---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '20924'
abstract:
- lang: eng
  text: "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.\r\nFor complete
    details on the use and execution of this protocol, please refer to Michael et
    al.1"
acknowledgement: We thank R.H. Kim, A. Casper, and R. Gautsch for sequencing at the
  NGS facility (RRID:SCR_025746). K.T. is an Honorary Professor at the Department
  of Biology, Ludwig-Maximilians-University, Munich, Germany. This study was funded
  by European Research Council grant ERC-CoG-818556 TotipotentZygotChrom (K.T.), Max
  Planck Society (K.T.), and ERC Starting Grant “ChromaChrono” 101162145 (A.K.M.).
article_number: '104295'
article_processing_charge: Yes
article_type: original
author:
- first_name: Wataru
  full_name: Kobayashi, Wataru
  last_name: Kobayashi
- first_name: Alicia
  full_name: Michael, Alicia
  id: 6437c950-2a03-11ee-914d-d6476dd7b75c
  last_name: Michael
  orcid: 0000-0002-6080-839X
- first_name: Siwat
  full_name: Ruangroengkulrith, Siwat
  last_name: Ruangroengkulrith
- first_name: Maximilian
  full_name: Kümmecke, Maximilian
  last_name: Kümmecke
- first_name: Kikuë
  full_name: Tachibana, Kikuë
  last_name: Tachibana
citation:
  ama: Kobayashi W, Michael AK, Ruangroengkulrith S, Kümmecke M, Tachibana K. Protocol
    for integrative analysis of transcription factor-nucleosome interactions using
    SeEN-seq and cryo-EM structure determination. <i>STAR Protocols</i>. 2026;7(1).
    doi:<a href="https://doi.org/10.1016/j.xpro.2025.104295">10.1016/j.xpro.2025.104295</a>
  apa: Kobayashi, W., Michael, A. K., Ruangroengkulrith, S., Kümmecke, M., &#38; Tachibana,
    K. (2026). Protocol for integrative analysis of transcription factor-nucleosome
    interactions using SeEN-seq and cryo-EM structure determination. <i>STAR Protocols</i>.
    Elsevier. <a href="https://doi.org/10.1016/j.xpro.2025.104295">https://doi.org/10.1016/j.xpro.2025.104295</a>
  chicago: Kobayashi, Wataru, Alicia K. Michael, Siwat Ruangroengkulrith, Maximilian
    Kümmecke, and Kikuë Tachibana. “Protocol for Integrative Analysis of Transcription
    Factor-Nucleosome Interactions Using SeEN-Seq and Cryo-EM Structure Determination.”
    <i>STAR Protocols</i>. Elsevier, 2026. <a href="https://doi.org/10.1016/j.xpro.2025.104295">https://doi.org/10.1016/j.xpro.2025.104295</a>.
  ieee: W. Kobayashi, A. K. Michael, S. Ruangroengkulrith, M. Kümmecke, and K. Tachibana,
    “Protocol for integrative analysis of transcription factor-nucleosome interactions
    using SeEN-seq and cryo-EM structure determination,” <i>STAR Protocols</i>, vol.
    7, no. 1. Elsevier, 2026.
  ista: Kobayashi W, Michael AK, Ruangroengkulrith S, Kümmecke M, Tachibana K. 2026.
    Protocol for integrative analysis of transcription factor-nucleosome interactions
    using SeEN-seq and cryo-EM structure determination. STAR Protocols. 7(1), 104295.
  mla: Kobayashi, Wataru, et al. “Protocol for Integrative Analysis of Transcription
    Factor-Nucleosome Interactions Using SeEN-Seq and Cryo-EM Structure Determination.”
    <i>STAR Protocols</i>, vol. 7, no. 1, 104295, Elsevier, 2026, doi:<a href="https://doi.org/10.1016/j.xpro.2025.104295">10.1016/j.xpro.2025.104295</a>.
  short: W. Kobayashi, A.K. Michael, S. Ruangroengkulrith, M. Kümmecke, K. Tachibana,
    STAR Protocols 7 (2026).
corr_author: '1'
das_tickbox: '1'
dataavailabilitystatement: Raw SeEN-seq data of ESRRB nucleosome binding have been
  deposited on the Sequence Read Achieve database under the accession PRJNA1305216.
  Example analysis scripts and input files for SeEN-seq analysis can be found at https://doi.org/10.5281/zenodo.17665082.
date_created: 2026-01-04T23:01:33Z
date_published: 2026-03-20T00:00:00Z
date_updated: 2026-07-23T06:34:37Z
day: '20'
ddc:
- '570'
department:
- _id: AlMi
doi: 10.1016/j.xpro.2025.104295
external_id:
  pmid:
  - '41455105'
file:
- access_level: open_access
  checksum: cf04b061a48548a649e6a2435bf120db
  content_type: application/pdf
  creator: dernst
  date_created: 2026-07-23T06:33:24Z
  date_updated: 2026-07-23T06:33:24Z
  file_id: '22389'
  file_name: 2026_StarProtocols_Kobayashi.pdf
  file_size: 5531906
  relation: main_file
  success: 1
file_date_updated: 2026-07-23T06:33:24Z
has_accepted_license: '1'
intvolume: '         7'
issue: '1'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 9136c684-16d5-11f0-9cad-91c0177b365f
  grant_number: '101162145'
  name: Circadian structural transitions of chromatin
publication: STAR Protocols
publication_identifier:
  eissn:
  - 2666-1667
publication_status: published
publisher: Elsevier
quality_controlled: '1'
researchdata_availability: yes
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Protocol for integrative analysis of transcription factor-nucleosome interactions
  using SeEN-seq and cryo-EM structure determination
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2026'
...
---
_id: '14794'
abstract:
- lang: eng
  text: "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.\r\n\r\nFor 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"
acknowledged_ssus:
- _id: Bio
- _id: PreCl
acknowledgement: We thank Florian Pauler for discussion and his expert technical support.
  This research was supported by the Scientific Service Units (SSU) at IST Austria
  through resources provided by the Imaging and Optics Facility (IOF) and Preclinical
  Facility (PCF). A.H.H. was a recipient of a DOC Fellowship (24812) of the Austrian
  Academy of Sciences.
article_number: '102795'
article_processing_charge: Yes
article_type: review
author:
- first_name: Andi H
  full_name: Hansen, Andi H
  id: 38853E16-F248-11E8-B48F-1D18A9856A87
  last_name: Hansen
- first_name: Simon
  full_name: Hippenmeyer, Simon
  id: 37B36620-F248-11E8-B48F-1D18A9856A87
  last_name: Hippenmeyer
  orcid: 0000-0003-2279-1061
citation:
  ama: Hansen AH, Hippenmeyer S. Time-lapse imaging of cortical projection neuron
    migration in mice using mosaic analysis with double markers. <i>STAR Protocols</i>.
    2024;5(1). doi:<a href="https://doi.org/10.1016/j.xpro.2023.102795">10.1016/j.xpro.2023.102795</a>
  apa: Hansen, A. H., &#38; Hippenmeyer, S. (2024). Time-lapse imaging of cortical
    projection neuron migration in mice using mosaic analysis with double markers.
    <i>STAR Protocols</i>. Elsevier. <a href="https://doi.org/10.1016/j.xpro.2023.102795">https://doi.org/10.1016/j.xpro.2023.102795</a>
  chicago: Hansen, Andi H, and Simon Hippenmeyer. “Time-Lapse Imaging of Cortical
    Projection Neuron Migration in Mice Using Mosaic Analysis with Double Markers.”
    <i>STAR Protocols</i>. Elsevier, 2024. <a href="https://doi.org/10.1016/j.xpro.2023.102795">https://doi.org/10.1016/j.xpro.2023.102795</a>.
  ieee: A. H. Hansen and S. Hippenmeyer, “Time-lapse imaging of cortical projection
    neuron migration in mice using mosaic analysis with double markers,” <i>STAR Protocols</i>,
    vol. 5, no. 1. Elsevier, 2024.
  ista: Hansen AH, Hippenmeyer S. 2024. Time-lapse imaging of cortical projection
    neuron migration in mice using mosaic analysis with double markers. STAR Protocols.
    5(1), 102795.
  mla: Hansen, Andi H., and Simon Hippenmeyer. “Time-Lapse Imaging of Cortical Projection
    Neuron Migration in Mice Using Mosaic Analysis with Double Markers.” <i>STAR Protocols</i>,
    vol. 5, no. 1, 102795, Elsevier, 2024, doi:<a href="https://doi.org/10.1016/j.xpro.2023.102795">10.1016/j.xpro.2023.102795</a>.
  short: A.H. Hansen, S. Hippenmeyer, STAR Protocols 5 (2024).
corr_author: '1'
date_created: 2024-01-14T23:00:56Z
date_published: 2024-03-15T00:00:00Z
date_updated: 2025-04-15T07:32:40Z
day: '15'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.1016/j.xpro.2023.102795
external_id:
  pmid:
  - '38165800'
file:
- access_level: open_access
  checksum: 4644d537451c5c114a9d7c7829b65bba
  content_type: application/pdf
  creator: dernst
  date_created: 2024-07-16T12:04:46Z
  date_updated: 2024-07-16T12:04:46Z
  file_id: '17264'
  file_name: 2024_STARProtoc_Hansen.pdf
  file_size: 3758943
  relation: main_file
  success: 1
file_date_updated: 2024-07-16T12:04:46Z
has_accepted_license: '1'
intvolume: '         5'
issue: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 2625A13E-B435-11E9-9278-68D0E5697425
  grant_number: '24812'
  name: Molecular mechanisms of radial neuronal migration
publication: STAR Protocols
publication_identifier:
  eissn:
  - 2666-1667
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
  link:
  - relation: software
    url: http://github.com/hippenmeyerlab
scopus_import: '1'
status: public
title: Time-lapse imaging of cortical projection neuron migration in mice using mosaic
  analysis with double markers
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2024'
...
---
APC_amount: 804 EUR
OA_place: publisher
OA_type: gold
_id: '17187'
abstract:
- lang: eng
  text: "The generation of diverse cell types during development is fundamental to
    brain\r\nfunctions. We outline a protocol to quantitatively assess the clonal
    output of individual neural progenitors using mosaic analysis with double markers
    (MADM) in\r\nmice. We first describe steps to acquire and reconstruct adult MADM
    clones in\r\nthe superior colliculus. Then we detail analysis pipelines to determine
    clonal\r\ncomposition and architecture. This protocol enables the buildup of quantitative\r\nframeworks
    of lineage progression with precise spatial resolution in the brain.\r\nFor complete
    details on the use and execution of this protocol, please refer to\r\nCheung et
    al.1"
acknowledged_ssus:
- _id: Bio
- _id: PreCl
acknowledgement: We thank A. Heger for mouse breeding support. This work was supported
  by the Scientific Service Units of IST Austria through resources provided by the
  Imaging & Optics and Preclinical facilities. G.C. received funding from the European
  Commission (IST plus postdoctoral fellowship); S.H. was funded by ISTA institutional
  funds and the Austrian Science Fund Special Research Programmes (FWF SFB-F78 Neuro
  Stem Modulation).
article_number: '103157'
article_processing_charge: Yes
article_type: original
author:
- first_name: Giselle T
  full_name: Cheung, Giselle T
  id: 471195F6-F248-11E8-B48F-1D18A9856A87
  last_name: Cheung
  orcid: 0000-0001-8457-2572
- first_name: Carmen
  full_name: Streicher, Carmen
  id: 36BCB99C-F248-11E8-B48F-1D18A9856A87
  last_name: Streicher
- first_name: Simon
  full_name: Hippenmeyer, Simon
  id: 37B36620-F248-11E8-B48F-1D18A9856A87
  last_name: Hippenmeyer
  orcid: 0000-0003-2279-1061
citation:
  ama: Cheung GT, Streicher C, Hippenmeyer S. Protocol for quantitative reconstruction
    of cell lineage using mosaic analysis with double markers in mice. <i>STAR Protocols</i>.
    2024;5(3). doi:<a href="https://doi.org/10.1016/j.xpro.2024.103157">10.1016/j.xpro.2024.103157</a>
  apa: Cheung, G. T., Streicher, C., &#38; Hippenmeyer, S. (2024). Protocol for quantitative
    reconstruction of cell lineage using mosaic analysis with double markers in mice.
    <i>STAR Protocols</i>. Elsevier. <a href="https://doi.org/10.1016/j.xpro.2024.103157">https://doi.org/10.1016/j.xpro.2024.103157</a>
  chicago: Cheung, Giselle T, Carmen Streicher, and Simon Hippenmeyer. “Protocol for
    Quantitative Reconstruction of Cell Lineage Using Mosaic Analysis with Double
    Markers in Mice.” <i>STAR Protocols</i>. Elsevier, 2024. <a href="https://doi.org/10.1016/j.xpro.2024.103157">https://doi.org/10.1016/j.xpro.2024.103157</a>.
  ieee: G. T. Cheung, C. Streicher, and S. Hippenmeyer, “Protocol for quantitative
    reconstruction of cell lineage using mosaic analysis with double markers in mice,”
    <i>STAR Protocols</i>, vol. 5, no. 3. Elsevier, 2024.
  ista: Cheung GT, Streicher C, Hippenmeyer S. 2024. Protocol for quantitative reconstruction
    of cell lineage using mosaic analysis with double markers in mice. STAR Protocols.
    5(3), 103157.
  mla: Cheung, Giselle T., et al. “Protocol for Quantitative Reconstruction of Cell
    Lineage Using Mosaic Analysis with Double Markers in Mice.” <i>STAR Protocols</i>,
    vol. 5, no. 3, 103157, Elsevier, 2024, doi:<a href="https://doi.org/10.1016/j.xpro.2024.103157">10.1016/j.xpro.2024.103157</a>.
  short: G.T. Cheung, C. Streicher, S. Hippenmeyer, STAR Protocols 5 (2024).
corr_author: '1'
date_created: 2024-06-30T22:01:04Z
date_published: 2024-09-20T00:00:00Z
date_updated: 2025-12-30T10:54:11Z
day: '20'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.1016/j.xpro.2024.103157
ec_funded: 1
external_id:
  pmid:
  - '38935508'
file:
- access_level: open_access
  checksum: d8a8cdba82a394e731aa699ace1ae433
  content_type: application/pdf
  creator: dernst
  date_created: 2025-01-09T12:12:40Z
  date_updated: 2025-01-09T12:12:40Z
  file_id: '18809'
  file_name: 2024_STARProtoc_Cheung.pdf
  file_size: 5186071
  relation: main_file
  success: 1
file_date_updated: 2025-01-09T12:12:40Z
has_accepted_license: '1'
intvolume: '         5'
issue: '3'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '754411'
  name: ISTplus - Postdoctoral Fellowships
- _id: 059F6AB4-7A3F-11EA-A408-12923DDC885E
  grant_number: F7805
  name: Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular
    Mechanisms of Neural Stem Cell Lineage Progression
publication: STAR Protocols
publication_identifier:
  eissn:
  - 2666-1667
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Protocol for quantitative reconstruction of cell lineage using mosaic analysis
  with double markers in mice
tmp:
  image: /images/cc_by_nc_nd.png
  legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
  name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
    (CC BY-NC-ND 4.0)
  short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2024'
...
---
APC_amount: 804 EUR
OA_place: publisher
OA_type: gold
_id: '17232'
abstract:
- lang: eng
  text: "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.\r\nFor complete details on the use and execution of this
    protocol, please refer to Cheung et al.\r\n1"
acknowledged_ssus:
- _id: Bio
- _id: M-Shop
- _id: PreCl
acknowledgement: We thank R. Beattie and T. Asenov for designing and producing components
  of the multi-well slice recover chamber. We thank R. Shigemoto for providing equipment
  access. We thank C. Streicher and A. Heger for mouse breeding support. This work
  was supported by the Scientific Service Units of IST Austria through resources provided
  by the Imaging & Optics, Miba Machine Shop, and Preclinical facilities. G.C. received
  funding from the European Commission (IST plus postdoctoral fellowship) and S.H.
  was funded by ISTA institutional funds and the Austrian Science Fund Special Research
  Programmes (FWF SFB-F78 Neuro Stem Modulation).
article_number: '103168'
article_processing_charge: Yes
article_type: original
author:
- first_name: Giselle T
  full_name: Cheung, Giselle T
  id: 471195F6-F248-11E8-B48F-1D18A9856A87
  last_name: Cheung
  orcid: 0000-0001-8457-2572
- first_name: Florian
  full_name: Pauler, Florian
  id: 48EA0138-F248-11E8-B48F-1D18A9856A87
  last_name: Pauler
  orcid: 0000-0002-7462-0048
- first_name: Peter
  full_name: Koppensteiner, Peter
  id: 3B8B25A8-F248-11E8-B48F-1D18A9856A87
  last_name: Koppensteiner
  orcid: 0000-0002-3509-1948
- first_name: Simon
  full_name: Hippenmeyer, Simon
  id: 37B36620-F248-11E8-B48F-1D18A9856A87
  last_name: Hippenmeyer
  orcid: 0000-0003-2279-1061
citation:
  ama: Cheung GT, Pauler F, Koppensteiner P, Hippenmeyer S. Protocol for mapping cell
    lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq.
    <i>STAR Protocols</i>. 2024;5(3). doi:<a href="https://doi.org/10.1016/j.xpro.2024.103168">10.1016/j.xpro.2024.103168</a>
  apa: Cheung, G. T., Pauler, F., Koppensteiner, P., &#38; Hippenmeyer, S. (2024).
    Protocol for mapping cell lineage and cell-type identity of clonally-related cells
    in situ using MADM-CloneSeq. <i>STAR Protocols</i>. Elsevier. <a href="https://doi.org/10.1016/j.xpro.2024.103168">https://doi.org/10.1016/j.xpro.2024.103168</a>
  chicago: Cheung, Giselle T, Florian Pauler, Peter Koppensteiner, and Simon Hippenmeyer.
    “Protocol for Mapping Cell Lineage and Cell-Type Identity of Clonally-Related
    Cells in Situ Using MADM-CloneSeq.” <i>STAR Protocols</i>. Elsevier, 2024. <a
    href="https://doi.org/10.1016/j.xpro.2024.103168">https://doi.org/10.1016/j.xpro.2024.103168</a>.
  ieee: G. T. Cheung, F. Pauler, P. Koppensteiner, and S. Hippenmeyer, “Protocol for
    mapping cell lineage and cell-type identity of clonally-related cells in situ
    using MADM-CloneSeq,” <i>STAR Protocols</i>, vol. 5, no. 3. Elsevier, 2024.
  ista: Cheung GT, Pauler F, Koppensteiner P, Hippenmeyer S. 2024. Protocol for mapping
    cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq.
    STAR Protocols. 5(3), 103168.
  mla: Cheung, Giselle T., et al. “Protocol for Mapping Cell Lineage and Cell-Type
    Identity of Clonally-Related Cells in Situ Using MADM-CloneSeq.” <i>STAR Protocols</i>,
    vol. 5, no. 3, 103168, Elsevier, 2024, doi:<a href="https://doi.org/10.1016/j.xpro.2024.103168">10.1016/j.xpro.2024.103168</a>.
  short: G.T. Cheung, F. Pauler, P. Koppensteiner, S. Hippenmeyer, STAR Protocols
    5 (2024).
corr_author: '1'
date_created: 2024-07-14T22:01:10Z
date_published: 2024-09-20T00:00:00Z
date_updated: 2025-12-30T10:54:12Z
day: '20'
ddc:
- '570'
department:
- _id: SiHi
- _id: PreCl
doi: 10.1016/j.xpro.2024.103168
external_id:
  pmid:
  - '38968076'
file:
- access_level: open_access
  checksum: 464f52ecc6ec92f509552823bb82bf79
  content_type: application/pdf
  creator: dernst
  date_created: 2025-01-09T12:16:53Z
  date_updated: 2025-01-09T12:16:53Z
  file_id: '18810'
  file_name: 2024_STARProtoc_Cheung2.pdf
  file_size: 6445556
  relation: main_file
  success: 1
file_date_updated: 2025-01-09T12:16:53Z
has_accepted_license: '1'
intvolume: '         5'
issue: '3'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 059F6AB4-7A3F-11EA-A408-12923DDC885E
  grant_number: F7805
  name: Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular
    Mechanisms of Neural Stem Cell Lineage Progression
publication: STAR Protocols
publication_identifier:
  eissn:
  - 2666-1667
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Protocol for mapping cell lineage and cell-type identity of clonally-related
  cells in situ using MADM-CloneSeq
tmp:
  image: /images/cc_by_nc_nd.png
  legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
  name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
    (CC BY-NC-ND 4.0)
  short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2024'
...
---
APC_amount: 804 EUR
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '18601'
abstract:
- lang: eng
  text: "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.\r\nFor complete details on the use and
    execution of this protocol, please refer to Lehr et al.1"
acknowledged_ssus:
- _id: NanoFab
acknowledgement: We thank the nanofabrication facility at ISTA for technical assistance.
  Work in the A.K. lab is supported by ISTA, the European Research Council under Horizon
  Europe (grant 101044579), and the Austrian Science Fund (FWF) (grant https://doi.org/10.55776/F78).
  S.L. is supported by Gesellschaft für Forschungsförderung Niederösterreich m.b.H.
  fellowship SC19-011.
article_number: '103187'
article_processing_charge: Yes
article_type: original
author:
- first_name: Stefanie
  full_name: Rus, Stefanie
  id: 4D9EC9B6-F248-11E8-B48F-1D18A9856A87
  last_name: Rus
  orcid: 0000-0001-8703-1093
- first_name: Jack
  full_name: Merrin, Jack
  id: 4515C308-F248-11E8-B48F-1D18A9856A87
  last_name: Merrin
  orcid: 0000-0001-5145-4609
- first_name: Monika Aleksandra
  full_name: Kulig, Monika Aleksandra
  id: 3331f5ae-e896-11ec-af79-eeb79769bcb7
  last_name: Kulig
- first_name: Thomas
  full_name: Minchington, Thomas
  id: 7d1648cb-19e9-11eb-8e7a-f8c037fb3e3f
  last_name: Minchington
- first_name: Anna
  full_name: Kicheva, Anna
  id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
  last_name: Kicheva
  orcid: 0000-0003-4509-4998
citation:
  ama: Rus S, Merrin J, Kulig MA, Minchington T, Kicheva A. Protocol for fabricating
    elastomeric stencils for patterned stem cell differentiation. <i>STAR Protocols</i>.
    2024;5(4). doi:<a href="https://doi.org/10.1016/j.xpro.2024.103187">10.1016/j.xpro.2024.103187</a>
  apa: Rus, S., Merrin, J., Kulig, M. A., Minchington, T., &#38; Kicheva, A. (2024).
    Protocol for fabricating elastomeric stencils for patterned stem cell differentiation.
    <i>STAR Protocols</i>. Elsevier. <a href="https://doi.org/10.1016/j.xpro.2024.103187">https://doi.org/10.1016/j.xpro.2024.103187</a>
  chicago: Rus, Stefanie, Jack Merrin, Monika Aleksandra Kulig, Thomas Minchington,
    and Anna Kicheva. “Protocol for Fabricating Elastomeric Stencils for Patterned
    Stem Cell Differentiation.” <i>STAR Protocols</i>. Elsevier, 2024. <a href="https://doi.org/10.1016/j.xpro.2024.103187">https://doi.org/10.1016/j.xpro.2024.103187</a>.
  ieee: S. Rus, J. Merrin, M. A. Kulig, T. Minchington, and A. Kicheva, “Protocol
    for fabricating elastomeric stencils for patterned stem cell differentiation,”
    <i>STAR Protocols</i>, vol. 5, no. 4. Elsevier, 2024.
  ista: Rus S, Merrin J, Kulig MA, Minchington T, Kicheva A. 2024. Protocol for fabricating
    elastomeric stencils for patterned stem cell differentiation. STAR Protocols.
    5(4), 103187.
  mla: Rus, Stefanie, et al. “Protocol for Fabricating Elastomeric Stencils for Patterned
    Stem Cell Differentiation.” <i>STAR Protocols</i>, vol. 5, no. 4, 103187, Elsevier,
    2024, doi:<a href="https://doi.org/10.1016/j.xpro.2024.103187">10.1016/j.xpro.2024.103187</a>.
  short: S. Rus, J. Merrin, M.A. Kulig, T. Minchington, A. Kicheva, STAR Protocols
    5 (2024).
corr_author: '1'
date_created: 2024-12-01T23:01:53Z
date_published: 2024-12-20T00:00:00Z
date_updated: 2026-08-23T22:30:37Z
day: '20'
ddc:
- '570'
department:
- _id: AnKi
- _id: NanoFab
doi: 10.1016/j.xpro.2024.103187
external_id:
  pmid:
  - '39602310'
file:
- access_level: open_access
  checksum: 0c61a6f9978608a103865905e06f4581
  content_type: application/pdf
  creator: dernst
  date_created: 2024-12-03T10:53:23Z
  date_updated: 2024-12-03T10:53:23Z
  file_id: '18610'
  file_name: 2024_STARProtoc_Lehr.pdf
  file_size: 4989169
  relation: main_file
  success: 1
file_date_updated: 2024-12-03T10:53:23Z
has_accepted_license: '1'
intvolume: '         5'
issue: '4'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: bd7e737f-d553-11ed-ba76-d69ffb5ee3aa
  grant_number: '101044579'
  name: Mechanisms of tissue size regulation in spinal cord development
- _id: 9B9B39FA-BA93-11EA-9121-9846C619BF3A
  grant_number: SC19-011
  name: The regulatory logic of pattern formation in the vertebrate dorsal neural
    tube
publication: STAR Protocols
publication_identifier:
  eissn:
  - 2666-1667
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
  record:
  - id: '19763'
    relation: dissertation_contains
    status: public
scopus_import: '1'
status: public
title: Protocol for fabricating elastomeric stencils for patterned stem cell differentiation
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2024'
...
---
_id: '10321'
abstract:
- lang: eng
  text: 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).
acknowledged_ssus:
- _id: Bio
- _id: PreCl
acknowledgement: This research was supported by the Scientific Service Units (SSU)
  at IST Austria through resources provided by the Bioimaging (BIF) and Preclinical
  Facilities (PCF). We particularly thank Mohammad Goudarzi for assistance with photography
  of mouse perfusion and dissection. N.A. received support from FWF Firnberg-Programm
  (T 1031). This work was also supported by IST Austria institutional funds; FWF SFB
  F78 to S.H.; and the European Research Council (ERC) under the European Union’s
  Horizon 2020 research and innovation programme (grant agreement no. 725780 LinPro)
  to S.H.
article_number: '100939'
article_processing_charge: Yes
article_type: original
author:
- first_name: Nicole
  full_name: Amberg, Nicole
  id: 4CD6AAC6-F248-11E8-B48F-1D18A9856A87
  last_name: Amberg
  orcid: 0000-0002-3183-8207
- first_name: Simon
  full_name: Hippenmeyer, Simon
  id: 37B36620-F248-11E8-B48F-1D18A9856A87
  last_name: Hippenmeyer
  orcid: 0000-0003-2279-1061
citation:
  ama: Amberg N, Hippenmeyer S. Genetic mosaic dissection of candidate genes in mice
    using mosaic analysis with double markers. <i>STAR Protocols</i>. 2021;2(4). doi:<a
    href="https://doi.org/10.1016/j.xpro.2021.100939">10.1016/j.xpro.2021.100939</a>
  apa: Amberg, N., &#38; Hippenmeyer, S. (2021). Genetic mosaic dissection of candidate
    genes in mice using mosaic analysis with double markers. <i>STAR Protocols</i>.
    Cell Press. <a href="https://doi.org/10.1016/j.xpro.2021.100939">https://doi.org/10.1016/j.xpro.2021.100939</a>
  chicago: Amberg, Nicole, and Simon Hippenmeyer. “Genetic Mosaic Dissection of Candidate
    Genes in Mice Using Mosaic Analysis with Double Markers.” <i>STAR Protocols</i>.
    Cell Press, 2021. <a href="https://doi.org/10.1016/j.xpro.2021.100939">https://doi.org/10.1016/j.xpro.2021.100939</a>.
  ieee: N. Amberg and S. Hippenmeyer, “Genetic mosaic dissection of candidate genes
    in mice using mosaic analysis with double markers,” <i>STAR Protocols</i>, vol.
    2, no. 4. Cell Press, 2021.
  ista: Amberg N, Hippenmeyer S. 2021. Genetic mosaic dissection of candidate genes
    in mice using mosaic analysis with double markers. STAR Protocols. 2(4), 100939.
  mla: Amberg, Nicole, and Simon Hippenmeyer. “Genetic Mosaic Dissection of Candidate
    Genes in Mice Using Mosaic Analysis with Double Markers.” <i>STAR Protocols</i>,
    vol. 2, no. 4, 100939, Cell Press, 2021, doi:<a href="https://doi.org/10.1016/j.xpro.2021.100939">10.1016/j.xpro.2021.100939</a>.
  short: N. Amberg, S. Hippenmeyer, STAR Protocols 2 (2021).
corr_author: '1'
date_created: 2021-11-21T23:01:28Z
date_published: 2021-11-10T00:00:00Z
date_updated: 2025-04-15T08:23:07Z
day: '10'
ddc:
- '573'
department:
- _id: SiHi
doi: 10.1016/j.xpro.2021.100939
ec_funded: 1
file:
- access_level: open_access
  checksum: 9e3f6d06bf583e7a8b6a9e9a60500a28
  content_type: application/pdf
  creator: cchlebak
  date_created: 2021-11-22T08:23:58Z
  date_updated: 2021-11-22T08:23:58Z
  file_id: '10329'
  file_name: 2021_STARProtocols_Amberg.pdf
  file_size: 7309464
  relation: main_file
  success: 1
file_date_updated: 2021-11-22T08:23:58Z
has_accepted_license: '1'
intvolume: '         2'
issue: '4'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
project:
- _id: 260018B0-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '725780'
  name: Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development
- _id: 268F8446-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: T01031
  name: Role of Eed in neural stem cell lineage progression
- _id: 059F6AB4-7A3F-11EA-A408-12923DDC885E
  grant_number: F7805
  name: Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular
    Mechanisms of Neural Stem Cell Lineage Progression
publication: STAR Protocols
publication_identifier:
  eissn:
  - 2666-1667
publication_status: published
publisher: Cell Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Genetic mosaic dissection of candidate genes in mice using mosaic analysis
  with double markers
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 2
year: '2021'
...
---
_id: '10565'
abstract:
- lang: eng
  text: '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).'
acknowledged_ssus:
- _id: Bio
acknowledgement: This research was supported by the European Research Council (grant
  715571 to S.S.). We thank Rouven Schulz, Michael Schunn, Claudia Gold, Gabriel Krens,
  Sarah Gorkiewicz, Margaret Maes, Jürgen Siegert, Marco Benevento, and Sara Oakeley
  for comments on the manuscript and the IST Austria Bioimaging Facility for the technical
  support.
article_number: '101012'
article_processing_charge: Yes
article_type: original
author:
- first_name: Alessandro
  full_name: Venturino, Alessandro
  id: 41CB84B2-F248-11E8-B48F-1D18A9856A87
  last_name: Venturino
  orcid: 0000-0003-2356-9403
- first_name: Sandra
  full_name: Siegert, Sandra
  id: 36ACD32E-F248-11E8-B48F-1D18A9856A87
  last_name: Siegert
  orcid: 0000-0001-8635-0877
citation:
  ama: Venturino A, Siegert S. Minimally invasive protocols and quantification for
    microglia-mediated perineuronal net disassembly in mouse brain. <i>STAR Protocols</i>.
    2021;2(4). doi:<a href="https://doi.org/10.1016/j.xpro.2021.101012">10.1016/j.xpro.2021.101012</a>
  apa: Venturino, A., &#38; Siegert, S. (2021). Minimally invasive protocols and quantification
    for microglia-mediated perineuronal net disassembly in mouse brain. <i>STAR Protocols</i>.
    Elsevier. <a href="https://doi.org/10.1016/j.xpro.2021.101012">https://doi.org/10.1016/j.xpro.2021.101012</a>
  chicago: Venturino, Alessandro, and Sandra Siegert. “Minimally Invasive Protocols
    and Quantification for Microglia-Mediated Perineuronal Net Disassembly in Mouse
    Brain.” <i>STAR Protocols</i>. Elsevier, 2021. <a href="https://doi.org/10.1016/j.xpro.2021.101012">https://doi.org/10.1016/j.xpro.2021.101012</a>.
  ieee: A. Venturino and S. Siegert, “Minimally invasive protocols and quantification
    for microglia-mediated perineuronal net disassembly in mouse brain,” <i>STAR Protocols</i>,
    vol. 2, no. 4. Elsevier, 2021.
  ista: Venturino A, Siegert S. 2021. Minimally invasive protocols and quantification
    for microglia-mediated perineuronal net disassembly in mouse brain. STAR Protocols.
    2(4), 101012.
  mla: Venturino, Alessandro, and Sandra Siegert. “Minimally Invasive Protocols and
    Quantification for Microglia-Mediated Perineuronal Net Disassembly in Mouse Brain.”
    <i>STAR Protocols</i>, vol. 2, no. 4, 101012, Elsevier, 2021, doi:<a href="https://doi.org/10.1016/j.xpro.2021.101012">10.1016/j.xpro.2021.101012</a>.
  short: A. Venturino, S. Siegert, STAR Protocols 2 (2021).
date_created: 2021-12-19T23:01:32Z
date_published: 2021-12-17T00:00:00Z
date_updated: 2025-05-14T11:26:30Z
day: '17'
ddc:
- '573'
department:
- _id: SaSi
doi: 10.1016/j.xpro.2021.101012
ec_funded: 1
file:
- access_level: open_access
  checksum: 9ea2501056c5df99e84726b845e9b976
  content_type: application/pdf
  creator: cchlebak
  date_created: 2021-12-20T08:58:40Z
  date_updated: 2021-12-20T08:58:40Z
  file_id: '10570'
  file_name: 2021_STARProt_Venturino.pdf
  file_size: 6207060
  relation: main_file
  success: 1
file_date_updated: 2021-12-20T08:58:40Z
has_accepted_license: '1'
intvolume: '         2'
issue: '4'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: 25D4A630-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '715571'
  name: Microglia action towards neuronal circuit formation and function in health
    and disease
publication: STAR Protocols
publication_identifier:
  eissn:
  - 2666-1667
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Minimally invasive protocols and quantification for microglia-mediated perineuronal
  net disassembly in mouse brain
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2
year: '2021'
...