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Distinct signaling center and progenitor identity dynamics initiate human forebrain patterning

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The authors' code

Jupyter notebook · 110 lines · 4.3 KB · no license

  1. # %% [markdown]
  2. # Pybridizer basic usage example:
  3. #
  4. # This notebook demonstrates how to use Pybridizer to design HCR probes
  6. # %% [markdown]
  7. # Import essential functions from the pybridizer probe design module
  9. # %%
  10. from pybridizer import read_fasta, create_oligos, blast_oligos, fetch_geneIDs, filter_and_rank, add_hairpin, plot_sequence_alignment
  12. # %% [markdown]
  13. # Read a FASTA file containing the transcript sequence for which HCR probes need to be designed. The file should be in a .fasta/.fa/.faa format.
  15. # %%
  16. ID, desc, sequence = read_fasta("Pybridizer\\input\\sox10_zebrafish.fasta")
  18. # %% [markdown]
  19. # Now, the transcript sequence needs to be tiled into oligos (default:25 base length, 2 base gap).
  20. #
  21. # Optional: You can also adjust the length of the oligo, gap between oligos and frame start position (0 i.e. beginning of the transcript by default)
  23. # %%
  24. oligos_all = create_oligos(sequence,oligo_length=25,gap_length=2,frame_start_position=0)
  26. # %% [markdown]
  27. # Next, perform a batch BLAST for each of the oligos against your database and save the BLAST results.
  28. #
  29. # !!!Warning!!! : BLAST+ must be installed and a BLAST database should be built using 'makeblastdb' command on the data downloaded from vector base. This is a pre-requisite for the BLAST function to work.
  30. #
  31. # The database name ('dbname') should be your custom BLAST database and the taxonomy ID ('taxid') argument is optional.
  32. # Taxonomy ID is essential if you want to run BLAST for a specific species in a database with multiple species.
  34. # %%
  35. blast_result = blast_oligos(oligos_all, dbname='refseq', taxid=7955)
  37. # %% [markdown]
  38. # You can view the BLAST results now.
  39. #
  40. # The dataframe lists the query results for each oligo including hits (matches with other transcripts) in the database, length of the matches, match positions and match scores.
  42. # %%
  43. blast_result.head()
  45. # %% [markdown]
  46. # The next step is to retreive gene IDs that correspond to transcript IDs. This would be useful if multiple transcript IDs exist for a single gene.
  47. #
  48. # This step is completely optional.
  50. # %%
  51. blast_result_genes = fetch_geneIDs(blast_result,taxid='zebrafish')
  53. # %% [markdown]
  54. # View the blast results with gene IDs appended
  56. # %%
  57. blast_result_genes.head()
  59. # %% [markdown]
  60. # The oligos need to be filtered based on the GC content and the Melting Temperature. Default range for GC: 37-85 % & Default range for MT: 47-85 C These can also be adjusted in the 'filter and rank' function but is optional.
  61. #
  62. # Based on the BLAST results, neighbouring oligos that hit the same transcript (other than our target gene) should be filtered out. This is to ensure specificity of HCR probes
  63. #
  64. # Lastly, the neighbouring oligo pairs are ranked according to their specificity
  66. # %%
  67. probe_datasheet = filter_and_rank(oligos_all,blast_result_genes,Tm_range=[47,85],GC_range=[0.37,0.85])
  69. # %% [markdown]
  70. # View the probe datasheet for the optimal set of HCR oligo pairs after filtering
  72. # %%
  73. probe_datasheet.head()
  75. # %% [markdown]
  76. # Choose hairpin (B1-B5) for the selected probes to generate final HCR probe pairs
  78. # %%
  79. hcr_probes = add_hairpin(probe_datasheet,'B3')
  81. # %% [markdown]
  82. # View final HCR probes for the chosen hairpin.
  83. # The hcr_probes datasheet has the following columns:
  84. #
  85. # 'Oligo1_position' and 'Oligo2_position' columns represent the location of the oligo along the transcript
  86. #
  87. # 'Oligo1_Sequence' and 'Oligo2_Sequence' are reverse complement oligos of the two neighbouring 25 base sequence along the transcript
  88. #
  89. # 'Score (avg hits)' represents how many other transcripts on average could partially bind to one of the two oligos, but not both. Lower the score, higher the specificity of the probe pair
  90. #
  91. # 'HCRprobe1' and 'HCRprobe2' are the final hairpin appended oligos that should be ordered as ssDNA.
  93. # %%
  94. hcr_probes.head()
  96. # %% [markdown]
  97. # Now we can visualize the alignment of the probe pairs to our target transcript sequence and save the output alignment as an image and a FASTA file.
  99. # %%
  100. fig_path = "Pybridizer\\output\\sox10_zebrafish_probe_alignment.png"
  101. align_fasta_path = "Pybridizer\\output\\sox10_zebrafish_probe_alignment.fasta"
  103. # %%
  104. fig,records = plot_sequence_alignment(sequence, ID, probe_datasheet, top_n=None,figsize=(16,8),save_path=fig_path,output_fasta=align_fasta_path)
  106. # %% [markdown]
  107. # You can save the designed hcr probes datasheet as an excel file
  109. # %%
  110. hcr_probes.to_excel('Pybridizer\\output\\sox10_hcr_probes_B3.xlsx')

pybridizer_basic_usage.ipynb at commit 28caf8b, no license · at the source

Overview

Authors: Afnan Azizi1,2, Dana Fakhreddine1,2, Fursham Hamid1, Zeno Messi2, Stephanie Strohbuecker2, Francois Guillemot2, Corinne Houart1,2
ORCID iDs: Afnan Azizi, Dana Fakhreddine, Fursham Hamid, Zeno Messi, Stephanie Strohbuecker, Corinne Houart
  1. Centre for Developmental Neuroscience, King’s College London, London, United Kingdom
  2. The Francis Crick Institute, London, United Kingdom
Institutions: King's College London (United Kingdom); The Francis Crick Institute (United Kingdom)
Journal: bioRxiv (preprint)
Dates: published online 25 March 2026
Type: Preprint
License: CC BY
Identifiers: DOI 10.64898/2026.03.25.714146 · OpenAlex W7140648434
Open access: green, a free copy (OpenAlex)
Status: code verified (how the code is found and verified)
Categories: genetics / omics (modality), human (organism), mouse (organism), developmental (subfield)
Methods: Smoothing, state filtering, decompositions, Evoked potentials
Keywords: Evolutionary heterochrony, Telencephalon patterning, Human embryonic development, Single cell RNA sequencing, Hybridization chain reaction, 3D imaging, SHH signaling
Topic: Neurogenesis and neuroplasticity mechanisms (Developmental Neuroscience, Neuroscience), according to OpenAlex
Funding: Wellcome Trust (220861/Z/20/Z, 215116/Z/18/Z); Biotechnology and Biological Sciences Research Council (BB/T008709/1)
Citations: not cited yet (Europe PMC); 56 references in the paper

Abstract

At which developmental stage does the human brain start to differ from other mammals? We uncover human features of telencephalic patterning as early as the fourth post-conception week, comparing the early mouse and human forebrains using single-cell transcriptomics and 3D spatial multi-transcript imaging. In comparison to mice, the human telencephalon is delayed in ventral SHH signaling, accompanied by a human signature of anterior FGF signaling. These observations correlate with a less-resolved patterning and reduced progenitor diversity along the dorsoventral and anteroposterior axes, as well as a human early neurogenic signature. Our complementary approaches reveal a human divergence in allocation of telencephalic progenitor identities, propelled by temporal and qualitative differences in ventro-anterior signals following neural tube closure in the developing forebrain.

Reproduced under the paper's license (CC BY), from the paper cited above.

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ctucl/pybridizer

License: none: the authors keep all their rights
State: the link answers, verified on 30 September 2026
Evidence: files inventoried
Commit: 28caf8bd6f48145e334fd39afc5585bd5c76117b, 31 October 2025
Languages: Python (3), Jupyter (1)
Size: 15 files, 4 scripts
Software Heritage: not archived
Found in: the text, “Wholemount HCR and tissue clearing”
Holds: README, environment (requirements.txt, setup.py), 1 notebook
Not found: license file, CITATION.cff, tests, continuous integration, documentation
Tools: Biopython (2 files), Matplotlib (2 files), NumPy (2 files), pandas (2 files), seaborn (2 files)
Availability: 1 check, the latest on 30 September 2026: the link answers
  • 30 September 2026: the link answers
5 files
At the source: github.com/ctucl/pybridizer

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Recorded: type, journal, dates, 7 authors, 7 keywords, 2 funders, 55 references.

Cite

This paper

Azizi, A., Fakhreddine, D., Hamid, F., Messi, Z., Strohbuecker, S., Guillemot, F., & Houart, C. (2026). Distinct signaling center and progenitor identity dynamics initiate human forebrain patterning. bioRxiv (preprint). https://doi.org/10.64898/2026.03.25.714146

BibTeX

@article{azizi2026distinct,
author = {Azizi, Afnan and Fakhreddine, Dana and Hamid, Fursham and Messi, Zeno and Strohbuecker, Stephanie and Guillemot, Francois and Houart, Corinne},
title = {{Distinct signaling center and progenitor identity dynamics initiate human forebrain patterning}},
journal = {bioRxiv (preprint)},
year = {2026},
month = mar,
publisher = {bioRxiv},
issn = {2692-8205},
doi = {10.64898/2026.03.25.714146},
url = {https://doi.org/10.64898/2026.03.25.714146}
}

RIS

TY - JOUR
AU - Azizi, Afnan
AU - Fakhreddine, Dana
AU - Hamid, Fursham
AU - Messi, Zeno
AU - Strohbuecker, Stephanie
AU - Guillemot, Francois
AU - Houart, Corinne
TI - Distinct signaling center and progenitor identity dynamics initiate human forebrain patterning
T2 - bioRxiv (preprint)
J2 - bioRxiv
PY - 2026
DA - 2026/03/25
SN - 2692-8205
PB - bioRxiv
DO - 10.64898/2026.03.25.714146
UR - https://doi.org/10.64898/2026.03.25.714146
ER -

CSL-JSON

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"id": "10.64898/2026.03.25.714146",
"type": "article",
"title": "Distinct signaling center and progenitor identity dynamics initiate human forebrain patterning",
"container-title": "bioRxiv (preprint)",
"author": [
{
"family": "Azizi",
"given": "Afnan"
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{
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"given": "Dana"
},
{
"family": "Hamid",
"given": "Fursham"
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{
"family": "Messi",
"given": "Zeno"
},
{
"family": "Strohbuecker",
"given": "Stephanie"
},
{
"family": "Guillemot",
"given": "Francois"
},
{
"family": "Houart",
"given": "Corinne"
}
],
"container-title-short": "bioRxiv",
"DOI": "10.64898/2026.03.25.714146",
"ISSN": "2692-8205",
"publisher": "bioRxiv",
"URL": "https://doi.org/10.64898/2026.03.25.714146",
"issued": {
"date-parts": [
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2026,
3,
25
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]
}
}

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