A Single-Cell and Spatial 3D Multi-omic Atlas of Developing Human Basal Ganglia and Inhibitory Neurons

Name: Verified Rigor Record — A Single-Cell and Spatial 3D Multi-omic Atlas of Developing Human Basal Ganglia and Inhibitory Neurons
Item: A Single-Cell and Spatial 3D Multi-omic Atlas of Developing Human Basal Ganglia and Inhibitory Neurons
Rating: 79
Author: Αlpha¹

Heffel, M. G.; Xu, H.; Pastor-Alonso, O.; Li, X.; Baig, M. S.; Irfan Ghoor, R.; Li, R.; Kern, C.; Kum, J.; Zhang, Y.; Paino, J.; Tsai, M. J.; Tai, C.-Y.; Tucker, G.; Zhao, Z.; Hou, A.; von Behren, Z.; Bhade, M.; Li, S.; Sandoval, K.; Scholes, J.; Codrea, F.; Calimlim, J.; Liao, E. K.; Leung, G.; Kim, J.; Eskin, E.; Flint, J.; Cotter, J. A.; Pasaniuc, B.; Bintu, B.; Zhu, Q.; Mukamel, E. A.; Ernst, J.; Paredes, M. F.; Luo, C.

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Αlpha¹ Rigor Review

Rigor Review Verified

Critical

High-priority

Action items to resolve · Critical / High

Confidence: highEngine: 7.6.0Source: full text

This Alpha1 Rigor Review uses AI Rigor Reviewers trained on a curated corpus of high-fidelity and retracted papers, with expert supervision and curation. It can still make mistakes; verify each finding against the source before relying on it.

The paper is a well-resourced observational atlas study with strong data and code sharing and a clear scientific premise. However, it has notable reporting gaps: missing ethics approval and consent statements, incomplete design criteria (inclusion/exclusion, outliers, power analysis), and statistical reporting that lacks effect sizes, confidence intervals, and assumption verification.

All three independent reviewers largely converged; the main divergence was on biological variables (Reviewer 3 rated warn due to sex not being in main text, but Table S1 includes it) and reporting transparency (Reviewer 2 passed while others warned due to missing STROBE). The statistics verification covered only 5 tests; the vast majority of reported statistics remain unverified. The copyedit pass found 15 minor typos/formatting issues. The reproducibility check found 1 dead link.

12 major claims checked against the paper's own evidence: all adequately supported.

partialResults, paragraph 17Reviewer 2
The SE chromatin conformation is associated with increased chromatin looping and transcriptional activity during OPC-to-ODC transition.
The paper shows correlation between SE and increased chromatin contacts in tOPC/tODC, and cites mouse ChAIR data for transcriptional activity, but direct evidence in human is limited.
Evidence: Increased chromatin loops at TNR locus in tOPC, and mouse ChAIR data showing elevated transcriptional activity in transitional cells.
“Consistent with our findings in the human brain, we observed that cells at the transitional stages... are strongly enriched for short-range chromatin contacts... these transitional cells exhibit elevated transcriptional activity.”
supportedAbstract and ResultsReviewer 1
A single-cell and spatial 3D multi-omic atlas of developing human basal ganglia and inhibitory neurons has been generated.
The paper presents snm3C-seq, spatial transcriptomics, and imaging-based chromatin tracing from 9 donors across developmental stages, providing a comprehensive dataset.
Evidence: Results section describes 155,225 new snm3C-seq profiles, spatial transcriptomics with a 6,175-transcript panel, and chromatin+RNA MERFISH. Data are deposited in public repositories.
“We generated 155,225 new snm3C-seq profiles sampled from nine developing brains”
supportedResults, paragraphs 2-3Reviewer 1
LGE shows declining neurogenic activity in mid-gestation and CGE exhibits ongoing developmental progression through infancy.
The paper provides pseudotime analysis, spatial transcriptomics showing higher immature neuron markers in CGE, and quantification of immature CGE neurons in post-natal samples.
Evidence: Results: 'CGE-derived immature neurons are the only type of immature neurons detected in post-natal brains at 1 month (14.2% of all CGE-derived cells)'. Spatial data show CGE highest in DCX, SOX11, MARCKSL1. Pseudotime differences are statistically significant.
“CGE-derived immature neurons are the only type of immature neurons detected in post-natal brains at 1 month (14.2% of all CGE-derived cells) or at 4–7 months (2.4%)”
supportedResults, 'Developmental trajectory of LGE-derived MSNs'Reviewer 1
MSNs exhibit synchronized maturation with discrete age groups, distinct from other neuron types.
The paper shows UMAP embedding with discrete MSN clusters by age, smaller within-age cell-to-cell distances, and both mCG and 3C pseudotime showing a major transition between 2T and 3T, unlike interneurons.
Evidence: Results: 'MSNs consistently exhibit smaller within-age-group distances among individual MSN cells and greater between-age-group distances'; 'UMAP embedding... revealed a more discrete distribution of MSNs across age groups compared to CGE- and MGE-derived inhibitory interneurons'.
“MSNs consistently exhibit smaller within-age-group distances among individual MSN cells and greater between-age-group distances”
supportedResults, 'Transient short-range chromatin conformation is associated with OPC to ODC differentiation'Reviewer 1
A transient short-range enriched (SE) chromatin conformation is found during the OPC-to-ODC transition in infant brains.
The paper identifies transitional OPC (tOPC) and tODC populations in 1-month brain samples, shows they are enriched for SE contacts, and validates with independent mouse ChAIR data.
Evidence: Results: 'tOPCs were enriched at 1 month in both cortex and striatum... SE chromatin organization was enriched in transitional tOPC and tODC populations'.
“tOPCs were enriched at 1 month in both cortex and striatum, whereas enrichment of tODCs at this stage was observed primarily in the striatum”
supportedResults, 'Neuropsychiatric risk across single cells in developing brains'Reviewer 1
Gene regulatory regions active in MSNs are enriched for loci associated with genetic risk for neuropsychiatric disease.
The paper uses met-scDRS and LDSC to show enrichment of SCZ, BIP, ADHD, and MDD risk in MSNs, particularly DRD1-eccentric and DRD2-striosome subtypes, with statistical tests supporting enrichment.
Evidence: Results: 'LGE-derived MSNs are more strongly enriched in the risk of SCZ than CGE and MGE-derived inhibitory neurons (p-value < 2.2e-16, chi-square test)'. Table and figures quantify enrichment.
“LGE-derived MSNs are more strongly enriched in the risk of SCZ than CGE and MGE-derived inhibitory neurons (p-value < 2.2e-16, chi-square test)”
supportedResults, paragraphs 2-4Reviewer 2
Multi-modal data support a heterogeneous temporal progression across GE subregions, with LGE showing declining neurogenic activity in mid-gestation and CGE exhibiting ongoing developmental progression through infancy.
The paper provides pseudotime analysis, spatial transcriptomics, and quantification of immature neurons to support this claim.
Evidence: Pseudotime scores, CosMx expression data, and quantification of immature neurons (40% CGE, 0.07% MGE, 1% LGE) in late gestation.
“CGE, MGE, and LGE develop at distinct rates, with the highest abundance of immature neurons in CGE, intermediate levels in MGE, and the lowest in LGE.”
supportedResults, paragraphs 5-8Reviewer 2
Identified regulatory programs that specify subtypes of BG principal cells, MSNs, via synchronized maturation of the 3D-epigenome.
The paper shows DMR analysis, TF motif enrichment, and synchronous maturation patterns in MSNs.
Evidence: DMR analysis, TF motif enrichment (AP-1, MEIS, etc.), and correlation analysis showing MSNs exhibit smaller within-age-group distances.
“MSNs exhibit smaller within-age-group distances among individual MSN cells and greater between-age-group distances, consistent with more synchronous maturation compared to inhibitory interneurons.”
supportedResults, paragraph 15-17Reviewer 2
In infant brains, we found a transient short-range enriched (SE) chromatin conformation during the transition between oligodendrocyte progenitors (OPCs) and oligodendrocytes (ODCs).
The paper identifies transitional OPC/ODC populations in 1-month brains and shows SE enrichment in these cells, supported by analysis of SE/LE ratios and trajectory analysis.
Evidence: SE/LE ratio analysis, identification of tOPC/tODC cells, and 3C pseudotime analysis.
“Transient short-range enriched (SE) chromatin conformation during the transition between oligodendrocyte progenitors (OPCs) and oligodendrocytes (ODCs)...”
supportedResults, paragraph 20-22Reviewers 2, 3
Gene regulatory regions active in MSNs were enriched in loci associated with genetic risk for neuropsychiatric disease.
The paper applies met-scDRS and LDSC to show enrichment of SCZ, BIP, ADHD, MDD risk in MSNs, especially in eccentric MSNs.
Evidence: met-scDRS scores, LDSC analysis, and chi-square test showing MSNs more enriched than other inhibitory neurons.
“LGE-derived MSNs are more strongly enriched in the risk of SCZ than CGE and MGE-derived inhibitory neurons (p-value < 2.2e-16, chi-square test).”
supportedAbstractReviewer 3
The study provides a single-cell and spatial 3D multi-omic atlas of developing human basal ganglia and inhibitory neurons.
The paper presents extensive snm3C-seq, spatial transcriptomics, and MERFISH data from multiple donors and brain regions, supporting the claim of a multi-omic atlas.
Evidence: The paper describes generating 155,225 new snm3C-seq profiles, integrating with existing datasets, and using spatial transcriptomics and MERFISH.
“A Single-Cell and Spatial 3D Multi-omic Atlas of Developing Human Basal Ganglia and Inhibitory Neurons”
supportedAbstractReviewer 3
The lateral GE (LGE) shows declining neurogenic activity in mid-gestation and caudal GE (CGE) exhibits ongoing developmental progression through infancy.
The paper provides pseudotime analysis, spatial transcriptomics, and quantification of immature neurons to support this claim.
Evidence: Results show lower pseudotime for CGE-derived cells in LV, higher expression of immature markers in CGE, and 40% of CGE-derived cells classified as immature in late gestation.
“the lateral GE (LGE) showing declining neurogenic activity in mid-gestation and caudal GE (CGE) exhibiting ongoing developmental progression through infancy.”

Recomputed 5 tests: 5 consistent, 0 inconsistent, 5 via agent-written checks.

Rigor

Eight Dimensions3 pass · 5 warn

12 major claims1 partial11 supported

15 copyedit issues flagged: mostly typo, consistency, clarity.

Checked 59 references: 57 verified — 2 not checked.

Reproducibility

6 data/code links checked; 5 live, 1 dead.

datahttps://assets.nemoarchive.org/dat-n5emc24LIVEHTTP 200
Resolved page looks like data.
datahttps://brainome.ucsd.edu/bg-epigenome-development-atlasLIVEHTTP 200
Resolves, but the content could not be matched to the paper.
dataDryadLIVEHTTP 200
https://doi.org/10.5061/dryad.3tx95x6wd
Resolves to Dryad (data repository).
dataDryadLIVEHTTP 200
http://datadryad.org/share/LINK_NOT_FOR_PUBLICATION/B0Eg_TOkYfJMyDacVNUQRydDXOhzM6njs9sHFNAwWA0
Resolves to Dryad (data repository).
codeGitHubLIVEHTTP 200
https://github.com/luke0321li/BICAN_ChromHMM
Resolves to GitHub (code repository).
dataDryadDEADHTTP 404
http://datadryad.org/share/LINK_NOT_FOR_PUBLICATION/B0Eg_TOkYfJMyDacVNU
Dead link — nothing to verify.

Alpha¹ Rigor Action ItemsFinal pass before journal submission

This is a post-publication audit. The published paper's conclusions are broadly supportable by the data, but an informed reader should weigh the missing ethics statement and the absence of effect sizes/CI as limitations. A correction adding the ethics approval and consent information is warranted. The dead link in the data/code statement should be repaired.

1.
HIGHethics
Add an IRB/ethics committee approval statement in the Methods section, naming the approving committee and protocol number, along with an informed consent statement (or exemption) for the use of post-mortem human brain tissue.
The study uses non-public human tissue; the complete absence of any ethics statement is a serious reporting gap that undermines transparency and could raise concerns about regulatory compliance.
2.
HIGHdata code
Fix or replace the dead link detected in the data/code availability resources (1 of 6 links checked was dead).
A dead link in the data/code statement prevents readers from accessing shared resources and undermines the otherwise strong data availability.
3.
HIGHreporting
Report pre-specified inclusion/exclusion criteria for brain specimens and cell-level filtering in the Methods section.
Without explicit criteria, readers cannot assess potential selection bias or how the final dataset was derived from the initial samples.
4.
HIGHreporting
Define how outliers were handled in the snm3C-seq and spatial transcriptomics data, including any exclusion thresholds.
Outlier handling is a key quality-control step in single-cell analysis; leaving it unreported reduces reproducibility.
5.
HIGHstatistics
Report effect sizes (e.g., Cohen's d, odds ratios, mean differences) with confidence intervals alongside all p-values.
P-values alone do not convey the magnitude or precision of effects; effect sizes and CIs are essential for interpretation and meta-analysis.
6.
HIGHstatistics
Verify and report the assumptions of statistical tests used (e.g., normality for Wilcoxon is not required, but for any parametric tests), or justify the choice of non-parametric tests.
Without assumption checks, the validity of reported p-values cannot be fully assessed.
7.
HIGHreporting
Reference an appropriate reporting guideline (e.g., STROBE for observational studies) in the Methods section.
Referencing a reporting guideline improves transparency and helps ensure all relevant elements are documented.
8.
MEDIUMreporting
Define error bars (SD, SEM, CI) in all figure legends and, where feasible, show individual data points in boxplots.
Undefined error bars prevent readers from interpreting the variability and precision of the presented data.
9.
MEDIUMreporting
Provide software version numbers (e.g., ChromHMM v1.22, DREM v2.0) for all computational tools used.
Version numbers are essential for reproducibility; different versions can produce different results.
10.
MEDIUMreporting
List key reagents and kits used in the snm3C-seq protocol with catalog numbers and manufacturers.
Reagent details enable independent replication of the wet-lab methods.
11.
MEDIUMreporting
Correct the typo 'MEG-derived' to 'MGE-derived' in the Discussion (paragraph 1) and Results (paragraph 2).
The abbreviation 'MEG' does not match the standard 'MGE' for medial ganglionic eminence; this could confuse readers.
12.
MEDIUMcopyedit
Correct the typo 'reassembled' to 'resembled' in Results, paragraph 5.
This typo changes the intended meaning and may confuse readers.
13.
MEDIUMcopyedit
Correct 'All together' to 'Altogether' in Results, paragraph 1.
Common grammatical error that should be corrected for clarity.
14.
LOWcopyedit
Standardize hyphenation of 'post-natal' to 'postnatal' throughout the manuscript.
Inconsistent hyphenation is a minor style issue that should be unified.
15.
LOWcopyedit
Remove duplicate URL in the Data and code availability section.
Duplicate listing of the same URL is a formatting error that should be cleaned up.

Full text (63,829 chars)Analyzed: Jul 7, 2026

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A Single-Cell and Spatial 3D Multi-omic Atlas of Developing Human Basal Ganglia and Inhibitory Neurons

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DOI

10.64898/2026.01.28.702385

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bc15a599b422d34944da184bc151b88ff279d868286eec64e8c984d64d80f132

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Issued Jul 7, 2026Engine 7.6.0

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