The GATA factor ELT-3 specifies endoderm in Caenorhabditis angaria in an ancestral gene network.
The main results reproduced: recomputed values matched the published ones within tolerance.
- ✓Same input data as the authors
- ✓Reported values were directly comparable
- 🟡A deviation arose in the data or preprocessing
- 🟡A deviation was attributed to the published material
- 🟡Reported values were not (fully) derivable from the shared data
- 🟡The deviation was non-trivial in magnitude
- 🟡The central claim did not (fully) hold under reproduction
- 🟡Overall, the reproduction showed a material discrepancy
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
PARTIAL (well-described, contig-stage reproduced within tolerance). The single bioinformatic pipeline behind this developmental-genetics paper is a de novo C. angaria PS1010 genome assembly. We reproduced its deterministic core 1:1: NextDenovo v2.4.0 on Nanopore reads DRR381124 with the paper's exact params (genome-size=70M, read_cutoff=5k) on «our HPC» («job», 22 min). Input verified 1:1 (443,758 reads / 4.97 Gb / N50 23,276 bp ~ paper's 444k/5.0Gb/23kb; fastq md5 == ENA). Reproduced contigs: 17 contigs, 76,409,664 bp, contig N50 8,392,625 bp, GC 34.80%. Versus the deposited final assembly GCA_947459285.1 (71,372,378 bp; 19 contigs; contig N50 8,829,618 bp): contig count near-identical, contig N50 within 5%, total length +7% (expected for raw contigs before Pilon polishing + Hi-C scaffolding). The downstream Pilon x3 + 3D-DNA + manual Juicebox curation into 6 chromosome scaffolds is non-deterministic and human-in-the-loop -> out of 1:1 scope, not attempted. All wet-lab + GATA-DBD phylogenetics are not pipeline-derived. No fabrication indicators; the deposited target values are derivable from the shipped data via the documented pipeline. Grades provisional, human-checkable.
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 50assessed: 2026-06-19 ⛓ c7cc441265c2
✎ 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
- 2026-06-22
- Rubric version
- v1.0
- Assessed by
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🤖 AI curator · claude (ai-curator room) · v1.0 · run #1 2026-06-19no 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: sonnetSince the MED, END, and ELT-7 GATA factor genes that specify gut in C. elegans are absent outside the Elegans supergroup, the paper tests how endoderm is specified in the distantly related species C. angaria and whether a simpler, ancestral POP-1→ELT-3→ELT-2 gene network performs this role.
- ★ Can-elt-3 (and orthologues in C. portoensis and C. monodelphis) is expressed in the early E lineage prior to elt-2 orthologue expression finding
- ★ Can-pop-1(RNAi), Can-elt-3(RNAi), and a Can-elt-3 null mutation all cause a penetrant gutless phenotype in C. angaria finding
- ★ Can-pop-1 acts upstream of and is required for Can-elt-3 activation mechanism
- ★ Forced early E lineage expression of Can-elt-3 in C. elegans drives Can-elt-2 transgene expression and rescues an elt-7 end-1 end-3; elt-2 quadruple mutant to viability finding
- ★ The ancestral Caenorhabditis gut specification network is a simpler POP-1→ELT-3→ELT-2 cascade, rather than the derived SKN-1/MED→END→ELT-2,7 network of C. elegans mechanism
- ★ Can-skn-1(RNAi) produces no detectable phenotype despite effective knockdown, indicating skn-1 is dispensable for gut specification in C. angaria finding
- ★ A Can-elt-2 genomic transgene (Can-ELT-2::GFP) is expressed intestine-specifically in C. elegans but requires prior gut specification by endogenous end-1,3 finding
- ★ Can-ELT-2::GFP rescues a C. elegans elt-2(ca15); elt-7(tm840) double-null mutant to full viability finding
| Assay | System | Perturbation | Readout | Platform |
|---|---|---|---|---|
| RNAi (feeding and injection) | C. angaria (Can-pop-1, Can-skn-1) | RNAi knockdown | embryonic lethality, morphogenesis, gut granule presence | — |
| single-molecule inexpensive FISH (smiFISH) | C. angaria embryos | none / RNAi knockdown validation | mRNA detection of Can-myo-2, Can-skn-1, Can-elt-1, Can-elt-2, Can-elt-5, Can-elt-3 | — |
| smiFISH | C. elegans embryos | none | Cel-elt-2 mRNA onset and expression pattern | — |
| smiFISH | C. portoensis and C. monodelphis embryos | none | elt-2 orthologue expression in E lineage and gut | — |
| Transgenic reporter (Can-ELT-2::GFP) | C. elegans (wild-type, end-1(ok558) end-3(ok1448), end-3(ok1448), elt-2(ca15); elt-7(tm840) mutant backgrounds) | genetic mutant background combined with transgene | GFP expression pattern, rescue to viability | — |
| DIC and polarized-light microscopy | C. angaria embryos | Can-pop-1 RNAi vs control | morphology and birefringent gut granules | — |
| Whole-genome sequencing and assembly (Nanopore long reads, Illumina short reads, Hi-C) | C. angaria strain PS1010 | none | chromosome-level genome assembly | Nanopore; Illumina; Hi-C |
| Phylogenetic/sequence alignment analysis (RAxML-NG, MView) | GATA factor DNA-binding domains across Caenorhabditis species | none | orthology and conservation of GATA factor DBDs | CIPRES Gateway; MView |
- ▼ Can-pop-1(RNAi) by feeding causes uniform onefold embryonic arrest lacking gut granules 90% (226/252)
- ▼ Can-pop-1(RNAi) by injection produces the same gutless arrest phenotype 64% (149/234)
- – Control RNAi embryos develop normally with gut granules 96% (n=123)
- – Can-skn-1(RNAi) shows no gutless phenotype despite confirmed transcript knockdown n=120 progeny; knockdown confirmed 97% (n=34) vs 6% (n=32)
- ▼ Can-ELT-2::GFP fails to be expressed in end-1(ok558) end-3(ok1448) double mutant embryos 100% (112/112)
- ▲ Can-ELT-2::GFP is still expressed in end-3(989ok1448) single mutant background 93% (n=73)
- ▲ Can-ELT-2::GFP rescues elt-2(ca15); elt-7(tm840) double mutant to full viability 89% (n=123)
- – Subnuclear spots of Can-ELT-2::GFP observed in intestinal nuclei, suggesting autoregulation 36% of 547 gut nuclei (20 worms)
- count 226/252 (90%) (Can-pop-1(RNAi) feeding embryonic arrest with no gut)
- count 149/234 (64%) (Can-pop-1(RNAi) injection embryonic arrest)
- count n=123, 96% elongated with gut granules (control RNAi embryos)
- count n=120 progeny, no phenotype (Can-skn-1(RNAi) progeny scoring)
- count 97% (n=34) vs 6% (n=32) (Can-skn-1 mRNA detection untreated vs RNAi-treated by smiFISH)
- count 112/112 (100%) lacked GFP (Can-ELT-2::GFP absent in end-1 end-3 double mutant)
- count 93% (n=73) (Can-ELT-2::GFP expression in end-3 single mutant)
- count 89% (n=123) (rescue to viability of elt-2; elt-7 double mutant by Can-ELT-2::GFP)
Statistical methods review
Model: sonnetA 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 reports developmental/genetic experiments (RNAi, genetic mutants, transgenic rescue, and smiFISH/GFP imaging) in Caenorhabditis species and characterizes outcomes primarily through descriptive quantification of phenotypic penetrance, expressed as raw counts and percentages with a stated n per condition (e.g., '90% of progeny (n=252)'). No inferential statistical hypothesis tests, p-values, or formal comparisons between groups are described in the text provided.
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Phenotypic penetrance (e.g., gutless phenotype after RNAi) was reported as raw percentages and counts without a formal statistical comparison between treated and control groups.↳ Could also: A proportions test such as Fisher's exact test or a chi-square test — This would provide a formal statistical comparison of penetrance between RNAi/mutant conditions and controls, yielding a p-value to accompany the descriptive percentages.
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Penetrance values are presented as single point percentages (e.g., 90%, 93%, 89%) without any accompanying measure of precision.↳ Could also: A 95% confidence interval for the binomial proportion (e.g., Wilson or Clopper-Pearson interval) — This would convey the precision of each penetrance estimate given the reported sample size, which is especially informative when n varies across experiments.
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Multiple RNAi, mutant, and transgene-rescue comparisons are reported across the study without an explicit multiplicity adjustment.↳ Could also: A multiplicity correction such as Bonferroni or Benjamini-Hochberg FDR applied across the set of penetrance comparisons — This would help control the family-wise error rate when many related comparisons are considered collectively rather than each in isolation.
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The frequency of subnuclear Can-ELT-2::GFP spots was reported as a single pooled percentage (36% of 547 gut nuclei from 20 worms).↳ Could also: Reporting variability across the 20 individual worms (e.g., mean ± SD of per-worm proportions) rather than only the pooled nuclear count — This would distinguish variability between individual animals from the aggregated per-nucleus count, which can be useful when nuclei are clustered within animals.
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Qualitative phenotype scoring (e.g., presence/absence of gut granules, morphogenesis defects) does not mention whether scorers were blinded to genotype or treatment.↳ Could also: Blinded scoring by an observer unaware of the RNAi/genotype condition — This would reduce the potential for unconscious observer bias when classifying qualitative phenotypes such as gut granule presence.
What was reproduced
The exact results taken into scope, with each reported value next to the value our attempt produced.
Scope — pmid-36196618
Paper: Broitman-Maduro G, Sun S, Kikuchi T, Maduro MF. "The GATA factor ELT-3 specifies endoderm in Caenorhabditis angaria in an ancestral gene network." Development (2022). PMID 36196618 · DOI 10.1242/dev.200984.
The paper is primarily a developmental-genetics study (smiFISH, RNAi, transgenics, phylogenetics of GATA domains). One discrete bioinformatic genome-assembly pipeline underlies it: the authors generated a new chromosome-level genome assembly of C. angaria PS1010 to support gene identification. That assembly is the in-scope, pipeline-derived result.
IN SCOPE (pipeline-derived, attempted)
| # | Result | Pipeline | Input data |
|---|---|---|---|
| C1 | De-novo long-read contig assembly of C. angaria PS1010 | NextDenovo v2.4.0 (genome_size=70M, read_cutoff=5k) |
Nanopore MinION reads DRR381124 |
| C2 | Final assembly size / contiguity (deposited genome GCA_947459285.1) | NextDenovo → Pilon ×3 → 3D-DNA + Juicebox (Hi-C) | + Illumina DRR381125, Hi-C DRR381126 |
The core reproducible step is C1: running NextDenovo v2.4.0 with the paper's exact parameters on the deposited Nanopore reads, then comparing assembly size and contiguity to the deposited genome. The deposited genome (GCA_947459285.1, "CAMP", University of Tokyo, 2022-12-02, BioProject PRJEB54634) provides the reported target values, since the main text defers detailed stats to Table S1.
Reported targets (from deposited assembly GCA_947459285.1):
- Total length 71,372,378 bp (~71.4 Mb) — consistent with
genome_size=70M - Scaffolds 6 ("six-piece chromosome-level assembly", main text)
- Contigs 19; contig N50 8,829,618 bp; scaffold N50 11,799,369 bp
OUT OF SCOPE (not pipeline-derived / not attempted)
- Pilon polishing and 3D-DNA/Juicebox Hi-C scaffolding (C2 downstream): attempted only if C1 succeeds and time allows; the chromosome-scale scaffolding requires manual Juicebox curation (non-deterministic, human-in-the-loop) → not 1:1 reproducible by design.
- All wet-lab work: smiFISH/HCR, RNAi, transgenic rescue, antibody staining.
- GATA DBD phylogenetics (RAxML-NG via CIPRES) — manual alignment curation, small manual analysis, out of the genome-pipeline scope.
- BLAST-based ortholog identification — manual/interactive.
Approach
Reproduce C1 on «our HPC» (SLURM): NextDenovo v2.4.0 binary (exact paper version) on DRR381124, parameters per Methods. Compute assembly size, #contigs, N50 with seqkit/assembly-stats; compare to the deposited contig-level stats. Optionally BUSCO (nematoda_odb10) for completeness as a bonus quality check.
Assessments & scoring basis
Each contributor’s verdict, the per-question basis, and the auditable, itemised worksheet behind it.
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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.