CUT&RUN sequencing (English Wikipedia)

Analysis of information sources in references of the Wikipedia article "CUT&RUN sequencing" in English language version.

refsWebsite

Global rank English rank

24nih.gov

4^th place

16doi.org

2^nd place

4protocols.io

low place

3semanticscholar.org

11^th place

8^th place

1fredhutch.org

low place

1epicypher.com

low place

1harvard.edu

18^th place

17^th place

doi.org

Meyer CA, Liu XS (November 2014). "Identifying and mitigating bias in next-generation sequencing methods for chromatin biology". Nature Reviews. Genetics. 15 (11): 709–21. doi:10.1038/nrg3788. PMC 4473780. PMID 25223782.
Baranello L, Kouzine F, Sanford S, Levens D (May 2016). "ChIP bias as a function of cross-linking time". Chromosome Research. 24 (2): 175–81. doi:10.1007/s10577-015-9509-1. PMC 4860130. PMID 26685864.
He C, Bonasio R (February 2017). "A cut above". eLife. 6. doi:10.7554/eLife.25000. PMC 5310838. PMID 28199181.
Skene PJ, Henikoff S (January 2017). "An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites". eLife. 6. doi:10.7554/eLife.21856. PMC 5310842. PMID 28079019.
Janssens, Derek; Henikoff, Steven (9 May 2019). "CUT&RUN: Targeted in situ genome-wide profiling with high efficiency for low cell numbers v3 (protocols.io.zcpf2vn)". protocols.io. doi:10.17504/protocols.io.zcpf2vn.
Ahmad, Kami (2 December 2018). "CUT&RUN with Drosophila tissues v1 (protocols.io.umfeu3n)". protocols.io. doi:10.17504/protocols.io.umfeu3n. S2CID 216840246.
Janssens, Derek; Ahmad, Kami; Henikoff, Steven (27 November 2018). "AutoCUT&RUN: genome-wide profiling of chromatin proteins in a 96 well format on a Biomek v1 (protocols.io.ufeetje)". protocols.io. doi:10.17504/protocols.io.ufeetje. S2CID 216872521.
antibodies-online (19 March 2020). "Bench top CUT&RUN with antibodies-online CUT&RUN Sets (protocols.io.bdwni7de)". protocols.io. doi:10.17504/protocols.io.bdwni7de.
Zambanini, Gianluca; Nordin, Anna; Jonasson, Mattias; Pagella, Pierfrancesco; Cantù, Claudio (1 December 2022). "A new CUT&RUN low volume-urea (LoV-U) protocol optimized for transcriptional co-factors uncovers Wnt/β-catenin tissue-specific genomic targets". Development. 149 (23). doi:10.1242/dev.201124. PMC 10112916. PMID 36355069. S2CID 253445603.
Huang P, Keller CA, Giardine B, Grevet JD, Davies JO, Hughes JR, Kurita R, Nakamura Y, Hardison RC, Blobel GA (August 2017). "Comparative analysis of three-dimensional chromosomal architecture identifies a novel fetal hemoglobin regulatory element". Genes & Development. 31 (16): 1704–1713. doi:10.1101/gad.303461.117. PMC 5647940. PMID 28916711.
Liu N, Hargreaves VV, Zhu Q, Kurland JV, Hong J, Kim W, Sher F, Macias-Trevino C, Rogers JM, Kurita R, Nakamura Y, Yuan GC, Bauer DE, Xu J, Bulyk ML, Orkin SH (April 2018). "Direct Promoter Repression by BCL11A Controls the Fetal to Adult Hemoglobin Switch". Cell. 173 (2): 430–442.e17. doi:10.1016/j.cell.2018.03.016. PMC 5889339. PMID 29606353.
Ramachandran S, Ahmad K, Henikoff S (December 2017). "Transcription and Remodeling Produce Asymmetrically Unwrapped Nucleosomal Intermediates". Molecular Cell. 68 (6): 1038–1053.e4. doi:10.1016/j.molcel.2017.11.015. PMC 6421108. PMID 29225036.
Kasinathan S, Henikoff S (April 2017). "Non-B-Form DNA Is Enriched at Centromeres". Molecular Biology and Evolution. 35 (4): 949–962. doi:10.1093/molbev/msy010. PMC 5889037. PMID 29365169.
Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS (2008). "Model-based analysis of ChIP-Seq (MACS)". Genome Biology. 9 (9): R137. doi:10.1186/gb-2008-9-9-r137. PMC 2592715. PMID 18798982.
Meers MP, Tenenbaum D, Henikoff S (July 2019). "Peak calling by Sparse Enrichment Analysis for CUT&RUN chromatin profiling". Epigenetics & Chromatin. 12 (1): 42. doi:10.1186/s13072-019-0287-4. PMC 6624997. PMID 31300027.
Bailey T, Krajewski P, Ladunga I, Lefebvre C, Li Q, Liu T, Madrigal P, Taslim C, Zhang J (2013). "Practical guidelines for the comprehensive analysis of ChIP-seq data". PLOS Computational Biology. 9 (11): e1003326. Bibcode:2013PLSCB...9E3326B. doi:10.1371/journal.pcbi.1003326. PMC 3828144. PMID 24244136.

epicypher.com

"Still Using ChIP? Try CUT&RUN for Enhanced Chromatin Profiling". EpiCypher. Retrieved 2019-07-26.

fredhutch.org

"Lay off the ChIPs: CUT&RUN instead". Fred Hutchinson Cancer Research Center. 20 February 2017.

harvard.edu

ui.adsabs.harvard.edu

Bailey T, Krajewski P, Ladunga I, Lefebvre C, Li Q, Liu T, Madrigal P, Taslim C, Zhang J (2013). "Practical guidelines for the comprehensive analysis of ChIP-seq data". PLOS Computational Biology. 9 (11): e1003326. Bibcode:2013PLSCB...9E3326B. doi:10.1371/journal.pcbi.1003326. PMC 3828144. PMID 24244136.

nih.gov

ncbi.nlm.nih.gov

Meyer CA, Liu XS (November 2014). "Identifying and mitigating bias in next-generation sequencing methods for chromatin biology". Nature Reviews. Genetics. 15 (11): 709–21. doi:10.1038/nrg3788. PMC 4473780. PMID 25223782.
Baranello L, Kouzine F, Sanford S, Levens D (May 2016). "ChIP bias as a function of cross-linking time". Chromosome Research. 24 (2): 175–81. doi:10.1007/s10577-015-9509-1. PMC 4860130. PMID 26685864.
He C, Bonasio R (February 2017). "A cut above". eLife. 6. doi:10.7554/eLife.25000. PMC 5310838. PMID 28199181.
Skene PJ, Henikoff S (January 2017). "An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites". eLife. 6. doi:10.7554/eLife.21856. PMC 5310842. PMID 28079019.
Zambanini, Gianluca; Nordin, Anna; Jonasson, Mattias; Pagella, Pierfrancesco; Cantù, Claudio (1 December 2022). "A new CUT&RUN low volume-urea (LoV-U) protocol optimized for transcriptional co-factors uncovers Wnt/β-catenin tissue-specific genomic targets". Development. 149 (23). doi:10.1242/dev.201124. PMC 10112916. PMID 36355069. S2CID 253445603.
Huang P, Keller CA, Giardine B, Grevet JD, Davies JO, Hughes JR, Kurita R, Nakamura Y, Hardison RC, Blobel GA (August 2017). "Comparative analysis of three-dimensional chromosomal architecture identifies a novel fetal hemoglobin regulatory element". Genes & Development. 31 (16): 1704–1713. doi:10.1101/gad.303461.117. PMC 5647940. PMID 28916711.
Liu N, Hargreaves VV, Zhu Q, Kurland JV, Hong J, Kim W, Sher F, Macias-Trevino C, Rogers JM, Kurita R, Nakamura Y, Yuan GC, Bauer DE, Xu J, Bulyk ML, Orkin SH (April 2018). "Direct Promoter Repression by BCL11A Controls the Fetal to Adult Hemoglobin Switch". Cell. 173 (2): 430–442.e17. doi:10.1016/j.cell.2018.03.016. PMC 5889339. PMID 29606353.
Ramachandran S, Ahmad K, Henikoff S (December 2017). "Transcription and Remodeling Produce Asymmetrically Unwrapped Nucleosomal Intermediates". Molecular Cell. 68 (6): 1038–1053.e4. doi:10.1016/j.molcel.2017.11.015. PMC 6421108. PMID 29225036.
Kasinathan S, Henikoff S (April 2017). "Non-B-Form DNA Is Enriched at Centromeres". Molecular Biology and Evolution. 35 (4): 949–962. doi:10.1093/molbev/msy010. PMC 5889037. PMID 29365169.
Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS (2008). "Model-based analysis of ChIP-Seq (MACS)". Genome Biology. 9 (9): R137. doi:10.1186/gb-2008-9-9-r137. PMC 2592715. PMID 18798982.
Meers MP, Tenenbaum D, Henikoff S (July 2019). "Peak calling by Sparse Enrichment Analysis for CUT&RUN chromatin profiling". Epigenetics & Chromatin. 12 (1): 42. doi:10.1186/s13072-019-0287-4. PMC 6624997. PMID 31300027.
Bailey T, Krajewski P, Ladunga I, Lefebvre C, Li Q, Liu T, Madrigal P, Taslim C, Zhang J (2013). "Practical guidelines for the comprehensive analysis of ChIP-seq data". PLOS Computational Biology. 9 (11): e1003326. Bibcode:2013PLSCB...9E3326B. doi:10.1371/journal.pcbi.1003326. PMC 3828144. PMID 24244136.

pubmed.ncbi.nlm.nih.gov

Meyer CA, Liu XS (November 2014). "Identifying and mitigating bias in next-generation sequencing methods for chromatin biology". Nature Reviews. Genetics. 15 (11): 709–21. doi:10.1038/nrg3788. PMC 4473780. PMID 25223782.
Baranello L, Kouzine F, Sanford S, Levens D (May 2016). "ChIP bias as a function of cross-linking time". Chromosome Research. 24 (2): 175–81. doi:10.1007/s10577-015-9509-1. PMC 4860130. PMID 26685864.
He C, Bonasio R (February 2017). "A cut above". eLife. 6. doi:10.7554/eLife.25000. PMC 5310838. PMID 28199181.
Skene PJ, Henikoff S (January 2017). "An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites". eLife. 6. doi:10.7554/eLife.21856. PMC 5310842. PMID 28079019.
Zambanini, Gianluca; Nordin, Anna; Jonasson, Mattias; Pagella, Pierfrancesco; Cantù, Claudio (1 December 2022). "A new CUT&RUN low volume-urea (LoV-U) protocol optimized for transcriptional co-factors uncovers Wnt/β-catenin tissue-specific genomic targets". Development. 149 (23). doi:10.1242/dev.201124. PMC 10112916. PMID 36355069. S2CID 253445603.
Huang P, Keller CA, Giardine B, Grevet JD, Davies JO, Hughes JR, Kurita R, Nakamura Y, Hardison RC, Blobel GA (August 2017). "Comparative analysis of three-dimensional chromosomal architecture identifies a novel fetal hemoglobin regulatory element". Genes & Development. 31 (16): 1704–1713. doi:10.1101/gad.303461.117. PMC 5647940. PMID 28916711.
Liu N, Hargreaves VV, Zhu Q, Kurland JV, Hong J, Kim W, Sher F, Macias-Trevino C, Rogers JM, Kurita R, Nakamura Y, Yuan GC, Bauer DE, Xu J, Bulyk ML, Orkin SH (April 2018). "Direct Promoter Repression by BCL11A Controls the Fetal to Adult Hemoglobin Switch". Cell. 173 (2): 430–442.e17. doi:10.1016/j.cell.2018.03.016. PMC 5889339. PMID 29606353.
Ramachandran S, Ahmad K, Henikoff S (December 2017). "Transcription and Remodeling Produce Asymmetrically Unwrapped Nucleosomal Intermediates". Molecular Cell. 68 (6): 1038–1053.e4. doi:10.1016/j.molcel.2017.11.015. PMC 6421108. PMID 29225036.
Kasinathan S, Henikoff S (April 2017). "Non-B-Form DNA Is Enriched at Centromeres". Molecular Biology and Evolution. 35 (4): 949–962. doi:10.1093/molbev/msy010. PMC 5889037. PMID 29365169.
Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS (2008). "Model-based analysis of ChIP-Seq (MACS)". Genome Biology. 9 (9): R137. doi:10.1186/gb-2008-9-9-r137. PMC 2592715. PMID 18798982.
Meers MP, Tenenbaum D, Henikoff S (July 2019). "Peak calling by Sparse Enrichment Analysis for CUT&RUN chromatin profiling". Epigenetics & Chromatin. 12 (1): 42. doi:10.1186/s13072-019-0287-4. PMC 6624997. PMID 31300027.
Bailey T, Krajewski P, Ladunga I, Lefebvre C, Li Q, Liu T, Madrigal P, Taslim C, Zhang J (2013). "Practical guidelines for the comprehensive analysis of ChIP-seq data". PLOS Computational Biology. 9 (11): e1003326. Bibcode:2013PLSCB...9E3326B. doi:10.1371/journal.pcbi.1003326. PMC 3828144. PMID 24244136.

protocols.io

Janssens, Derek; Henikoff, Steven (9 May 2019). "CUT&RUN: Targeted in situ genome-wide profiling with high efficiency for low cell numbers v3 (protocols.io.zcpf2vn)". protocols.io. doi:10.17504/protocols.io.zcpf2vn.
Ahmad, Kami (2 December 2018). "CUT&RUN with Drosophila tissues v1 (protocols.io.umfeu3n)". protocols.io. doi:10.17504/protocols.io.umfeu3n. S2CID 216840246.
Janssens, Derek; Ahmad, Kami; Henikoff, Steven (27 November 2018). "AutoCUT&RUN: genome-wide profiling of chromatin proteins in a 96 well format on a Biomek v1 (protocols.io.ufeetje)". protocols.io. doi:10.17504/protocols.io.ufeetje. S2CID 216872521.
antibodies-online (19 March 2020). "Bench top CUT&RUN with antibodies-online CUT&RUN Sets (protocols.io.bdwni7de)". protocols.io. doi:10.17504/protocols.io.bdwni7de.

semanticscholar.org

api.semanticscholar.org

Ahmad, Kami (2 December 2018). "CUT&RUN with Drosophila tissues v1 (protocols.io.umfeu3n)". protocols.io. doi:10.17504/protocols.io.umfeu3n. S2CID 216840246.
Janssens, Derek; Ahmad, Kami; Henikoff, Steven (27 November 2018). "AutoCUT&RUN: genome-wide profiling of chromatin proteins in a 96 well format on a Biomek v1 (protocols.io.ufeetje)". protocols.io. doi:10.17504/protocols.io.ufeetje. S2CID 216872521.
Zambanini, Gianluca; Nordin, Anna; Jonasson, Mattias; Pagella, Pierfrancesco; Cantù, Claudio (1 December 2022). "A new CUT&RUN low volume-urea (LoV-U) protocol optimized for transcriptional co-factors uncovers Wnt/β-catenin tissue-specific genomic targets". Development. 149 (23). doi:10.1242/dev.201124. PMC 10112916. PMID 36355069. S2CID 253445603.