanoparticles and lowering the disease protein in six patients.

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Guide RNA screen in HEK293T40%
Read and annotate Hsu et al. on targeting specificity
Clone the 12 guide RNAs into the vector
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Sequence the predicted off-target sites
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Guide RNA screen in HEK293T · due Nov 14
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Search my library and the web thoroughly: compare what different studies find about off-target editing by Cas9, and check each paper individually.
Deep research71 found · 55 screened · 14 included · 14 extracted
SearchScreenExtractSynthesize

Off-target editing by Cas9: what 14 studies say

How much off-target editing is found depends on how it is looked for: cell-based assays report many sites, while whole-genome sequencing of edited animals finds very few Hsu et al., 2013 Iyer et al., 2018. The larger risk may be at the target site itself, where repair can leave long deletions Kosicki et al., 2018.

Guide design and delivery matter more than the nuclease: shorter exposure and careful guide choice cut off-target editing in every comparison Tsai et al., 2015.

Evidence14 included, 5 shown
TitleYearDesignMethodOutcomeEffect
DNA targeting specificity of RNA-guided Cas9 nucleases2013Cell assayTargeted sequencingMismatch toleranceMany sites cut
GUIDE-seq enables genome-wide profiling of off-target cleavage2015Genome-wide mapGUIDE-seqSites in cellsFew, guide-dependent
Repair of double-strand breaks leads to large deletions and complex rearrangements2018Cell linesLong-read sequencingOn-target repairLarge deletions found
Exome sequencing of CRISPR-edited mice reveals few off-target events2018Edited miceExome sequencingGenome-wide variantsFew off-target events
Digenome-seq: genome-wide profiling of Cas9 off-target effects2015In vitro mapDigenome-seqCleavage sitesN/A
Sources · 3
DNA targeting specificity of RNA-guided Cas9 nucleasesHsu PD and 11 others · 2013In library
Exome sequencing of CRISPR-edited mice reveals few off-target eventsIyer V, Boroviak K, Thomas M, et al. · 2018
GUIDE-seq enables genome-wide profiling of off-target cleavageTsai SQ, Zheng Z, Nguyen NT, et al. · 2015In library
Run it again but only whole-genome methods.
Deep researchCancelledpartial results below · 23 found, 9 screened

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Inhibition of inflammatory microglia by dietary fiber and short-chain fatty acids
Authors Caetano-Silva ME, Rund L, Hutchinson NT, Woods JA, Steelman AJ, Johnson RW
Journal Scientific Reports·2023PubMed10.1038/s41598-022-27086-x·PDF attached

Microglia play a vital role maintaining brain homeostasis but can also cause persistent neuroinflammation. Short-chain fatty acids (SCFAs) produced by the intestinal microbiota have been suggested to regulate microglia inflammation indirectly by signaling through the gut-brain axis or directly by reaching the brain. The present work evaluated the anti-inflammatory effects of SCFAs on lipopolysaccharide (LPS)-stimulated microglia from mice fed inulin, a soluble fiber that is fermented by intestinal microbiota to produce SCFAs in vivo, and SCFAs applied to primary microglia in vitro.

Host microbiota constantly control maturation and function of microglia in the CNS
Authors Erny D, Hrabě de Angelis AL, Jaitin D, et al.
Journal Nature Neuroscience·2015PubMed10.1038/nn.4030·PDF attached

Microglia in germ-free mice were immature and responded poorly to infection. Recolonizing the mice with a complex microbiota restored them, and short-chain fatty acids alone, given in drinking water, were enough to restore microglial maturation. Mice lacking the receptor FFAR2 showed similar microglial defects.

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Page 4 of Caetano-Silva et al. 2023, Inhibition of inflammatory microglia by dietary fiber and short-chain fatty acids
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Gut bacteria ferment dietary fibre into short-chain fatty acids, mainly acetate, propionate and butyrate. Short-chain fatty acids from the gut microbiota are needed for microglia to mature (Erny et al., 2015). Germ-free mice also have a leakier blood–brain barrier (Braniste et al., 2014) and an exaggerated stress response (Sudo et al., 2004), and these fatty acids may act on the brain directly (Dalile et al., 2019).

How they reach the brain remains debated. Proposed routes include the vagus nerve, immune signalling and transport across the blood–brain barrier.

References

Braniste, V., Al-Asmakh, M., Kowal, C., Anuar, F., Abbaspour, A., Tóth, M., … Pettersson, S. (2014). The gut microbiota influences blood-brain barrier permeability in mice. Science Translational Medicine.

Dalile, B., Van Oudenhove, L., Vervliet, B., & Verbeke, K. (2019). The role of short-chain fatty acids in microbiota–gut–brain communication. Nature Reviews Gastroenterology & Hepatology.

Erny, D., Hrabě de Angelis, A. L., Jaitin, D., Wieghofer, P., Staszewski, O., David, E., … Prinz, M. (2015). Host microbiota constantly control maturation and function of microglia in the CNS. Nature Neuroscience, 18(7), 965–977.

Sudo, N., Chida, Y., Aiba, Y., Sonoda, J., Oyama, N., Yu, X.-N., Kubo, C., & Koga, Y. (2004). Postnatal microbial colonization programs the hypothalamic–pituitary–adrenal system for stress response in mice. The Journal of Physiology.

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Short-chain fatty acids, products of bacterial fermentation, were enough to restore the maturation of microglia in germ-free mice.
Host microbiota constantly control maturation and function of microglia in the CNS
Erny, Hrabě de Angelis, Jaitin, et al. · Nat Neurosci · 2015
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Read and annotate Erny et al. on microglia maturation
Erny 2015 · Library
In progressAWOct 13
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Stain brain sections for Iba1-positive microgliaTo doSMOct 24
Analyse the 16S sequencing reads in QIIME 2To doAWOct 29
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Oct 24
Pilot the butyrate diet on 3 cages/dueDue Oct 24
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Draft methods section (husbandry, diets and sampling)
FriAW
Email the gnotobiotic facility about cage space
Oct 20SM
Germ-free mouse SCFA study
2 of 5 doneDue Nov 14
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TodayAW
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Found by the project-wide search rather than by one of the themes above.
/
Compare the studies in my library: model, design, measure and finding
Thinking

Four of the seven papers carry the fields you asked for. The other three are reviews, without a single model or measure to extract.

PaperModelDesignMeasureFinding vs control
Erny et al. (2015)
Microbiota and microglia
Germ-free miceRecolonization; SCFAs in waterMicroglial maturationSCFAs alone restore maturation
Braniste et al. (2014)
Microbiota and the blood–brain barrier
Germ-free miceRecolonization; butyrateBarrier permeabilityBarrier tightened
Sudo et al. (2004)
Colonization and the stress axis
Germ-free miceRestraint stressACTH and corticosteroneExaggerated stress response
Caetano-Silva et al. (2023)
Fibre, SCFAs and microglia
Mice; primary microgliaInulin diet; SCFAs in vitroTNF-α secretionAcetate, butyrate lower it
4 papers · every field found

Want me to search PubMed for more germ-free studies of microglia to add to the table?

Sources · 2
Compare the studies in my library: model, design, measure and finding
All7Unread7Key sources2
Chain-of-thought prompting elicits reasoning in large language models
Authors Wei J, Wang X, Schuurmans D, Bosma M, Ichter B, Xia F, Chi E, Le Q, Zhou D
Journal NeurIPS·2022arXiv·PDF attached
Shows that prompting with a few worked examples that spell out intermediate steps markedly improves large models on arithmetic, commonsense and symbolic reasoning, with the gains appearing only at large scale.
OverviewOpen readerCite
Large language models are zero-shot reasoners
Authors Kojima T, Gu SS, Reid M, Matsuo Y, Iwasawa Y
Journal NeurIPS·2022arXiv·PDF attached
Shows that adding one instruction, to think step by step, lets large models work through arithmetic and logic problems without any worked examples.
OverviewOpen readerCite
Read

Every paper you read, in one library. Open any of them to highlight a passage and ask about it.

Language models often fail at multi-step arithmetic when asked for the answer directly. Writing out intermediate steps makes a model more accurate on reasoning tasks. Even one instruction to think step by step helps [2].
Best match
Generating a chain of thought, a series of intermediate reasoning steps, significantly improves the ability of large language models to perform complex reasoning.
Chain-of-thought prompting elicits reasoning in large language models
Wei, Wang, Schuurmans, et al. · NeurIPS · 2022
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Write

Highlight a claim in Word or Google Docs and insert the paper that backs it.

4 references · IEEECopy all
[1]
J. Wei et al., “Chain-of-thought prompting elicits reasoning in large language models,” in Proc. NeurIPS, 2022, pp. 24824–24837.
[2]
T. Kojima, S. S. Gu, M. Reid, Y. Matsuo, and Y. Iwasawa, “Large language models are zero-shot reasoners,” in Proc. NeurIPS, 2022.
[3]
K. Cobbe et al., “Training verifiers to solve math word problems,” arXiv:2110.14168, 2021.
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d.okafor@lab.eduInvite as CollaboratorAir Pollution & HealthSend invite
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SMSofia Morenos.moreno@lab.eduMember
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Methods: We estimated the effects of air pollution on mortality, while controlling for individual risk factors, in a prospective cohort study of 8111 adults in six U.S. cities. Methods: The adjusted mortality-rate ratio for the most polluted of the cities as compared with the least polluted was 1.26 (95 percent confidence interval, 1.08 to 1.47). Air pollution was positively associated with death from lung cancer and cardiopulmonary disease.

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PM2.5 and asthma admissions GoalMCNov 14
Read and annotate Dockery et al. (1993)SMOct 13
SMSofia MorenoLead
DODaniel Okafor
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Link monitor readings to ZIP codesDOToday
Clean the hospital admissions dataKWOct 24
Get IRB approval for the recordsSTOct 9
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Species are moving toward the poles and uphill as the climate warms.
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Rapid range shifts of species associated with high levels of climate warming
Chen et al. · Science · 2011
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Genome editing once meant engineering a new protein for every target sequence. Cas9 can be pointed at a chosen DNA sequence by a single guide RNA (Jinek et al., 2012). Bacteria use the same system to remember and destroy viruses (Barrangou et al., 2007), and within a year it was editing human cells (Cong et al., 2013; Mali et al., 2013).

How precisely it cuts remains a concern. Off-target edits, delivery and immune responses all limit its use in patients.

References

Barrangou, R., Fremaux, C., Deveau, H., Richards, M., Boyaval, P., Moineau, S., Romero, D. A., & Horvath, P. (2007). CRISPR provides acquired resistance against viruses in prokaryotes. Science, 315(5819), 1709–1712.

Cong, L., Ran, F. A., Cox, D., Lin, S., Barretto, R., Habib, N., … Zhang, F. (2013). Multiplex genome engineering using CRISPR/Cas systems. Science, 339(6121), 819–823.

Jinek, M., Chylinski, K., Fonfara, I., Hauer, M., Doudna, J. A., & Charpentier, E. (2012). A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science, 337(6096), 816–821.

Mali, P., Yang, L., Esvelt, K. M., Aach, J., Guell, M., DiCarlo, J. E., … Church, G. M. (2013). RNA-guided human genome engineering via Cas9. Science, 339(6121), 823–826.

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The Cas9 endonuclease can be programmed with a single guide RNA to cleave a chosen site in double-stranded DNA.
A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity
Jinek, Chylinski, Fonfara, et al. · Science · 2012
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Precision and off-target effects in genome editing
CRISPR-Cas9 in vivo gene editing for transthyretin amyloidosis
Authors Gillmore JD, Gane E, Taubel J, et al.
Journal New England Journal of Medicine·2021PubMed

A first-in-human trial of editing inside the body, delivering Cas9 to the liver in lipid nanoparticles and lowering the disease protein in six patients.

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Guide RNA screen in HEK293T40%
Read and annotate Hsu et al. on targeting specificity
Clone the 12 guide RNAs into the vector
Run the T7 endonuclease assay on each pool
Sequence the predicted off-target sites
Methods section0%
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Search my library and the web thoroughly: compare what different studies find about off-target editing by Cas9, and check each paper individually.
Deep research71 found · 55 screened · 14 included · 14 extracted
SearchScreenExtractSynthesize

Off-target editing by Cas9: what 14 studies say

How much off-target editing is found depends on how it is looked for: cell-based assays report many sites, while whole-genome sequencing of edited animals finds very few Hsu et al., 2013 Iyer et al., 2018. The larger risk may be at the target site itself, where repair can leave long deletions Kosicki et al., 2018.

Guide design and delivery matter more than the nuclease: shorter exposure and careful guide choice cut off-target editing in every comparison Tsai et al., 2015.

Evidence14 included, 5 shown
TitleYearDesignMethodOutcomeEffect
DNA targeting specificity of RNA-guided Cas9 nucleases2013Cell assayTargeted sequencingMismatch toleranceMany sites cut
GUIDE-seq enables genome-wide profiling of off-target cleavage2015Genome-wide mapGUIDE-seqSites in cellsFew, guide-dependent
Repair of double-strand breaks leads to large deletions and complex rearrangements2018Cell linesLong-read sequencingOn-target repairLarge deletions found
Exome sequencing of CRISPR-edited mice reveals few off-target events2018Edited miceExome sequencingGenome-wide variantsFew off-target events
Digenome-seq: genome-wide profiling of Cas9 off-target effects2015In vitro mapDigenome-seqCleavage sitesN/A
Sources · 3
DNA targeting specificity of RNA-guided Cas9 nucleasesHsu PD and 11 others · 2013In library
Exome sequencing of CRISPR-edited mice reveals few off-target eventsIyer V, Boroviak K, Thomas M, et al. · 2018
GUIDE-seq enables genome-wide profiling of off-target cleavageTsai SQ, Zheng Z, Nguyen NT, et al. · 2015In library
Run it again but only whole-genome methods.
Deep researchCancelledpartial results below · 23 found, 9 screened

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