@article{20924,
  abstract     = {Pioneer transcription factors (TFs) possess the ability to read out DNA motifs embedded within nucleosomes, driving changes in gene expression during cellular differentiation and reprogramming. Here, we present selected engagement on nucleosome sequencing (SeEN-seq), a protocol designed to systematically identify potential TF-binding sites on the nucleosome. We describe steps for nucleosome library assembly, SeEN-seq assay, and cryoelectron microscopy (cryo-EM) sample preparation. This protocol facilitates the preparation of homogeneous pioneer TF-nucleosome complexes for cryo-EM structure determination using single-particle analysis.
For complete details on the use and execution of this protocol, please refer to Michael et al.1},
  author       = {Kobayashi, Wataru and Michael, Alicia and Ruangroengkulrith, Siwat and Kümmecke, Maximilian and Tachibana, Kikuë},
  issn         = {2666-1667},
  journal      = {STAR Protocols},
  number       = {1},
  publisher    = {Elsevier},
  title        = {{Protocol for integrative analysis of transcription factor-nucleosome interactions using SeEN-seq and cryo-EM structure determination}},
  doi          = {10.1016/j.xpro.2025.104295},
  volume       = {7},
  year         = {2026},
}

@article{14794,
  abstract     = {Mosaic analysis with double markers (MADM) technology enables the sparse labeling of genetically defined neurons. We present a protocol for time-lapse imaging of cortical projection neuron migration in mice using MADM. We describe steps for the isolation, culturing, and 4D imaging of neuronal dynamics in MADM-labeled brain tissue. While this protocol is compatible with other single-cell labeling methods, the MADM approach provides a genetic platform for the functional assessment of cell-autonomous candidate gene function and the relative contribution of non-cell-autonomous effects.

For complete details on the use and execution of this protocol, please refer to Hansen et al. (2022),1 Contreras et al. (2021),2 and Amberg and Hippenmeyer (2021).3},
  author       = {Hansen, Andi H and Hippenmeyer, Simon},
  issn         = {2666-1667},
  journal      = {STAR Protocols},
  number       = {1},
  publisher    = {Elsevier},
  title        = {{Time-lapse imaging of cortical projection neuron migration in mice using mosaic analysis with double markers}},
  doi          = {10.1016/j.xpro.2023.102795},
  volume       = {5},
  year         = {2024},
}

@article{17187,
  abstract     = {The generation of diverse cell types during development is fundamental to brain
functions. We outline a protocol to quantitatively assess the clonal output of individual neural progenitors using mosaic analysis with double markers (MADM) in
mice. We first describe steps to acquire and reconstruct adult MADM clones in
the superior colliculus. Then we detail analysis pipelines to determine clonal
composition and architecture. This protocol enables the buildup of quantitative
frameworks of lineage progression with precise spatial resolution in the brain.
For complete details on the use and execution of this protocol, please refer to
Cheung et al.1},
  author       = {Cheung, Giselle T and Streicher, Carmen and Hippenmeyer, Simon},
  issn         = {2666-1667},
  journal      = {STAR Protocols},
  number       = {3},
  publisher    = {Elsevier},
  title        = {{Protocol for quantitative reconstruction of cell lineage using mosaic analysis with double markers in mice}},
  doi          = {10.1016/j.xpro.2024.103157},
  volume       = {5},
  year         = {2024},
}

@article{17232,
  abstract     = {The lineage relationship of clonally-related cells offers important insights into the ontogeny and cytoarchitecture of the brain in health and disease. Here, we provide a protocol to concurrently assess cell lineage relationship and cell-type identity among clonally-related cells in situ. We first describe the preparation and screening of acute brain slices containing clonally-related cells labeled using mosaic analysis with double markers (MADM). We then outline steps to collect RNA from individual cells for downstream applications and cell-type identification using RNA sequencing.
For complete details on the use and execution of this protocol, please refer to Cheung et al.
1},
  author       = {Cheung, Giselle T and Pauler, Florian and Koppensteiner, Peter and Hippenmeyer, Simon},
  issn         = {2666-1667},
  journal      = {STAR Protocols},
  number       = {3},
  publisher    = {Elsevier},
  title        = {{Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq}},
  doi          = {10.1016/j.xpro.2024.103168},
  volume       = {5},
  year         = {2024},
}

@article{18601,
  abstract     = {Geometrically controlled stem cell differentiation promotes reproducible pattern formation. Here, we present a protocol to fabricate elastomeric stencils for patterned stem cell differentiation. We describe procedures for using photolithography to produce molds, followed by molding polydimethylsiloxane (PDMS) to obtain stencils with through holes. We then provide instructions for culturing cells on stencils and, finally, removing stencils to allow colony growth and cell migration. This approach yields reproducible two-dimensional organoids tailored for quantitative studies of growth and pattern formation.
For complete details on the use and execution of this protocol, please refer to Lehr et al.1},
  author       = {Rus, Stefanie and Merrin, Jack and Kulig, Monika Aleksandra and Minchington, Thomas and Kicheva, Anna},
  issn         = {2666-1667},
  journal      = {STAR Protocols},
  number       = {4},
  publisher    = {Elsevier},
  title        = {{Protocol for fabricating elastomeric stencils for patterned stem cell differentiation}},
  doi          = {10.1016/j.xpro.2024.103187},
  volume       = {5},
  year         = {2024},
}

@article{10321,
  abstract     = {Mosaic analysis with double markers (MADM) technology enables the generation of genetic mosaic tissue in mice. MADM enables concomitant fluorescent cell labeling and introduction of a mutation of a gene of interest with single-cell resolution. This protocol highlights major steps for the generation of genetic mosaic tissue and the isolation and processing of respective tissues for downstream histological analysis. For complete details on the use and execution of this protocol, please refer to Contreras et al. (2021).},
  author       = {Amberg, Nicole and Hippenmeyer, Simon},
  issn         = {2666-1667},
  journal      = {STAR Protocols},
  number       = {4},
  publisher    = {Cell Press},
  title        = {{Genetic mosaic dissection of candidate genes in mice using mosaic analysis with double markers}},
  doi          = {10.1016/j.xpro.2021.100939},
  volume       = {2},
  year         = {2021},
}

@article{10565,
  abstract     = {Enzymatic digestion of the extracellular matrix with chondroitinase-ABC reinstates juvenile-like plasticity in the adult cortex as it also disassembles the perineuronal nets (PNNs). The disadvantage of the enzyme is that it must be applied intracerebrally and it degrades the ECM for several weeks. Here, we provide two minimally invasive and transient protocols for microglia-enabled PNN disassembly in mouse cortex: repeated treatment with ketamine-xylazine-acepromazine (KXA) anesthesia and 60-Hz light entrainment. We also discuss how to analyze PNNs within microglial endosomes-lysosomes. For complete details on the use and execution of this protocol, please refer to Venturino et al. (2021).},
  author       = {Venturino, Alessandro and Siegert, Sandra},
  issn         = {2666-1667},
  journal      = {STAR Protocols},
  number       = {4},
  publisher    = {Elsevier},
  title        = {{Minimally invasive protocols and quantification for microglia-mediated perineuronal net disassembly in mouse brain}},
  doi          = {10.1016/j.xpro.2021.101012},
  volume       = {2},
  year         = {2021},
}