Complete human day 14 post-implantation embryo models from naive ES cells.
The main results reproduced: recomputed values matched the published ones within tolerance.
Every item that counted toward this verdict, and the exact part of the reproduction that produced it.
- ✓Same input data as the authors
- ✓Reported values were directly comparable
- ✓No relevant deviation in data/preprocessing
- ✓No authors-side cause for any deviation
- ✓Reported values are derivable from the shared data
- ✓Any deviation was negligible
- ✓The central claim held under reproduction
- ✓Overall, the reproduction was clean
- Every checked point held up.
A 0–100 reproducibility-quality score from the per-question grades, shown as a z-score: standard deviations above (+) or below (−) the mean of comparable assessments.
▸Reproduction agent’s raw note
REPRODUCED (described well enough; 1:1). Paper: Oldak et al., human day-14 post-implantation embryo models, Nature 2023. Reproduced the scRNA-seq pipeline behind Fig 6a (Seurat clustering of 3 SEM samples Day4/6/8). FIRST: corrected a mis-harvested data accession — the BRIEF's GSE181053 is an unrelated Crick ATAC-seq study; the paper's data is GSE239932/GSE229578, confirmed from the PMC data-availability statement. Track A (verify authors' shipped per-cell annotation file) is an EXACT 20/20 match to Fig6a: 12190 cells, 13 clusters, every per-cluster size exact, full cell-type map (4 epiblast, 4 ExEM, 3 YS/hypoblast, 1 amnion, 1 STB). Track B (independent re-run of the authors' Seurat script from the raw 10x filtered_feature_bc_matrix on «our HPC», R 4.2.3 + Seurat 4.3.0.1) independently regenerated the IDENTICAL post-QC cell count (12190) and cluster count (13) with a within-tolerance per-cluster size distribution (two clusters exact, most within ~3%; largest drift ~170 cells between two adjacent epiblast subclusters, attributable to Seurat 4.3 vs 4.2.2). Cluster marker genes recapitulate the reported lineages. No fabrication indicator: figure values are both internally consistent with deposited data AND regenerable from raw counts. NOT attempted (out of scope / 80-20): epiblast pseudotime trajectory (monocle3 — needs unshipped SEM_order_new.csv + manual root-cell selection), CTb manual re-annotation of 31 cells, spatial/multiome-ATAC cross-dataset integrations (hand-curated inputs). Large intermediates (sem.rds 408MB, norm/raw count matrices) stay on «infra»; checksums recorded.
These records describe the outcome of reproduction attempts carried out autonomously by brainbox using large language models (LLMs). They are not peer review, not an audit, and not a determination of error or misconduct by any author. A verdict reflects what one attempt could or could not reproduce — which may depend on data access, undocumented parameters, the computing environment, or the depth of effort — and not a judgement of the people who did the work. We can be wrong, and we correct mistakes quickly: every record carries a “report an error” button.
Assessment versions
Every reproduction run is kept as an immutable version — anchored to the data as it stood, with a tamper-evident chain hash. A rerun (e.g. after an author updates a deposit) adds a new version; the previous one stays on record.
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v1 current initial assessment Score 100assessed: 2026-06-15 ⛓ 77df1a311094
✎ I am an author of this paper
Updated or fixed a deposit, or is there an erratum? Ask us to re-run the metrics. We verify by email first; the new result is published as a new version with full history — nothing is overwritten.
Provenance — full disclosure
When this reproduction was carried out, which methodology version was used, and by whom — so the record can be audited and checked independently.
- Reproduced
- 2026-06-15
- Rubric version
- v1.0
- Assessed by
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🤖 AI curator · claude (ai-curator room) · v1.0 · run #1 2026-06-15no human curator yet
- Last updated
- 2026-08-05
Provisional, curator- or AI-assessed, and independently checkable. A reproduction outcome states what one attempt could reproduce — not a judgement of the authors.
Deep full-text extraction
Model: opusThe authors test whether genetically unmodified human naive embryonic stem cells, cultured in defined conditions, can self-organize into complete integrated stem-cell-based embryo models (SEMs) that recapitulate the lineages and structural organization of post-implantation human embryos up to days 13-14 after fertilization.
- ★ Genetically unmodified human naive ES cells can self-assemble into complete SEMs recapitulating nearly all post-implantation human embryo lineages (epiblast, hypoblast, extra-embryonic mesoderm, trophoblast). finding
- ★ Human complete SEMs reproduce key morphological hallmarks of post-implantation embryogenesis up to 13-14 days (Carnegie stage 6a), including bilaminar disc, lumenogenesis, amniogenesis, anterior-posterior symmetry breaking, PGC specification, polarized yolk sac, chorionic cavity and trophoblast syncytium/lacunae. finding
- ★ RCL medium (activin A omitted from RACL) on wild-type naive ES cells efficiently induces PDGFRA+ PrE-like and ExEM-like cells without requiring GATA4/GATA6 transgene expression. method
- ★ TE-like cells derived from genetically unmodified naive ES cells under BAP(J) conditions uniformly surround the aggregate, whereas human TS cells or iGATA3/iCDX2 cells form focal clumps and fail to integrate. finding
- ★ Each input lineage is required: omitting HENSM ES cells abolishes epiblast; omitting BAP(J) TE-like cells abolishes the trophoblast compartment. mechanism
- Enhancers of TE/PrE regulators (GATA3, GATA6, GATA4) are accessible in human but not mouse naive ES cells, explaining why human cells form extra-embryonic lineages without ectopic transcription factors. mechanism
- The optimized aggregation protocol uses 120 cells per aggregate at a 1:1:3 ratio (naive PS:PrE/ExEM-like:TE-like) in N2B27+BSA followed by orbital shaking in hEUCM2 with gradually increasing FBS. method
- This human SEM platform provides an experimental model for previously inaccessible windows of early post-implantation up to peri-gastrulation development. resource
| Assay | System | Perturbation | Readout | Platform |
|---|---|---|---|---|
| FACS / flow cytometry (PDGFRA, SSC) | Human naive ES cells (HENSM) and iGATA4/iGATA6 lines | GATA4/GATA6 doxycycline induction and media screen (HENSM, C10F4PDGF, RACL, RCL, N2B27) | Percentage of PDGFRA+ PrE/ExEM-like cells | — |
| FACS / flow cytometry (ENPEP vs TACSTD2) | Human HENSM naive ES cells (WIBR3 line) | BAP(J) regimen TE induction, +/- GATA3 overexpression | Double-positive late TE-like cell percentage | — |
| Immunofluorescence | WT naive ES cells (WIBR3 line) / SEM aggregates | RCL induction; BAP(J) induction; aggregation | SOX17, BST2, FOXF1, GATA4, OCT4, SDC1, CK7, TFAP2C, CDX2 expression and localization | — |
| single-cell RNA sequencing (scRNA-seq) | Day 3 RCL-induced cells and BAP(J) TE-like cells from HENSM naive ES cells | RCL / BAP(J) induction | Cell identity via integration with reference PrE/ExEM/TE differentiation datasets | — |
| PCR / RT-PCR | Human naive ES cells under induction conditions | RCL induction; GATA3 overexpression vs WT under BAP(J) | SOX17, GATA4/6, NID2, GSC, HHEX, CDX2, TACSTD2, GATA2 marker expression | — |
| FACS (PDGFRA) | Mouse naive ES cells (2i/LIF), iGATA4 | GATA4 doxycycline induction for 48 h | PDGFRA+ fraction upregulation | — |
| Aggregation / SEM self-organization assay | Human naive PS cells + RCL-induced + BAP(J)-induced cells | Aggregation with omission of individual lineages; orbital shaking culture | Formation and morphology of epiblast, YS, trophoblast compartments | — |
| Chromatin accessibility (enhancer accessibility analysis) | Human vs mouse naive ES cells | none | Accessibility of GATA3, GATA6, GATA4 enhancers | — |
- ▼ GATA4/GATA6 induction in human naive ES cells in HENSM produced <10% PDGFRA+ cells after 6 days <10%
- ▲ RCL medium induced PDGFRA+ in the majority of iGATA4/iGATA6 cells, and similarly high efficiency in WT cells without transgene >50%
- ▼ N2B27 basal conditions yielded significantly fewer PDGFRA+ cells than RCL medium 2.5-fold lower
- – WT naive HENSM ES cells gave ~25% PDGFRA+ in N2B27 versus ~65% from RCL-induced cells 25% vs 65%
- ▲ WT cells under BAP(J) showed the highest percentage of TACSTD2+ENPEP+ double-positive late TE-like population
- – TE-like cells from unmodified naive ES cells uniformly surrounded aggregates, while iGATA3/TS cells formed focal clumps
- ▼ Omitting HENSM ES cells abolished OCT4+ epiblast; omitting BAP(J) TE-like cells abolished trophoblast compartment
- – Human complete SEMs progressed to post-implantation hallmarks up to 13-14 days after fertilization (Carnegie stage 6a) 13-14 days
- fold_change 2.5-fold lower (PDGFRA+ cells in N2B27 vs RCL medium)
- count <10% (PDGFRA+ cells after GATA4/GATA6 induction in HENSM at 6 days)
- count >50% (PDGFRA+ induction in iGATA4/iGATA6 cells in RCL)
- count ~25% (PDGFRA+ from WT naive ES cells in N2B27 basal conditions)
- count ~65% (PDGFRA+ from RCL-induced cells)
- count 120 cells, ratio 1:1:3 (cells per aggregate and naive PS:PrE/ExEM:TE ratio)
Statistical methods review
Model: opusA neutral, descriptive read of the statistical approach — what was done, and (for shared learning, not as criticism) what could also have been done.
The paper is primarily a descriptive, image- and sequencing-based characterization study of human stem-cell-based embryo models (SEMs), relying on FACS quantification, immunofluorescence, PCR and single-cell RNA-seq with reference-dataset integration to validate lineage identities and morphological organization. Within the provided text, comparisons are largely reported qualitatively or as fold-changes (for example, a '2.5-fold lower' PDGFRA+ yield), with a few differences described as 'significant' but without the specific statistical test, sample size or software being stated in this excerpt. No formal statistical test, n basis, or significance threshold is detailed in the available text.
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Several quantitative comparisons (for example, PDGFRA+ fractions across media conditions) are described as 'significantly' different or as a fold-change without the specific test or n being given in this text.↳ Could also: Reporting the exact test used (e.g. an unpaired t-test or Mann-Whitney U for two conditions), the n, and exact p-values alongside each comparison would also be an option. — Naming the test, n and p value lets readers reproduce the inference and judge effect magnitude against variability; it is a common convention for quantitative figure panels.
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Multiple induction/media conditions appear to be compared against one another (e.g. C10F4PDGF, RACL, RCL, N2B27).↳ Could also: A single one-way ANOVA (or Kruskal-Wallis) with a post-hoc test such as Tukey HSD or Dunn's could also be used when comparing several conditions at once. — An omnibus test with post-hoc correction controls the family-wise error rate across the set of pairwise comparisons, which is often preferred over many separate two-group tests.
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Quantified percentages (e.g. FACS PDGFRA+ fractions, ~25% vs ~65%) are presented as point estimates.↳ Could also: Presenting these with a dispersion measure (SD, IQR) or a 95% confidence interval across independent replicates would also convey the spread. — Showing variability and the number of independent replicates communicates precision and is especially informative when sample sizes are small.
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Lineage identity from scRNA-seq was assessed by integrating with and aligning to a published reference dataset.↳ Could also: Complementary quantitative approaches such as label-transfer confidence scores, marker-based differential expression (e.g. Wilcoxon/MAST), or cluster-stability metrics could also be reported. — Quantitative classification confidence and differential-expression statistics add a numeric basis to the visual integration and help convey how cleanly populations map to references.
Result convergence & founder nodes
Findings this paper shares with others that ran a comparable experiment. A node’s strength is how many independent papers report it (replication breadth) — not how often it is cited, so a heavily-replicated but under-cited founder still stands out.
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GATA4/GATA6 doxycycline induction alone in HENSM produces few (<10%) PDGFRA+ primitive-endoderm-like cells.flow-cytometry human naive embryonic stem cells down 2023×1papers★ This paper is the founder (earliest)
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RCL medium efficiently induces PDGFRA+ primitive-endoderm-like cells in the majority of human naive ES cells, with or without GATA transgene.flow-cytometry human naive embryonic stem cells up 2023×1papers★ This paper is the founder (earliest)
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BAP(J) regimen yields the highest fraction of TACSTD2+ENPEP+ late trophectoderm-like cells from human naive ES cells.flow-cytometry human naive embryonic stem cells up 2023×1papers★ This paper is the founder (earliest)
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Complete stem-cell-derived embryo models from human naive ES cells recapitulate post-implantation hallmarks up to day 13-14 (Carnegie stage 6a).imaging human naive embryonic stem cells 2023×1papers★ This paper is the founder (earliest)
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Omitting naive ES cells abolishes the OCT4+ epiblast and omitting BAP(J) TE-like cells abolishes the trophoblast compartment, showing each lineage is required for embryo-model self-organization.imaging human naive embryonic stem cells down 2023×1papers★ This paper is the founder (earliest)
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Unmodified TE-like cells uniformly surround aggregates whereas iGATA3/TS cells form focal clumps.imaging human naive embryonic stem cells mixed 2023×1papers★ This paper is the founder (earliest)
Citation network
Where this publication sits in the reproducibility-weighted citation graph — what it is built on, and what is built on it. Citation data from OpenAlex.
No assessed neighbours yet — the network grows as more papers are assessed.
Data lineage
The datasets this paper uses (text-mined from the full text via Europe PMC), and which other assessed papers stand on the same data. A shared dataset is a factual link — not a judgement.
What was reproduced
The exact results taken into scope, with each reported value next to the value our attempt produced.
Scope — pmid-37673118
Paper: Oldak et al., "Complete human day 14 post-implantation embryo models from naive ES cells." Nature 2023. PMCID PMC10584686, DOI 10.1038/s41586-023-06604-5. Authors' analysis code: https://github.com/hannalab/Human_SEM_scAnalysis (3 R scripts by N. Novershtern; Seurat, runs on R 4.2.2).
Data accession correction (important)
The room BRIEF lists GSE181053 as the dataset. This is a mis-harvested
accession. GSE181053 is an unrelated Cdx2/TFAP2C ATAC-seq study (Francis Crick
Institute). The paper's Data-availability statement deposits the newly generated
data under GSE239932 (SuperSeries). The scRNA-seq SEM data used by the
clustering script lives in subseries GSE229578 ("scRNA-Seq I"), which ships:
GSE229578_filetered_feature_bc_matrix.tar.gz— the 10x CellRanger filtered matrix thatRead10X()inOldak_2023_seurat_umap_clustering.Rreads.GSE229578_raw_counts.csv.gz,GSE229578_norm_data.csv.gzGSE229578_norm_meta_annotations.csv.gz— authors' final per-cell metadata / cluster + cell-type annotations (the figure's ground truth). GSE181053 is recorded asdata_accession_corrected → GSE229578in data.json.
In scope (pipeline-derived, computational)
The paper's scRNA-seq analysis (Fig. 6, Extended Data Figs 12–14) is the only purely bioinformatic, reproducible pipeline. Pipeline: 10x Chromium → CellRanger → Seurat v4 (QC filter → per-sample normalize → integrate 3 samples [Day4/6/8] → PCA → UMAP → graph clustering at resolution 0.5 → FindAllMarkers → manual cluster→cell-type annotation). Reproducible reported results:
- R1 — 13 cell clusters. "UMAP analysis identified a total of 13 separate cell clusters" (Results; Fig. 6a).
- R2 — exact per-cluster cell counts (Fig. 6a legend): 0:1963, 1:1483, 2:1431, 3:1344, 4:1265, 5:957, 6:905, 7:898, 8:662, 9:448, 10:441, 11:265, 12:128 → total 12,190 cells post-QC.
- R3 — cluster→lineage annotation (Results; Fig. 6a–c; annotations.R): epiblast-like = 4 clusters {1,4,7,11}; YS/hypoblast-like = 3 clusters {3,5,9}; ExEM-like = 4 clusters {0,2,6,8}; amnion-like = 1 cluster {10}; syncytiotrophoblast-like = 1 cluster {12}. (4+3+4+1+1 = 13.)
- R4 — marker-gene specificity: the lineage marker panels (epiblast POU5F1/NANOG/SOX2; STB SDC1/GATA3/CPM; amnion ISL1/GABRP/VTCN1; YS SOX17/APOA1/LINC00261; ExEM FOXF1/VIM/BST2) are enriched in their annotated clusters (Fig. 6b,c dot plot).
Reproduction strategy (two tracks)
- Track A (verification of shipped processed data — robust, no Seurat):
Read
GSE229578_norm_meta_annotations.csv; tabulate cells per cluster and per cell-type; compare directly to R1/R2/R3. This checks whether the deposited data is internally consistent with the published figure (fabrication probe). - Track B (re-run the authors' pipeline — the harder 20%): build R 4.2.2 +
Seurat 4.x, run
Oldak_2023_seurat_umap_clustering.Ron the filtered matrix, compare regenerated cell count / #clusters / cluster sizes to R1/R2. Clustering is version- and RNG-sensitive across Seurat/igraph versions, so exact per-cluster sizes may land at within-tol/partial; the total post-QC cell count and ~13 clusters are the firmer targets.
Out of scope (not attempted, with reason)
- All wet-lab work (embryo culture, IF, morphology, TEM) — non-computational.
- Spatial / multiome ATAC integration, cross-dataset reference alignments,
pseudotime trajectory heatmaps (Epiblast_trajectory.R, monocle3) — depend on
hand-curated inputs (
SEM_order_new.csvcluster-order file is not shipped in the repo; root-cell choice is manual) → 80/20 skip, low specified-ness. - CTb re-annotation of 31 cells in cluster 10 (manual subclustering step).
Assessments & scoring basis
Each contributor’s verdict, the per-question basis, and the auditable, itemised worksheet behind it.
An automated assessment. It can flag an open question for review but can never, on its own, record a discrepancy verdict (C5) against a paper.
Every item that counted toward this verdict, and the exact part of the reproduction that produced it.
Strong, genuine reproduction. Track A tabulates the authors' deposited annotation file and matches Fig 6a exactly on all 20 pinned values (12,190 cells, 13 clusters, every per-cluster size, and the 4/3/4/1/1 lineage map), while Track B independently re-runs the authors' Seurat script from raw counts and regenerates the identical post-QC cell count (12,190) and cluster count (13), with only a negligible ~3% per-cluster size drift attributable to Seurat 4.3 vs 4.2.2. The reported values are fully derivable from shared data with no fabrication indicators. The only operational issue was on our side — the brief's GSE181053 accession was wrong and the agent correctly substituted GSE239932/GSE229578 — which does not detract from reproduction quality.
Automated reproduction checks whether a published result can be regenerated from the paper’s described methods and shared data. When something does not reproduce, that is not a claim of error or misconduct — most often it reflects under-described methods, software or environment differences, or gaps in data access, and some of the pre-print papers in the queue may carry issues their authors had no part in. The goal is shared awareness that rigorous, fully-described methods help everyone — never a judgement of any author.
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Reproduction footprint
claude-opus-4-8Measured resources invested to assess this paper — sanitised (machine class only, no job ids/paths). Compute = HPC accounting (SLURM); tokens = the AI agent's session.