3XFlag-pA-Tn5-Fl Citations (29)
Originally described in: CUT&Tag for efficient epigenomic profiling of small samples and single cells.Kaya-Okur HS, Wu SJ, Codomo CA, Pledger ES, Bryson TD, Henikoff JG, Ahmad K, Henikoff S Nat Commun. 2019 Apr 29;10(1):1930. doi: 10.1038/s41467-019-09982-5. PubMed Journal
Articles Citing 3XFlag-pA-Tn5-Fl
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| The Polycomb group protein Ring1 regulates dorsoventral patterning of the mouse telencephalon. Eto H, Kishi Y, Yakushiji-Kaminatsui N, Sugishita H, Utsunomiya S, Koseki H, Gotoh Y. Nat Commun. 2020 Nov 11;11(1):5709. doi: 10.1038/s41467-020-19556-5. PubMed |
Genomic profiling of native R loops with a DNA-RNA hybrid recognition sensor.
Wang K, Wang H, Li C, Yin Z, Xiao R, Li Q, Xiang Y, Wang W, Huang J, Chen L, Fang P, Liang K.
Sci Adv. 2021 Feb 17;7(8). pii: 7/8/eabe3516. doi: 10.1126/sciadv.abe3516. Print 2021 Feb.
PubMed
Associated Plasmids |
| UTX promotes CD8(+) T cell-mediated antiviral defenses but reduces T cell durability. Mitchell JE, Lund MM, Starmer J, Ge K, Magnuson T, Shpargel KB, Whitmire JK. Cell Rep. 2021 Apr 13;35(2):108966. doi: 10.1016/j.celrep.2021.108966. PubMed |
| Chromatin and transcription factor profiling in rare stem cell populations using CUT&Tag. Li Y, Nakka K, Olender T, Gingras-Gelinas P, Wong MM, Robinson DCL, Bandukwala H, Palii CG, Neyret O, Brand M, Blais A, Dilworth FJ. STAR Protoc. 2021 Aug 19;2(3):100751. doi: 10.1016/j.xpro.2021.100751. eCollection 2021 Sep 17. PubMed |
| Variant PCGF1-PRC1 links PRC2 recruitment with differentiation-associated transcriptional inactivation at target genes. Sugishita H, Kondo T, Ito S, Nakayama M, Yakushiji-Kaminatsui N, Kawakami E, Koseki Y, Ohinata Y, Sharif J, Harachi M, Blackledge NP, Klose RJ, Koseki H. Nat Commun. 2021 Sep 9;12(1):5341. doi: 10.1038/s41467-021-24894-z. PubMed |
| Defining Proximity Proteomics of Histone Modifications by Antibody-mediated Protein A-APEX2 Labeling. Li X, Zhou J, Zhao W, Wen Q, Wang W, Peng H, Gao Y, Bouchonville KJ, Offer SM, Chan K, Wang Z, Li N, Gan H. Genomics Proteomics Bioinformatics. 2021 Sep 20. pii: S1672-0229(21)00182-0. doi: 10.1016/j.gpb.2021.09.003. PubMed |
| Distal and proximal cis-regulatory elements sense X chromosome dosage and developmental state at the Xist locus. Gjaltema RAF, Schwammle T, Kautz P, Robson M, Schopflin R, Ravid Lustig L, Brandenburg L, Dunkel I, Vechiatto C, Ntini E, Mutzel V, Schmiedel V, Marsico A, Mundlos S, Schulz EG. Mol Cell. 2022 Jan 6;82(1):190-208.e17. doi: 10.1016/j.molcel.2021.11.023. Epub 2021 Dec 20. PubMed |
| H3K27me3 Demethylase UTX Restrains Plasma Cell Formation. Kania AK, Price MJ, George-Alexander LE, Patterson DG, Hicks SL, Scharer CD, Boss JM. J Immunol. 2022 Apr 15;208(8):1873-1885. doi: 10.4049/jimmunol.2100948. Epub 2022 Mar 28. PubMed |
| MOZ and Menin-MLL Complexes Are Complementary Regulators of Chromatin Association and Transcriptional Output in Gastrointestinal Stromal Tumor. Hemming ML, Benson MR, Loycano MA, Anderson JA, Andersen JL, Taddei ML, Krivtsov AV, Aubrey BJ, Cutler JA, Hatton C, Sicinska E, Armstrong SA. Cancer Discov. 2022 Jul 6;12(7):1804-1823. doi: 10.1158/2159-8290.CD-21-0646. PubMed |
| Thymic epithelial cells co-opt lineage-defining transcription factors to eliminate autoreactive T cells. Michelson DA, Hase K, Kaisho T, Benoist C, Mathis D. Cell. 2022 Jul 7;185(14):2542-2558.e18. doi: 10.1016/j.cell.2022.05.018. Epub 2022 Jun 16. PubMed |
| Tip60-mediated H2A.Z acetylation promotes neuronal fate specification and bivalent gene activation. Janas JA, Zhang L, Luu JH, Demeter J, Meng L, Marro SG, Mall M, Mooney NA, Schaukowitch K, Ng YH, Yang N, Huang Y, Neumayer G, Gozani O, Elias JE, Jackson PK, Wernig M. Mol Cell. 2022 Dec 15;82(24):4627-4646.e14. doi: 10.1016/j.molcel.2022.11.002. Epub 2022 Nov 22. PubMed |
| Reconstituting human somitogenesis in vitro. Yamanaka Y, Hamidi S, Yoshioka-Kobayashi K, Munira S, Sunadome K, Zhang Y, Kurokawa Y, Ericsson R, Mieda A, Thompson JL, Kerwin J, Lisgo S, Yamamoto T, Moris N, Martinez-Arias A, Tsujimura T, Alev C. Nature. 2023 Feb;614(7948):509-520. doi: 10.1038/s41586-022-05649-2. Epub 2022 Dec 21. PubMed |
| Simultaneous profiling of histone modifications and DNA methylation via nanopore sequencing. Yue X, Xie Z, Li M, Wang K, Li X, Zhang X, Yan J, Yin Y. Nat Commun. 2022 Dec 24;13(1):7939. doi: 10.1038/s41467-022-35650-2. PubMed |
| A Cluster of Evolutionarily Recent KRAB Zinc Finger Proteins Protects Cancer Cells from Replicative Stress-Induced Inflammation. Martins F, Rosspopoff O, Carlevaro-Fita J, Forey R, Offner S, Planet E, Pulver C, Pak H, Huber F, Michaux J, Bassani-Sternberg M, Turelli P, Trono D. Cancer Res. 2024 Mar 15;84(6):808-826. doi: 10.1158/0008-5472.CAN-23-1237. PubMed |
| Atypical heat shock transcription factor HSF5 is critical for male meiotic prophase under non-stress conditions. Yoshimura S, Shimada R, Kikuchi K, Kawagoe S, Abe H, Iisaka S, Fujimura S, Yasunaga KI, Usuki S, Tani N, Ohba T, Kondoh E, Saio T, Araki K, Ishiguro KI. Nat Commun. 2024 Apr 29;15(1):3330. doi: 10.1038/s41467-024-47601-0. PubMed |
| YY1 is involved in homologous recombination inhibition at guanine quadruplex sites in human cells. Cui X, Zhang C, Fu C, Hu J, Li T, Li L. Nucleic Acids Res. 2024 Jul 22;52(13):7401-7413. doi: 10.1093/nar/gkae502. PubMed |
| Spatial 3D genome organization controls the activity of bivalent chromatin during human neurogenesis. Ahanger SH, Zhang C, Semenza ER, Gil E, Cole MA, Wang L, Kriegstein AR, Lim DA. bioRxiv [Preprint]. 2024 Aug 1:2024.08.01.606248. doi: 10.1101/2024.08.01.606248. PubMed |
| Clusters of lineage-specific genes are anchored by ZNF274 in repressive perinucleolar compartments. Begnis M, Duc J, Offner S, Grun D, Sheppard S, Rosspopoff O, Trono D. Sci Adv. 2024 Sep 13;10(37):eado1662. doi: 10.1126/sciadv.ado1662. Epub 2024 Sep 13. PubMed |
Single-cell mapping of regulatory DNA:Protein interactions.
Chi WY, Yoon SH, Mekerishvili L, Ganesan S, Potenski C, Izzo F, Landau D, Raimondi I.
bioRxiv [Preprint]. 2025 Jan 2:2024.12.31.630903. doi: 10.1101/2024.12.31.630903.
PubMed
Associated Plasmids |
| An eRNA transcription checkpoint for diverse signal-dependent enhancer activation programs. Wang L, Yuan W, Gamliel A, Ma W, Lee S, Tan Y, Chen Z, Taylor H, Ohgi K, Oh S, Aggarwal AK, Rosenfeld MG. Nat Genet. 2025 Apr;57(4):962-972. doi: 10.1038/s41588-025-02138-w. Epub 2025 Apr 4. PubMed |
| Iron-Dependent JMJD1A-Mediated Demethylation of H3K9me2 Regulates Gene Expression During Adipogenesis in a Spatial Genome Organization-Dependent Manner. Masuda S, Komatsu T, Atia S, Suzuki T, Hayashi M, Toyoda A, Kimura H, Inagaki T. Genes Cells. 2025 May;30(3):e70023. doi: 10.1111/gtc.70023. PubMed |
| Tissular chromatin-state cartography based on double-barcoded DNA arrays that capture unloaded PA-Tn5 transposase. Mendoza-Ferri MG, Lozachmeur G, Duvina M, Perret L, Merciris D, Gigout A, Mendoza-Parra MA. Genome Res. 2025 Jul 1;35(7):1633-1645. doi: 10.1101/gr.280305.124. PubMed |
| IT-scC&T-seq streamlines scalable, parallel profiling of protein-DNA interactions in single cells. Ma J, Jin W, Rong L, Gao Z, Hazrat Z, Shakhawat HM, Long F, Zhang Z, Huang J, Lu X, Jin G, Zhou Z. Genome Biol. 2025 Jul 7;26(1):196. doi: 10.1186/s13059-025-03661-z. PubMed |
| Antibody-Mediated Protein A-APEX2 Labeling (AMAPEX) for Proximity Proteome Exploration. Zhou J, Li X, Wen Q, Gan H. Methods Mol Biol. 2025;2953:295-310. doi: 10.1007/978-1-0716-4694-6_19. PubMed |
| DynaTag for efficient mapping of transcription factors in low-input samples and at single-cell resolution. Hunold P, Pizzolato G, Heramvand N, Kaiser L, Barbiera G, van Ray O, Thomas R, George J, Peifer M, Hansel-Hertsch R. Nat Commun. 2025 Jul 28;16(1):6585. doi: 10.1038/s41467-025-61797-9. PubMed |
| NanoTag is an improved method to map interactions between DNA and proteins not requiring IgG. Dimitriu MA, Arzate-Mejia RG, Steg LC, Germain PL, Mansuy IM. Sci Rep. 2025 Aug 6;15(1):28672. doi: 10.1038/s41598-025-13316-5. PubMed |
| Combinatorial profiling of multiple histone modifications and transcriptome in single cells using scMTR-seq. Wang Y, Li J, Malcolm AA, Mansfield W, Clark SJ, Argelaguet R, Biggins L, Acton RJ, Andrews S, Reik W, Kelsey G, Rugg-Gunn PJ. Sci Adv. 2025 Aug 8;11(32):eadu3308. doi: 10.1126/sciadv.adu3308. Epub 2025 Aug 6. PubMed |
| Cancer cells subvert the primate-specific KRAB zinc finger protein ZNF93 to control APOBEC3B. Forey R, Raclot C, Pulver C, Rosspopoff O, Offner S, Duc J, Planet E, Martins F, Turelli P, Trono D. Proc Natl Acad Sci U S A. 2025 Aug 26;122(34):e2505021122. doi: 10.1073/pnas.2505021122. Epub 2025 Aug 19. PubMed |
| Decoding transcriptional identity during neuron-astroglia cell fate driven by RAR-specific agonists. Galindo-Albarran A, Koshy A, Mendoza-Ferri MG, Mendoza-Parra MA. NAR Mol Med. 2025 May 7;2(2):ugaf018. doi: 10.1093/narmme/ugaf018. eCollection 2025 Apr. PubMed |
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