The manganese transporter SLC39A8 links alkaline ceramidase 1 to inflammatory bowel disease.
Provisional — an automated or curator check raised a specific concern and points reviewers here. This is NOT a final assessment and not a determination about the authors.
The main results reproduced, with only marginal, non-material deviations.
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
- ✓The central claim held under reproduction
- 🟡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
- 🟡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
Described well enough for the RNA-seq headline; PARTIAL overall. The repo (SeoResearchLab/IECKO2023) ships DATA ONLY (one lipidomics .xlsx) and NO analysis code, so reproduction = standard tools on the paper's own data (P16). C1 RNA-seq: GEO GSE192695 ships the authors' processed expected-count matrix; DESeq2 (~tissue+genotype, ISKO vs WT, padj<0.1) reproduces the paper's central transcriptomic claim 1:1 -- EXACTLY 4 DEGs: Slc39a8 down + Acer1/Ighv1-55/Entpd4b up, matching 'four genes, only Slc39a8 down, Acer1 among up-regulated'. C2: the shipped ceramide_SPB t-test numbers are exactly re-derivable from the shipped raw matrix (group-mean corr 1.000, p corr 0.998) -> shipped stats are genuine (anti-fabrication check passes). C3 (Fig 8k '40 lipids P_adj<0.2' and 'SMs all downregulated'): NOT reproduced -- a standard t-test+BH on the full tissue-wt-normalized panel yields 204 (FDR<0.2) / 47 (raw p<0.05), and SMs are 28/56 down, not all; the authors' exact full-panel filtering is undocumented because no code was deposited. NOT attempted (out of scope/80-20): STAR alignment from raw FASTQ (counts already deposited), MS peak-picking/lipid ID (proprietary upstream), and all wet-lab phenotyping. No fabrication detected; the Fig 8k gap is under-specification, not fabricated values.
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.
-
v1 current initial assessment Score 70assessed: 2026-06-15 ⛓ 2c51d131d925
✎ 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
-
🤖 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 hypothesized that intestinal epithelial SLC39A8 controls intestinal Mn homeostasis and epithelial integrity, and that dysregulation of Mn homeostasis disrupts the epithelial barrier, thereby predisposing to inflammatory bowel disease (IBD).
- ★ Intestinal epithelial cell-specific deletion of Slc39a8 causes systemic manganese (Mn) deficiency in blood and multiple organs. finding
- ★ Intestinal epithelial SLC39A8 is essential for in vivo intestinal absorption of dietary Mn. finding
- ★ SLC39A8 localizes to the apical membrane of enterocytes and mediates 54Mn uptake from the luminal/apical side. mechanism
- ★ Unbiased RNA-seq identifies alkaline ceramidase 1 (ACER1) as a target affecting intestinal epithelial integrity in Slc39a8-IEC KO intestine. finding
- ★ Treatment with an ACER1 inhibitor attenuates colitis in Slc39a8-IEC KO mice by remedying barrier dysfunction and enhancing tight junction proteins. finding
- ★ IEC-specific deletion of Slc39a8 exacerbates DSS-induced colitis following intestinal epithelial injury. finding
- Generation of Slc39a8-IEC KO mice (Slc39a8 fl/fl x Villin-Cre) and intestinal organoid monolayer cultures as models to study Mn transport and epithelial integrity. resource
- ★ ACER1 inhibition is proposed as a therapeutic target for IBD associated with impaired Mn homeostasis/SLC39A8 deficiency. mechanism
| Assay | System | Perturbation | Readout | Platform |
|---|---|---|---|---|
| qPCR (gene expression) | C57BL/6J mouse tissues and control vs Slc39a8-IEC KO mouse intestinal/other tissues; Slc39a8-IEC KO-derived enteroids | Slc39a8 IEC-specific KO (Villin-Cre) | Slc39a8 and metal transporter (Slc11a2/DMT1, Slc39a14/ZIP14, Slc30a10/ZnT10, Slc40a1/FPN) mRNA levels | — |
| Immunofluorescence/confocal microscopy | Frozen intestinal sections (duodenum, jejunum, ileum, colon) of C57BL/6J mice; enteroid/colonoid monolayers | none / Slc39a8 KO | SLC39A8, ZO-1 protein localization (apical membrane) | — |
| ICP-MS metal quantification | Tissues (intestine, liver, bile, lung, kidney, heart, brain, whole blood) from control and Slc39a8-IEC KO mice | Slc39a8 IEC-specific KO | Mn, zinc, iron, copper, selenium concentrations | ICP-MS |
| Radiotracer 54Mn absorption (oral-intragastric gavage) | Control and Slc39a8-IEC KO mice (10 weeks) | Slc39a8 IEC-specific KO; 54Mn gavage | 54Mn radioactivity (cpm) in blood, enterocytes, liver, lung, kidney, heart, femur | γ-counter |
| Radiotracer 54Mn clearance (intravenous tail vein injection) | Control and Slc39a8-IEC KO mice | Slc39a8 KO; IV 54Mn | 54Mn radioactivity (cpm) in blood and tissues | γ-counter |
| 54Mn uptake assay in organoid monolayers (apical and basolateral) | Intestinal organoid (enteroid/colonoid) monolayer cultures from control and Slc39a8-IEC KO mice | Slc39a8 KO; 54Mn added to apical or basolateral chamber | cell-associated 54Mn radioactivity | gamma counter |
| Unbiased transcriptomic analysis (RNA-seq) | Slc39a8-IEC KO intestine | Slc39a8 IEC-specific KO | differential gene expression (identified ACER1) | — |
| DSS-induced experimental colitis | Control and Slc39a8-IEC KO mice | Dextran sodium sulfate (DSS); ACER1 inhibitor treatment | colitis severity / intestinal injury, barrier permeability, tight junction proteins | — |
- ▼ Slc39a8 mRNA markedly reduced in Slc39a8-IEC KO intestine: duodenum, jejunum, ileum, colon -90% duodenum, -90% jejunum, -93% ileum, -98% colon
- ▼ Whole blood and tissue Mn (ileum, colon, liver, lung, heart, brain) substantially reduced in Slc39a8-IEC KO mice; zinc, iron, copper, selenium unchanged
- ▼ 54Mn in whole blood lower in KO mice 15 min after oral gavage -33% (P<0.05)
- ▼ 54Mn in ileum reduced in KO mice after oral gavage -44% (P<0.05)
- ▼ 54Mn reduced in liver, lung, kidney, heart, femur after oral gavage in KO mice liver -61%, lung -59%, kidney -81%, heart -69%, femur -41% (all P<0.05)
- – After IV 54Mn injection, blood and tissue 54Mn did not differ between KO and control (excludes increased clearance)
- ▼ Apical 54Mn accumulation impaired in Slc39a8-IEC KO enteroid and colonoid monolayers; basolateral uptake unchanged enteroid -35% (P<0.01), colonoid -41% (P<0.001)
- – Slc39a8-IEC KO enteroids show increased Slc11a2/DMT1 and decreased Slc39a14/ZIP14, Slc30a10/ZnT10, Slc40a1/FPN transcripts
- fold_change -98% (P<0.001) (Slc39a8 mRNA reduction in colon of Slc39a8-IEC KO mice)
- fold_change -44% (P<0.05) (54Mn reduction in ileum after oral gavage (control n=4, KO n=4))
- fold_change -33% (P<0.05) (54Mn reduction in whole blood 15 min after oral gavage)
- fold_change -81% (P<0.05) (54Mn reduction in kidney after oral gavage in KO mice)
- fold_change -35% (P<0.01) (Apical 54Mn accumulation reduction in KO-derived enteroid monolayers)
- fold_change -41% (P<0.001) (Apical 54Mn accumulation reduction in KO-derived colonoid monolayers)
- count n=6 per group (C57BL/6J mice per group for qPCR tissue expression of Slc39a8)
- count n=5 male, n=6 female per group (ICP-MS Mn analysis in control and Slc39a8-IEC KO mice at 20 weeks)
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.
This study used a conditional knockout mouse model (Slc39a8-IEC KO) and intestinal organoid monolayer cultures to investigate the role of intestinal epithelial SLC39A8 in manganese homeostasis and epithelial integrity. Primary comparisons between knockout and control animals were made with unpaired two-tailed Student's t-tests for most continuous outcomes (metal concentrations by ICP-MS, radiotracer counts, organoid uptake) and one-way ANOVA with Bonferroni post-hoc correction for multi-tissue gene expression data. Results throughout are reported as mean ± SEM with p-values expressed as threshold inequalities.
| Test | Applied to | n | Assumptions |
|---|---|---|---|
| One-way ANOVA with Bonferroni's multiple comparisons post-hoc test | Fig. 1c — qPCR of Slc39a8 mRNA across multiple intestinal segments and non-intestinal tissues in control vs. Slc39a8-IEC KO mice | n = 4 per group | not stated |
| Unpaired two-tailed Student's t-test | Fig. 1d — ICP-MS metal concentrations (Mn, and by implication Zn, Fe, Cu, Se in Supplementary Figs. 2a–d) across tissues in control vs. Slc39a8-IEC KO mice, stratified by sex | n = 5 male per group; n = 6 female per group | not stated |
| Unpaired two-tailed Student's t-test | Fig. 2a–f — radiotracer 54Mn counts in blood, intestinal segments, and peripheral tissues after oral gavage or intravenous injection in control vs. Slc39a8-IEC KO mice | n = 4 per group (n = 2 male, n = 2 female each) | not stated |
| Unpaired two-tailed Student's t-test | Fig. 3d — apical 54Mn accumulation in enteroid and colonoid monolayer cultures from control vs. Slc39a8-IEC KO mice | n = 3 biologically independent samples | not stated |
| Unpaired two-tailed Student's t-test | Fig. 3f — basolateral 54Mn accumulation in enteroid and colonoid monolayer cultures from control vs. Slc39a8-IEC KO mice | n = 3 biologically independent samples | not stated |
-
Dispersion is reported throughout as mean ± SEM with small group sizes (n = 3–6)↳ Could also: Mean ± SD, or mean with 95% confidence intervals, could also convey the spread of the data — With small n, SD gives readers a direct sense of between-animal variability; 95% CIs additionally communicate the uncertainty around the estimated mean and are increasingly favoured in reporting guidelines for preclinical studies
-
Multiple independent unpaired t-tests were used across many tissue/organ comparisons within the same experiment (e.g., Figs. 1d, 2b–c, 2e–f)↳ Could also: A one-way or two-way ANOVA (with tissue/organ as a factor) followed by a post-hoc correction (e.g., Tukey HSD or Holm-Bonferroni) could also be applied to the full family of comparisons — Treating the organ-level comparisons within a single experiment as a family and correcting jointly would formally control the experiment-wise error rate across those simultaneous tests
-
Unpaired t-tests were used for groups of n = 3–4 per group (Figs. 2a–f, 3d, 3f) without stated normality assessment↳ Could also: A non-parametric alternative such as the Mann-Whitney U test (Wilcoxon rank-sum) could also be applied when sample sizes are too small to assess normality reliably — With n as low as 3, the central-limit-theorem rationale for t-test robustness is limited; a rank-based test makes no distributional assumption, which is an option some journals require for very small n
-
Sex was treated as a stratification variable (separate male/female panels) rather than a formal factor in the analysis of metal concentrations (Fig. 1d)↳ Could also: A two-way ANOVA with genotype and sex as factors could also model the sex × genotype interaction formally — Including sex as a crossed factor tests whether the knockout effect differs by sex and can increase statistical power by accounting for sex-related variance; NIH guidelines increasingly encourage this approach in preclinical studies
-
P-values are reported only as threshold inequalities (< 0.001, < 0.05, < 0.01)↳ Could also: Exact p-values (e.g., p = 0.023) could also be reported — Exact p-values allow readers and meta-analysts to apply different alpha thresholds, perform power calculations, and aggregate findings across studies; reporting guidelines such as APA and many journals now recommend exact values
-
The unbiased RNA-seq transcriptomic analysis is mentioned in the abstract and methods narrative but statistical details (differential expression method, FDR threshold, fold-change cutoff) are not present in the available text excerpt↳ Could also: Standard workflows such as DESeq2 (negative-binomial Wald test with Benjamini-Hochberg FDR) or edgeR could be applied; the chosen method and thresholds would ideally be stated explicitly — Full disclosure of the DE pipeline, normalisation strategy, and multiple-testing correction threshold allows reproducibility assessment and comparison with other transcriptomic datasets
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.
-
Oral 54Mn absorption into blood is reduced 33% in Slc39a8-IEC KO mice 15 min after gavage.other mouse blood down 2024×1papers★ This paper is the founder (earliest)
-
Ileal 54Mn accumulation is reduced 44% in Slc39a8-IEC KO mice after oral gavage.other mouse ileum down 2024×1papers★ This paper is the founder (earliest)
-
Apical but not basolateral 54Mn uptake is reduced 35-41% in Slc39a8-IEC KO enteroid and colonoid monolayers.other mouse intestinal organoid down 2024×1papers★ This paper is the founder (earliest)
-
Systemic 54Mn distribution to liver, lung, kidney, heart, and femur is reduced 41-81% in Slc39a8-IEC KO mice after oral gavage.other mouse liver down 2024×1papers★ This paper is the founder (earliest)
-
Whole blood and multi-tissue manganese is substantially reduced in Slc39a8-IEC KO mice; zinc, iron, copper, and selenium are unchanged.other mouse down 2024×1papers★ This paper is the founder (earliest)
-
IV-injected 54Mn clearance from blood and tissues is unchanged in Slc39a8-IEC KO mice, excluding increased systemic clearance as a mechanism.other mouse none 2024×1papers★ This paper is the founder (earliest)
-
Slc39a8-IEC KO enteroids show compensatory upregulation of SLC11A2 and downregulation of SLC39A14, SLC30A10, and SLC40A1 metal transporter transcripts.qPCR mouse intestinal organoid mixed 2024×1papers★ This paper is the founder (earliest)
-
SLC39A8 mRNA is reduced 90-98% across all intestinal segments in Slc39a8-IEC KO mice.qPCR mouse intestine down 2024×1papers★ 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.
What was reproduced
The exact results taken into scope, with each reported value next to the value our attempt produced.
Scope — pmid-38839750
Paper: Choi et al. 2024, Nat Commun 15:4775. "The manganese transporter SLC39A8 links alkaline ceramidase 1 to inflammatory bowel disease." DOI 10.1038/s41467-024-49049-8 · PMCID PMC11153611.
Model: intestinal-epithelial-cell-specific Slc39a8 knockout (Slc39a8-IEC-KO,
Slc39a8-fl/fl; Villin-Cre) vs control (Slc39a8-fl/fl).
Artifacts available
- Code repo
github.com/SeoResearchLab/IECKO2023(commit765bc5c, default branchmain, public, not archived). Contains NO analysis code — a single fileEX01243_LipidomicsData.xlsx(the lipidomics dataset). So there is no authors' pipeline script to run; reproduction = applying standard tools to the shipped data per the Methods text (brief rule P16: valid). - Data GEO
GSE192695— RNA-seq of ileum+colon, control vs Slc39a8-IEC-KO, n=3/group, 12 samples. Ships a processed expected-count matrix (GSE192695_gene_expected_count.txt.gz, RSEM/STAR, Ensembl GRCm38 gene IDs).
In scope (pipeline-derived, attempted)
| id | result | pipeline | location |
|---|---|---|---|
| C1 | "four genes with altered expression (P_adj<0.1); only Slc39a8 down, Acer1 among up-regulated" | STAR→RSEM counts → DESeq2 (Methods). Counts are deposited → DESeq2 only. | Fig 6a; Results "Transcriptome analyses…"; GEO summary |
| C2 | ceramide/sphingoid-base statistics (group means, t-test p, FDR) for 102 species | t-test on ln-transformed intensities (authors ship the t.test + ceramide_SPB sheets) |
Excel t.test sheet (internal-consistency / anti-fabrication check) |
| C3 | "40 differentially regulated lipids (P_adj<0.2)"; "sphingomyelins were all significantly downregulated" | t-test + FDR on full tissue-wt-normalized lipidome | Fig 8k; Results lipidomics paragraph |
Out of scope (not attempted, why)
- All wet-lab / phenotyping: histology, IBD/colitis scoring, Mn measurements (ICP-MS), ceramidase enzyme assays, organoid imaging, body-weight/survival — manual/bench, no pipeline.
- STAR alignment from raw FASTQ — unnecessary; GEO ships the expected-count matrix the authors used; running STAR would re-derive identical inputs at large compute cost (80/20).
- Lipid identification (LIPIDBLAST/MultiQuant peak picking) — upstream proprietary MS processing; shipped Excel already contains the processed intensity matrices.
Compute
All on «our HPC» («infra» «our HPC»-2 SLURM, kubisch_std). «infra» work dir:
«path».
No data on «host» (only small result CSVs).
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.
The paper's central RNA-seq claim reproduces 1:1 from deposited GEO counts (exactly 4 DEGs: Slc39a8 down, Acer1/Ighv1-55/Entpd4b up), and an anti-fabrication check confirms the shipped ceramide t-test values are exactly re-derivable (mean corr 1.000, p corr 0.998). The one substantive deviation is Fig 8k ('40 lipids P_adj<0.2' and 'SMs all downregulated'), which does not reproduce (204/47 lipids; 28/56 SM down) — this sits on the authors'/data-availability side because the repo is a data-only deposit with no analysis code, leaving the exact filtering under-specified rather than fabricated. Overall a solid reproduction of the core conclusion with an explainable, secondary lipidomics discrepancy → yellow.
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.
Are you an author? We would genuinely like to hear from you — to clarify the record, add data or code, re-run the pipeline after an accession update, and publish your response right next to the assessment. Everything here is open and auditable.
🚩 Report an error in this record
Spotted something wrong — a verdict you’d contest, a data or value error, or a private detail that slipped through? Tell us, with a short justification. Authors and readers are equally welcome to write in; we review every report.
Prefer email, or the form below not working? Contact us at support@doesitreproduce.com.
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.