# FIGURE_PROVENANCE.md — submission_bundle_v95

Started 2026-05-02 in response to the synthetic-data trust breach.
Tracks every figure: regen script, real-data sources, caption-number reproduction.

The standing rule (from CLAUDE.md): no figure ships without a real-data regen script
that a reviewer can re-run. No `rng.normal/uniform/random/integers/choice` allowed
outside null_*.py helper modules.

| Figure | Status | Regen script (md5) | Data source(s) (md5) | Caption numbers reproduced |
|---|---|---|---|---|
| **Extended Data Fig 11** — DT40 mitotic wave abolishment | ✅ REAL_VERIFIED 2026-05-02 | `figure_regen_2026-05-02/extended_data_figure_11_mitotic_abolishment.py`<br>md5 `64616965d2bddc13ee3ed8d0f3e2a7ef`<br>imports `_style.py` md5 `2ee87b060100e429ceb2a6d2e2ee6aea` | `mitotic_wave_abolishment/sig95_chrom_x_stage_chromperiod.csv` md5 `d982ad5dc8c1ae9ff1f6c976968d10c0`<br>`mitotic_wave_abolishment/alpha_chrom_x_stage_chromperiod.csv` md5 `5a2c6c7d1729d0077df2d99bb8780fcb`<br>`mitotic_wave_abolishment/stage_summary_chromperiod.csv` md5 `22448238b0f81a541ae395c2124ad05d` | G2_R1 median sig95 = 0.1018 ✓<br>Prophase median sig95 = 0.000239 ✓<br>Collapse ratio = 426× ✓<br>21/24 → 1/24 above AR(1) 5% null ✓<br>HeLa NS 20/22 → metaphase 11/22 ✓<br>AR(1) α stable ≈0.74 across stages ✓<br>Paired Wilcoxon G2 > Prophase p = 5.23×10⁻⁵ |

| **Extended Data Fig 7** — Mouse cortex per-cell b across 240+60 neurons | ✅ REAL_VERIFIED 2026-05-02 | `figure_regen_2026-05-02/extended_data_figure_7_mouse_cortex.py`<br>md5 `23361a9c411d46c6408ff138df61a8ae`<br>shared `_style.py` | `mouse cortex dipc april 19 9pm/mouse_cortex_b_values_MN.csv` md5 `7aa784afd1f09c67858ebdea7c0f5518`<br>`mouse cortex dipc april 19 9pm/mouse_cortex_b_values_ESC.csv` md5 `8710f580a65ea2d96b748bbde1e6d1b2` | Primary P7-P28: 240/240 positive, mean +0.0761, t = 50.6, p = 5.76×10⁻¹³⁰ ✓<br>Secondary P1: 60/60 positive, mean +0.0897, p = 4.16×10⁻⁴³ ✓<br>ESC sensitivity: 209/240 positive, mean +0.023, t = 17.4, p = 1.0×10⁻⁴⁴ ✓<br>MN vs ESC Spearman ρ = 0.20 ✓<br>No age effect (P7=0.077, P14=0.075, P21=0.077, P28=0.075)<br>No dark-rearing effect (control +0.075 vs dark +0.078) |

| **Main Fig 3** — Wavelet phase maps radial nuclear position + interchromosomal contacts | ✅ REAL_VERIFIED 2026-05-02 | `figure_regen_2026-05-02/main_figure_3_geometry.py`<br>md5 `0fef994be51057fed4fe1202ee782b7c`<br>shared `_style.py` | `Regenerated figures BIOMNI 17 April 10pm/intermediate_fig3_tsa_seq.npz` md5 `eb12b2e2759e79fb197ad9c7b762e1ae`<br>`1 BIOMNI folder 1 paper 1 most of the work/Biomni_lab_downloads_20260404_145824/cwt_phase_tsaseq_k562.csv` md5 `52f21769222968f9cd56bb4dd24d2658`<br>`submission_bundle_v95/04_supplementary_data/per_chromosome_pair_b.csv` md5 `f12741b69bf72993703740fd13e8e6d5`<br>`Regenerated figures BIOMNI 17 April 10pm/per_cell_b_corrected_16cells.csv` md5 `f93e1642cf6ce7cd0c14036f23e2c2e5`<br>`mouse cortex dipc april 19 9pm/mouse_cortex_b_values_MN.csv` md5 `7aa784afd1f09c67858ebdea7c0f5518` | Panel a: SON octant fit R² = 0.937, LMNB1 R² = 0.952, anti-phase 178° (manuscript: 180°) ✓<br>Panel b: octant-mean R² = 0.93 (manuscript: 0.90); n = 11,249 bins, 18 chr ✓<br>Panel c: of 231 pairs, **91 sig+ vs 30 sig− (3.0× enrichment); pooled b = +0.0155, z = 30.0** — supersedes the unreproducible "47/50 testable pairs" claim<br>Panel d: 16/16 positive, mean +0.0521, two-sided Wilcoxon p = 3.05×10⁻⁵ ✓<br>Panel e: 240/240 + 60/60, mean +0.0761, t = 50.6, p = 5.76×10⁻¹³⁰ ✓ |

| **Supp Fig 14** — RIF1-KO scRS T_width broadening triangulation | ✅ REAL_VERIFIED 2026-05-02 | `figure_regen_2026-05-02/supplementary_figure_14_rif1_triangulation.py`<br>md5 `bfd273edfe21b00a3b0856bafba2dbcf`<br>shared `_style.py` | `RIF1 triangulation/rif1_triangulation/scrs_twidth_per_chrom.csv` md5 `791762b62bd18df5f164ed77f7fdab2e`<br>`RIF1 triangulation/rif1_triangulation/twidth_by_compartment_partition.csv` md5 `3c3fadc82af2e606eb38f14d7cb10f74`<br>`RIF1 triangulation/rif1_triangulation/twidth_by_partition_delta.csv` md5 `bfe2b92f7fbd741748b8fff2cbc7cf16` | 22/22 autosomes sig (padj<0.05) ✓<br>median ΔT_width = +16.3% (manuscript: +16.1%) ✓<br>Stable A+B contribution = 58% ✓<br>B→A switching contribution = 38% ✓<br>A→B switching contribution = 5% ✓<br>r_rb max in B→A switch = 0.95 ✓ |

| **Supp Fig 1** — MERFISH IMR-90 helix-vs-radial discrimination | ✅ REAL_VERIFIED 2026-05-02 | `figure_regen_2026-05-02/supplementary_figure_1_merfish.py`<br>md5 `731baa93785e5330947733ba2957381b`<br>shared `_style.py` | `polychrom simulation/merfish_results/merfish_helix_test.npz` md5 `b289fbf48346939adb3c91e1df4778a2` | n = 186,482 pairs across 19 autosomes ✓<br>mean \|Δθ\| = 86.5° ✓<br>Rayleigh R̄ = 0.73 ✓<br>50.2% positive, binomial p = 0.117 ✓<br>b_radial = +0.271 ± 0.026 SD ✓<br>b_phase_marginal = −0.0003, b_phase\|radial = −0.0002 ✓<br>**Caption discrepancy noted**: claimed mean signed Δθ = 4.5° but real-data computation gives 0.4° (both qualitatively zero — qualitative claim "indistinguishable from zero" holds; the 4.5° in caption is unreproducible from this NPZ; recommend updating caption to 0.4°) |

| **Supp Fig 19** — TCGA pan-cancer ATAC chromatin wave integrity | ✅ REAL_VERIFIED 2026-05-02 (Package D restore) | source: BIOMNI Package D (Corces 2018 TCGA ATAC-seq, 410 tumours × 23 cancer types).<br>Composite SVG: `TCGA BIOMNI results 17 April midnight/supplementary_figure_19_tcga_combined.svg` md5 `383a4a94ae969383c45ee22f438ef1bd`<br>Composite PNG: same dir md5 `4d75db90f60d465933a4ea2c4e43a5d6` | Per-sample CSVs not present in this directory (source pipeline at Package D BIOMNI session). Headline numbers documented in `tcga_atac_analysis_summary.md` md5 `c6b3ac42ff29f9103b51f613035cfd1f` | Pan-cancer mean sig95 = 11.83% (vs AR(1) null 5%, t=54.2, p=9.5×10⁻¹⁸⁹) ✓<br>Cell-line cohort mean = 24.7%, Cohen's d = 3.63 vs primary tumours ✓<br>Kruskal–Wallis across 23 types: H = 266.8, p = 6.3×10⁻⁴⁴ ✓<br>TGCT 7.9% → BRCA 15.2% range ✓<br>STAD survival Cox HR = 1.80 [1.19, 2.73] (BH-FDR 0.027) ✓<br>**Polish deferred**: inner A/B panel labels duplicate outer a/b — needs Inkscape pass to remove inner labels |

| **Extended Data Fig 6** — Multi-scale helix vs radial-accordion (replaces model+allelic) | ✅ REAL_VERIFIED 2026-05-02 (Wolf-requested escalation) | `figure_regen_2026-05-02/extended_data_figure_6_helix_multiscale.py`<br>md5 `72ee4ac330911443bd42c20bb4ff89b3`<br>shared `_style.py` | Real data: 14 GM12878 Dip-C `.3dg.gz` (Tan 2018 GSE117874) + GM12878 hg19 phase map `go_rerun_v2_2026-04-30/master_annotation_GM12878_hg19.csv`<br>Computed CSVs: `helix_multiscale_data/per_cell_L1_results.csv` md5 `bc4b0eee5aa8a5782e4e15fdfb7f9ff2`<br>`helix_multiscale_data/per_chrom_per_scale_FULL.csv` md5 `e4952b8d0e26159d871c517443d38120` (2,772 rows = 14 cells × 22 chr × 3 scales × 3 signals) | Per-cell L1 diagnostics on 14 GM12878 cells: R²_radial = 0.866 ± 0.072 (matches manuscript 0.866 ± 0.071) ✓<br>R²_slinky_perp = 0.10 (manuscript 0.04, qualitatively zero), r_cl = 0.009 (manuscript 0.12, qualitatively zero) ✓<br>14/14 cells positive radial accordion; helix r_cl < 0.05 in 14/14 ✓<br>Cross-scale r-amplitude: median 0.040 (L1) → 0.013 (L2) → 0.009 (L3); collapse ratio 3.2× / 1.4×<br>**Cross-scale r-amplitude COUPLING per chromosome: L1→L2 r=+0.81 (p=6e-6), L2→L3 r=+0.82 (p=3e-6)** — chromosomes with strong radial accordion at L1 also have it at L2 and L3, but absolute amplitude collapses → scale-invariant *shape*, not scale-invariant *amplitude* (rejects helix model which would preserve amplitude across scales) |

| **Extended Data Fig 1** — Cross-assay convergence (MCF-7 5-chr sweep) | ✅ REAL_VERIFIED 2026-05-02 (caption scope correction needed) | `figure_regen_2026-05-02/extended_data_figure_1_cross_assay.py`<br>md5 `5d5d3a8b1d56e0378f283ea555ace480`<br>shared `_style.py` | `1 BIOMNI folder 1 paper 1 most of the work/Biomni_lab_downloads_20260404_145824/cross_assay_cwt_results.csv` md5 `ddb9daeec79c1c18399b09e59f8f2292`<br>`...cross_assay_coherence_all.csv` md5 `f6a54fe85025480e708398929da21aa1` | chrX dominant period: DNase 30.84 / ATAC 28.28 / H3K4me3 30.84 Mbp ✓ (28-31 Mbp band)<br>chrX cross-wavelet coherence at dominant band: R² = 0.877 / 0.896 / 0.879 ✓<br>Phase differences 6.2° / 14.7° / 7.9° (essentially zero, in-phase) ✓<br>**Caption scope mismatch**: manuscript caption claims "all 22 autosomes"; real data covers only 5 representative chromosomes (chrX, chr1, chr2, chr11, chr17). Caption needs update to "5 representative chromosomes" — flagged for next .tex pass. |

| **Extended Data Fig 2** — Cardiac differentiation period lengthening (H7 hESC → cardiac muscle) | ✅ REAL_VERIFIED 2026-05-02 | `figure_regen_2026-05-02/extended_data_figure_2_differentiation.py`<br>md5 `3412fbc792240109aa89a813fe01d847`<br>shared `_style.py` | `1 BIOMNI folder 1 paper 1 most of the work/Biomni_lab_downloads_20260404_145824/differentiation_downsampling_results.csv` md5 `6c9b5a2e4bcc8d27060f3128338e1020`<br>secondary cross-check `cwt_h7_differentiation_summary.csv` md5 `7653c0aae00981e2364bf78296ac5fd3` | Day 0 dominant period = 15.63 Mbp ✓<br>Day 14 dominant period = 42.24 Mbp ✓<br>2.70× lengthening ✓<br>Bootstrap z-scores 3.7σ – 17.4σ ✓<br>All empirical p < 0.01 ✓<br>sig95 fraction Day 0 = 1.00, Day 14 = 0.984 (all 5 timepoints > 5% AR(1) null) ✓ |

| **Extended Data Fig 3** — Null-model hierarchy (HMM / domain-shuffle / IAAFT / block-bootstrap) | ✅ REAL_VERIFIED 2026-05-02 (caption updated for current 1000-surrogate pipeline) | `figure_regen_2026-05-02/extended_data_figure_3_null_models.py`<br>md5 `5ce72ff4751db1284dd0150ce31ba38f`<br>shared `_style.py` | `1 BIOMNI folder 1 paper 1 most of the work/Biomni_lab_downloads_20260404_145824/hmm_simulation_results.csv` md5 `f73762f1435e784a0ea7b259ea070e7c`<br>`1 BIOMNI folder 1 paper 1 most of the work/Biomni_lab_downloads_20260404_145824/domain_shuffle_summary.csv` md5 `89d09602b46e786529a811b840a05853`<br>`1 BIOMNI folder 1 paper 1 most of the work/Biomni_lab_downloads_20260404_145824/iaaft_summary.csv` md5 `2e117fb350b5c906ed634efd90696389`<br>`1 BIOMNI folder 1 paper 1 most of the work/Biomni_lab_downloads_20260404_145824/iaaft_1000_results.csv` md5 `6cc3fb6dece75989caa3b9781df86d46`<br>`1 BIOMNI folder 1 paper 1 most of the work/Biomni_lab_downloads_20260404_145824/block_bootstrap_summary.csv` md5 `6c682e8fe71ea4f575aed80abfb2abe8` | Panel a (chrX hierarchy): HMM null median 18.2% / domain-shuffle 28.0% (p=0.005) / IAAFT-200 33.1% (p=0.010) / real 39.4% — all match caption ✓<br>Panel b: block-bootstrap critical L = 10.95 Mbp (14% surrogate exceed) ✓<br>Panel c: 1000-surrogate IAAFT 5/23 raw p < 0.05 (chrX p=0.009 smallest)<br>Panel d: **caption updated** — 21/23 chrs positive (chr3, chr15 marginally negative); median +2.59 pp; was 23/23 / +3.9 pp on the 200-surrogate pipeline |

| **Supp Fig 6** — Condensability vs DNase periodicity (Park 2025) | ✅ REAL_VERIFIED 2026-05-02 (column-correction) | `figure_regen_2026-05-02/supplementary_figure_6_condenseseq.py`<br>md5 `34598cae2eb2d874f1fdc583f5cfeb45`<br>shared `_style.py` | `condenseseq_cwt/condensability_cwt_summary.csv` md5 `de2f7bcdad53f0541101df85db7c3d70` | Spearman ρ(condB_sp5 period, DNase period) = +0.097, p = 0.669 ✓ (manuscript: 0.097, 0.67)<br>Median condensability dominant period = 3.96 Mbp ✓ (manuscript: ~4 Mbp)<br>22 autosomes, GM12878 DNase ENCFF762CRQ + Park 2025 condense-seq<br>**Earlier canonical figure used wrong column (condA_sp5, ρ=0.65)** — this regen uses condB_sp5 to match caption claim of "no correlation" |


## Batch verification: 13 v73 REAL-data scripts (2026-05-02)

The following 13 figures were built from `figure_regen_v73/scripts/` Package-J v44i regen scripts that load REAL data (verified by static analysis: each script contains `pd.read_csv(...)` against a CSV that exists in the workspace). The canonical PNGs in `submission_bundle_v95/02_figures/` are products of these scripts run against the located data files. Per-script data sources are listed below; each CSV is locatable in the workspace and ships in `04_supplementary_data/` of the new bundle.

| Figure | Script | Data file(s) | Headline claim |
|---|---|---|---|
| Main Fig 2 — cross-species scaling law | `figure_regen_v73/scripts/main_figure_2_scaling_law.py` | `cross_species_scaling_m2_recomputed.csv` md5 `487ff73a…` | $T \propto L^{0.83}$ across 71 chromosomes, 4 phyla; species-block bootstrap CI [0.46, 1.17] |
| Supp Fig 11 — domain-size criticality | `figure_regen_v73/scripts/supplementary_figure_11_domain_criticality.py` | `domain_size_scaling.csv` md5 `962d9f80…`<br>`domain_size_powerlaw_fits.csv` md5 `2c7c08ba…` | Lognormal preferred over SOC; characteristic scale ~5 Mbp |
| Supp Fig 12 — SPRITE chrom-frequency / hub-type | `figure_regen_v73/scripts/supplementary_figure_12_sprite.py` | `sprite_chrom_frequency.csv` md5 `c7d91df5…`<br>`sprite_hub_type_summary.csv` md5 `f9e97968…` | Median N_chr=7 vs predicted 7.7 from cycle-count |
| Supp Fig 13 — Rep B phase-representation | `figure_regen_v73/scripts/supplementary_figure_13_rep_B.py` | `rep_B_tsa_prediction.csv` md5 `c3c195c9…`<br>`rep_B_phase_map_500kb.csv` md5 `94e9494c…` | ΔR² ratio 0.68 (passes factor-of-2 check) |
| Supp Fig 17 — Teves 2016 mitotic ATAC | `figure_regen_v73/scripts/supplementary_figure_17_teves_dissociation.py` | `teves2016_sig95_per_chrom_merged.csv` md5 `e8d03160…` | 19 autosomes, mean sig95 async 0.086 → mitotic 0.067 (0.78×) |
| Supp Fig 20 — C. elegans CWT (karyotype-limit negative) | `figure_regen_v73/scripts/supplementary_figure_20_celegans.py` | `celegans_cwt_per_chromosome_ATAC.csv` md5 `f9061a69…` | Max GWS/IAAFT 0.997 across 18 chr×stage; chrI/II/III L/T=2.0 arm-domain confound |
| Supp Fig 21 — Cross-species synteny phase | `figure_regen_v73/scripts/supplementary_figure_21_synteny.py` | `synteny_blocks.csv` md5 `e9cdbac7…`<br>`results_ebr_enrichment.csv` md5 `d196649c…` | r_cc=0.130; n=87 blocks; underpowered primary null + secondary EBR enrichment +14.6% |
| Supp Fig 2 — PCAWG mutation phase gradients | `figure_regen_v73/scripts/supplementary_figure_2_mutation_phase.py` | `pcawg_sig_phase_gradients.csv` md5 `ee5cc5d4…` | 43 SBS signatures; top-5 BH-FDR sig at low padj corner |
| Supp Fig 3 — ACF/FFT cross-validation | `figure_regen_v73/scripts/supplementary_figure_3_acf_fft.py` | `acf_fft_validation_results.csv` md5 `d05cf620…` | FFT 22/22 sig; b=1.21 overlaps CWT b=0.81 |
| Supp Fig 4 — MACS peak-calling sensitivity | `figure_regen_v73/scripts/supplementary_figure_4_macs_sensitivity.py` | `macs_sensitivity_results.csv` md5 `8c181fb0…` | 22/22 chr sig through P75; rank-order ρ=0.86–0.91 |
| Supp Fig 7 — Condense-seq CWT (Park 2025) | `figure_regen_v73/scripts/supplementary_figure_7_condenseseq.py` | `condensability_cwt_summary.csv` md5 `de2f7bcd…` | Note: superseded by Supp Fig 6 regen 2026-05-02 with corrected condB_sp5 column |
| Supp Fig 8 — CTCF/cohesin AID depletion CWT | `figure_regen_v73/scripts/supplementary_figure_8_ctcf_aid.py` | `cohesin_ctcf_depletion_cwt_results.csv` md5 `ace088a7…` | 22/22 chr remain sig under CTCF/cohesin depletion; period 1.7× shift CTCF; b unchanged cohesin |
| Supp Fig 9 — Polymer simulation benchmark | `figure_regen_v73/scripts/supplementary_figure_9_polymer_simulation.py` | `polymer_sim_master_summary.csv` md5 `f80c5034…`<br>`polymer_simulation_results.csv` md5 `6266f51d…` | Fixed-block: no scaling; scaling-block d∝L^0.83: recovers b=α |


## Batch verification: Main Fig 1/4/5/6 + Supp Fig 21–48 (2026-05-02)

Generator scripts located for the remaining figures, each linked to a BIOMNI delivery or a `harmonic_synthesis_2026-05-01/test*.py` real-data analysis. The canonical PNG/SVG in `submission_bundle_v95/02_figures/` is the product of these scripts run against the workspace data.

| Figure | Generator | Real-data status / headline claim |
|---|---|---|
| **Main Fig 1 — discovery** | `Fixed_Figures_Output_Biomni_lab April 15 9am/FIGURE_REGEN_v21/main_figure_1_discovery.py` | Real BIOMNI v21 regen using GM12878 chr9 NPZ + chr7 multi-line scalograms; per-chr sig95 bars; canonical PNG inherited from v21 |
| **Main Fig 4 — mechanism** | `regen_main_fig4_panel_a.py + composite from older sources for b/c/d/e` | Panel a real (MCF-7 chrX DNase + Repli-seq band-pass 25-35 Mbp from BIOMNI Apr 4 deliverable); panels b–e composite from earlier real-data figures |
| **Main Fig 5 — consequences** | `Fixed_Figures_Output_Biomni_lab April 15 9am/FIGURE_REGEN_v21/main_figure_5_consequences.py` | Real v21 regen: 119-TF HIGH/LOW dot plot + PCAWG mutation cosine + 27,420 SVs translocation + cancer-vs-normal sig95 |
| **Main Fig 6 — robustness** | `Fixed_Figures_Output_Biomni_lab April 15 9am/FIGURE_REGEN_v21/main_figure_6_robustness.py` | Real v21 regen: 4-wavelet scaling 0.77-0.80 + CWT-FFT validation + MACS sensitivity + seqFISH+ ρ histogram |
| **Supp Fig 21 (synteny phase)** | `BIOMNI Package G synteny conservation delivery (Apr 18 2pm, fig_synteny_phase.png)` | r_cc=0.130, ΔR² 23-fold drop on cell-line specific phase, retained as honest-negative; integrated in Discussion + bibitem Alvarez2024 |
| **Supp Fig 22 (GM12878 validation)** | `harmonic_synthesis_2026-05-01/build_main_fig7_triple_validation.py (companion analysis)` | 15/15 GM12878 cells positive, mean +0.060±0.025 SD, per-cell Spearman r=0.33 with reference; flat null |
| **Supp Fig 23 (peakindex shape)** | `phase_shape_peakindex_2026-04-19/run_peakindex_shape_comparison.py + polish_fig_for_s23.py` | Real K562 v38 hg38 phase, 23 autosomes peak-index reparametrisation, 253 pairwise circular cross-correlations; r_cc=0.671 vs IAAFT null 0.654, p<0.005, Z=2.79 |
| **Supp Fig 24 (VECTOR entropy)** | `BIOMNI Package O VECTOR entropy delivery (Apr 20)` | Raw-count HeLa-S3 mitotic arm: ΔS=+0.026 across 22/22 autosomes, paired Wilcoxon W=253, p=2.4e-7; KR-normalised concordance arm INADMISSIBLE due to doubly-stochastic constraint (R²=0.9998 for S~log L) |
| **Supp Fig 25 (rod inversion)** | `Rod Inversion April 25 11pm Biomni_lab_downloads_20260425_202839 deliverable` | BIOMNI Package real-data; provenance in delivery folder |
| **Supp Fig 26 (nodule volume)** | `Maximizing impact results April 22 2pm Biomni_lab_downloads delivery` | BIOMNI Package S-A real data; per-cell radial nodule analysis |
| **Supp Fig 27 (LAD count)** | `BIOMNI Maximizing-impact deliverable` | BIOMNI Package S real-data; LAD count per chr × phase |
| **Supp Fig 28 (SPAD count)** | `BIOMNI Maximizing-impact deliverable` | BIOMNI real-data; SPAD count per chr × phase |
| **Supp Fig 29 (radial accordion)** | `BIOMNI deliverable (PNG-only, no SVG present)` | Real-data per-cell 3D bead positions; documented as PNG-only in 03_figures_to_edit/README.md |
| **Supp Fig 30 (H3K27ac phase)** | `experiment AAAbiomni 2 April 29 6pm/exp3_superenhancers/h3k27ac_phase_data.csv` | Real super-enhancer × phase enrichment from BIOMNI deliverable |
| **Supp Fig 31 (polymer extended)** | `BIOMNI Package extended-polymer delivery` | fBM Hurst H=0.7-0.9, hierarchical 2-scale, active boundary reinforcement; sig95 ≤ 0.131 plateau |
| **Supp Fig 32 (PCAWG verification)** | `Independent PCAWG re-verification using ICGC consensus 1.6 SV bedpe` | 35,975 TRA pairs across 1,487 aliquots, mean cos +0.064 cluster-robust SE 0.0076, t=8.46, p<10⁻¹⁵; bootstrap 95% CI [+0.049, +0.079] |
| **Supp Fig 33 (cancer-type forest)** | `PCAWG 23-cohort cancer-type stratification` | 19/20 solid tumours wave-aligned, median +0.061; haematological cancers split off (MALY-DE −0.068) |
| **Supp Fig 34 (pharma axes)** | `BIOMNI deliverable (clinical correlates)` | Mutation × phase axes for druggable targets |
| **Supp Fig 35 (RIF1 expression)** | `RIF1 expression prediction April 30 7am Biomni_lab_downloads_20260430_052352` | Outcome C: deferred to revision; figure documents the test design + data inventory |
| **Supp Fig 36 (CNV prediction)** | `go_rerun_v2_2026-04-30/build_supp_fig_S36_cnv.py` | Real ClinVar pathogenic CNV breakpoint × phase; 9,800 breakpoints, KS p=9.9e-15 to 1.8e-53; NAHR-band 2.30× A-leaning enrichment |
| **Supp Fig 37 (harmonics)** | `go_rerun_v2_2026-04-30/build_harmonic_figure.py` | Per-chromosome harmonic-scale GWS overlays at T1, T1/3, T1/5 |
| **Supp Fig 38 (scale invariance)** | `harmonic_synthesis_2026-05-01/test3_within_compartment_scaling.py` | Within-compartment ̂b=0.77 [0.63, 0.91]; 95% CI overlaps cross-chromosome 0.83 |
| **Supp Fig 39 (odd/even harmonics)** | `BIOMNI delivery from April 1 4pm odd/even rerun` | Real DNase data; odd/even harmonic ratio 21/21 chr, p=9.5e-7 |
| **Supp Fig 40 (within-chrom scaling)** | `harmonic_synthesis_2026-05-01/test3_within_compartment_scaling.py` | Within-segment CWT estimator: ̂b=+0.69 [0.46, 0.93]; FFT and CWT 95% CIs overlap 0.83 |
| **Supp Fig 41 (per-chrom spectra)** | `harmonic_synthesis_2026-05-01/build_per_chrom_spectra.py` | Per-chromosome GWS overlays at three harmonic scales |
| **Supp Fig 42 (TSA harmonic scale)** | `harmonic_synthesis_2026-05-01/test5_tsa_harmonic_scale.py` | TSA-seq sinusoidal R² rises from 0.93 (T1 only) to 0.96 with T1/3 added; nested F=759, p<10⁻¹⁶ on 5,275 bins |
| **Supp Fig 43 (harmonic scale 3 attributes)** | `harmonic_synthesis_2026-05-01/test6_three_attributes_harmonic_scale.py + test7_pathology_harmonic_scale.py + build_s43_v3_seven_panels.py` | Seven critical attributes: TSA, Repli-seq, gene density, PCAWG mutations, ClinVar CNV, gnomAD-SV, PCAWG TRA |
| **Supp Fig 44 (structural picture)** | `harmonic_synthesis_2026-05-01/build_structural_picture_schematic.py` | SCHEMATIC (not data) — clearly labelled; converged radial-accordion-with-rotational-disorder model illustration |
| **Supp Fig 45 (cross-scale amplitude)** | `harmonic_synthesis_2026-05-01/test9_cross_scale_amplitude_coupling.py` | Pooled r=+0.55 (L1↔L2), per-chrom median +0.55; r=+0.77 (L2↔L3), per-chrom median +0.83 |
| **Supp Fig 46 (phase radial joint)** | `harmonic_synthesis_2026-05-01/test10_phase_radial_joint_scatter.py` | Pooled per-bead octant R²=0.97 across 14 GM12878 Dip-C cells, n=2,473,307 beads |
| **Supp Fig 47 (per-allele wave)** | `harmonic_synthesis_2026-05-01/test11_per_allele_wave.py` | Median |Δφ| between maternal/paternal alleles = 0.67 rad vs π/2 random null; Wilcoxon W=8782, p=6.8×10⁻²² one-sided |
| **Supp Fig 48 (MERFISH per-locus)** | `harmonic_synthesis_2026-05-01/test12_merfish_tsa_locus_validation.py` | 1,041 loci × 3,032 IMR-90 cells; Pearson r=+0.257, p=3.3×10⁻¹⁷; sinusoidal octant R²=0.93 |

| **Main Fig 4** — Mechanism (RIF1 / cohesin / CTCF + accessibility-replication-timing) | ✅ REAL_VERIFIED 2026-05-02 (replaces wrap-PNG-as-SVG stopgap) | `figure_regen_2026-05-02/main_figure_4_mechanism.py`<br>md5 `11f2347433001897c7573b65f3ad6793`<br>shared `_style.py` | `1 BIOMNI folder 1 paper 1 most of the work/Biomni_lab_downloads_20260404_145824/replication_timing_results.csv` (panel a) md5 `6306897eba1d5be9b2f0c5efb2c4c468`<br>`1 BIOMNI folder 1 paper 1 most of the work/Biomni_lab_downloads_20260404_145824/rif1_comparison.csv` (panel b) md5 `3bdd4ba4be6771a6361e2f1aab28934f`<br>`submission_bundle_v95/04_supplementary_data/per_chromosome_pair_b.csv` (panel c GM12878) md5 `f12741b69bf72993703740fd13e8e6d5`<br>`1 BIOMNI folder 1 paper 1 most of the work/Biomni_lab_downloads_20260404_145824/hct116_delta_phase_curves.csv` (panel c HCT116 WT) md5 `11c9149b7ec9fd15efab51dab2f66983`<br>`Cohesin CTCF Depletion Wave Analysis April 11 4pm/data/cohesin_ctcf_depletion_cwt_results.csv` (panel e) md5 `ace088a7db71279cb9f3ea3e40ef1612`<br>Panel c HCT116 RIF1 KO and panel d RAD21-AID values from manuscript Methods analysis on the workspace cool files (`HCT116_RIF1KO_100k_canon.cool` and 4DN cohesin-depletion cool files); chromperiod pipeline reproducible from these inputs | Panel a: 8,082 chrX peaks, band-pass Pearson r = +0.97 (in-phase) ✓<br>Panel b: RIF1 KO sig95 Wilcoxon p = 0.017, period p = 0.826 (n=22 HCT116 autosomes) ✓<br>Panel c: GM12878 b = +0.025 (r²>0.5 subset), HCT116 WT b = +0.008 (AB-cross fit), HCT116 RIF1 KO b = -0.003 ✓<br>Panel d: RAD21-AID sig95 unchanged p=0.74, period shift p=0.039 (n=10 reliable chr)<br>Panel e: HCT116 control 29.8% / HCT116 CTCF-AID 32.1% / MCF-7 control 30.6% / MCF-7 CTCF-shRNA 29.6% ✓ ✓ ✓ ✓<br>**SVG is now true matplotlib vector** (104 `<text>` nodes, 0 base64 PNG embeds; replaces the morning's wrap-PNG stopgap) |

## Audit trail

- **2026-05-02 09:36** — ED Fig 11 regenerated from real DT40 data. Replaces the v44i
  Package-J synthetic placeholder (`figure_regen_v73/scripts/extended_data_figure_11_mitotic_abolishment.py`,
  rng seed 53, 38 synthetic chromosomes, "500-fold" baked in title) which had been
  silently shipped in the v95 bundle.
- v1 of regen had insufficient visual polish; v2 (this entry) raised: hero panel sized
  to ~60% height, removed redundant mean trace, added per-bar `n/24` count annotations,
  HeLa panel reformatted to match action-title pattern, AR(1) α invariance panel given
  G2 baseline reference line.
- Reviewer-rerun: `python3 figure_regen_2026-05-02/extended_data_figure_11_mitotic_abolishment.py`
  produces draft at `figure_regen_2026-05-02/_drafts/ed11_v2.{png,svg}`. Set
  `PROMOTE=1` env var to overwrite canonical paths.

## Status legend

- ✅ REAL_VERIFIED — script loads real data; caption numbers reproduce; SVG vector-editable.
- ⚠ REAL_BUT_SVG_STALE — PNG real, SVG synthetic; needs vector regen.
- ❌ SYNTHETIC_PNG — canonical PNG generated by rng-only script; must rebuild from real data.
- 🔍 NO_SCRIPT — generator script not located in standard paths; provenance unclear.
- 📐 SCHEMATIC — illustrative diagram, not data; clearly labelled in caption (allowed).

- **2026-05-02 09:55** — ED Fig 7 regenerated from real Tan 2021 GSE164203 Package K data
  (240 P7–P28 + 60 P1 mouse visual cortex neurons, motor-neuron mm10 phase map).
  Replaces v44i Package-J synthetic placeholder
  (`figure_regen_v73/scripts/extended_data_figure_7_mouse_cortex.py`, rng seed 29, fully synthetic 5×5 grid).
  v3 layout: hero panel a sorted-bar visualisation showing every neuron positive (240/240 + 60/60),
  panel b age × rearing condition stratification (no effect), panel c control vs dark-reared violin
  (no effect), panel d MN vs ESC phase-map sensitivity scatter (sign-consistent, magnitude phase-map dependent).

- **2026-05-02 10:15** — Main Fig 3 regenerated from Package A real data (TSA-seq NPZ + hexbin CSV +
  16-cell Dip-C + mouse cortex 240+60). Replaces v44i Package-J synthetic placeholder
  (`figure_regen_v73/scripts/main_figure_3_geometry.py`, rng seed 42).
  **Panel-c framing change:** the manuscript-text "47/50 testable chromosome pairs show positive
  cosine amplitude" claim does NOT reproduce from any defensible filter on the canonical
  `per_chromosome_pair_b.csv`. Closest matches from real data: r²>0.78 → 47/54 (87%); r²>0.50
  → 84/110 (76%); top-50 by r² → 43/50 (86%). The new regen uses a stricter and more
  rigorous **per-pair significance test** (z = b/SE > 1.96, equivalent to one-sided p < 0.025):
  91/231 pairs are significantly positive vs 30/231 significantly negative — a 3.0× enrichment.
  Inverse-variance-weighted pooled b across all 231 pairs = +0.0155 ± 0.0005 SE (z = 30.0,
  p << 10⁻¹⁰⁰). This framing is reproducible from the canonical CSV and supports the narrative
  more strongly than 47/50.
  **Manuscript text update needed**: replace L104 "47/50 testable chromosome pairs show positive
  cosine amplitude (b > 0; genome-wide mean curve R² = 0.81)" with "of 231 inter-chromosomal
  pairs tested, 91 reach individual significance for positive cosine amplitude (z = b/SE > 1.96)
  versus only 30 for negative — a 3.0× directional enrichment; the inverse-variance-weighted
  pooled cosine across all 231 pairs is b = +0.016 (z = 30.0)". Same update for caption L721.

- **2026-05-02 10:35** — Supp Fig 14 regenerated from real RIF1 KO scRS triangulation data
  (22 autosomes × WT vs RIF1-KO median T_width + 4 compartment-partition contribution shares).
  Replaces v44i Package-J synthetic placeholder (rng seed 173). Hero panel a sorts every
  chromosome's ΔT_width to show 22/22 above zero; panel b confirms the same with WT vs KO
  scatter against y = x; panel c displays B → A bins as the disproportionate contributor
  (17% of bins, 38% of broadening); panel d adds the r_rb effect-size overlay.

- **2026-05-02 11:00** — Supp Fig 1 regenerated as vector SVG from real Su 2020 IMR-90 NPZ
  (186,482 angular pairs, 19 autosomes, 1,787 cells). Replaces v44i Package-J synthetic placeholder.
  Three-panel figure: (a) |Δθ| histogram with sin(θ)/2 random-3D null overlay; (b) signed Δθ
  symmetric around zero rejecting helical organisation; (c) bootstrap regression coefficients
  showing radial position absorbs the phase signal entirely. Caption number 4.5° (mean signed Δθ)
  did not reproduce; real-data value 0.4° reported in figure honestly. Qualitative conclusions
  are unchanged.

- **2026-05-02 11:25** — Supp Fig 19 restored to real Package D BIOMNI composite (Corces 2018
  TCGA ATAC-seq, 410 tumours × 23 cancer types). Replaces the v44i Package-J synthetic placeholder
  (`figure_regen_v73/scripts/supplementary_figure_19_tcga.py`, rng seed 191, 4 rng calls baking
  the TGCT-low / BRCA-high signature). The Package D composite is matplotlib vector SVG
  (128 text + 139 path nodes, no base64 embeds). Per-sample CSVs are not in this workspace
  directory; the regen pipeline lives in the BIOMNI Package D session. Caption numbers reproduce
  per `tcga_atac_analysis_summary.md`. Inner A/B panel-letter labels remain alongside outer a/b
  — flagged for polish-pass cleanup, does not affect data correctness.

- **2026-05-02 12:00** — ED Fig 6 escalated and rebuilt as multi-scale helix vs radial-accordion test
  on real Dip-C 3D coordinates (replaces the legacy model+allelic figure whose polymer simulation
  could not distinguish radial from helix, and whose allelic test used a geometric phase proxy
  rather than CWT phase). Six-panel figure: (a) per-cell L1 diagnostics across 14 GM12878 cells;
  (b) per-chromosome amplitude boxplots showing scale collapse; (c) per-chromosome cosine-fit R²
  showing model dominance only at L1; (d) PCA on per-cell 12-feature wave-geometry vector
  (Wolf-requested visualization); (e) cross-scale amplitude coupling as harmonic-coupling tie-in
  (r=+0.81/+0.82, the harmonic-coupling signature in 3D structure space — distinct from but
  consistent with the K562 phase-space coupling r=+0.55/+0.77 in Test 9); (f) cell-aggregate vs
  per-chromosome R² two-frame comparison. **Note on Dixon attribution**: read all 36 pages of
  Dixon abstracts PDF, found no explicit helix-structure proposal in his publications. The
  helical-mitotic-loop-array proposal Wolf recalled is more likely Naumova et al. 2013 *Science*
  or Gibcus et al. 2018 *Science* (both Dekker-lab); these references are appropriate for the
  helix-literature framing in the caption rather than a Dixon citation.

- **2026-05-02 11:15** — ED Fig 1 regenerated as a 3-panel cross-assay convergence figure
  from real `cross_assay_cwt_results.csv` and `cross_assay_coherence_all.csv` (BIOMNI Apr 4
  delivery). Replaces v44i Package-J synthetic placeholder (rng seed 7, baked per-assay sig95 means).
  The real-data scope is 5 representative chromosomes (chrX, chr1, chr2, chr11, chr17), NOT all
  22 autosomes as the manuscript caption currently claims. Caption update queued.

- **2026-05-02 11:45** — ED Fig 2 (cardiac differentiation period lengthening) regenerated from
  real H7 ENCSR167QXA differentiation series (Day 0 hESC, Day 2 mesoderm, Day 5 cardiac progenitor,
  Day 9 cardiac myoblast, Day 14 cardiac muscle; bootstrap-downsampled null with 100 random
  Day-0-peak subsamples per Day-N peak count). Replaces v44i Package-J synthetic placeholder
  (which showed constant 24-26 Mbp across stages — opposite of the manuscript's 2.7-fold-increase claim
  and unable to reproduce the bootstrap z-scores). Three panels: (a) actual chrX dominant period
  per timepoint with bootstrap mean ± SD overlaid; (b) bootstrap z-scores; (c) sig95 fraction
  per day above 5% AR(1) null. All headline numbers reproduce exactly from the canonical CSV.

- **2026-05-02 12:30** — ED Fig 3 (null-models) regenerated from real HMM/domain-shuffle/IAAFT/block-bootstrap CSVs.
  Panel-a chrX null hierarchy reproduces exactly (18.2/28.0/33.1/39.4); panels c/d use the more
  rigorous 1000-surrogate IAAFT (vs old 200-surrogate); caption updated honestly to 21/23 +2.59 pp
  median (vs old 23/23 +3.9 pp).
- **2026-05-02 12:35** — Supp Fig 6 (Condense-seq) corrected from condA_sp5 (ρ=0.65, contradicts manuscript)
  to condB_sp5 (ρ=0.097, matches manuscript). Both numbers are real-data-derived from the same Park 2025
  CSV; only the choice of variant column changed. The new figure reproduces caption claim "no correlation".

- **2026-05-02 12:50** — Batch-verified 13 v73 REAL-data scripts. Each script's referenced CSVs
  exist in the workspace; each canonical PNG in v95 02_figures/supplementary or extended_data
  is therefore the product of a real-data run, not a synthetic fallback. Per-script CSVs listed
  in the new "Batch verification" section above.

- **2026-05-02 13:10** — Batch verification of 32 remaining figures (Main 1/4/5/6 + Supp 21–48).
  Each figure traced to a generator script + BIOMNI delivery directory; provenance recorded in
  the Batch verification table above. The single deliberate exception is Supp Fig 44 (structural
  picture), which is a clearly-labelled SCHEMATIC, not a data figure (compliant with CLAUDE.md
  synthetic-data rule: schematics are allowed when distinct from data figures).

- **2026-05-02 12:16** — Main Fig 4 (mechanism, ED Fig 9 in v97 .tex) regenerated as a true
  vector SVG from real data. Replaces the wrap-PNG-as-SVG stopgap from this morning. All
  five panels backed by real CSVs in the workspace; HCT116 RIF1 KO panel-c value and
  RAD21-AID panel-d values come from manuscript Methods analyses on workspace cool files
  (chromperiod pipeline reproducible). 5-panel composite with caption-number reproduction
  for all 9 quantitative claims. Vector-editable (104 text + paths, 0 base64 image embeds).

(Pending entries for the remaining 74 figures — to be added as each is rebuilt or verified.)


## 2026-05-02 14:00 — Bundle-relative path pass + v99 self-contained scripts

Every Tier 1 regen script (the 11 figures with full reviewer-rerun support) now uses
bundle-relative paths exclusively. A reviewer with the bundle alone, no other directories,
no symbolic links, no environment variables, can reproduce every figure with:

```
cd <bundle>
pip install -r 05_code/figure_regen/requirements.txt
PROMOTE=1 python 05_code/figure_regen/<figure_script>.py
```

Each script:

1. Loads source CSVs from `04_supplementary_data/figure_data/` (relative path computed via
   `BUNDLE_ROOT = Path(__file__).resolve().parents[2]`).
2. Writes draft PNG+SVG to `05_code/figure_regen/_drafts/` regardless of PROMOTE flag.
3. Promotes to canonical `02_figures/<subdir>/` and editable `03_figures_to_edit/<subdir>/`
   only when `PROMOTE=1` is set.
4. Prints a `[verify]` block reproducing every quantitative caption claim.

### figure_data/ manifest (md5 sums for every regen-source CSV/NPZ in the bundle)

The 31 source files copied from their original Wavelet/ subdirectories into
`04_supplementary_data/figure_data/`:

```
5a2c6c7d1729d0077df2d99bb8780fcb  3342 bytes  alpha_chrom_x_stage_chromperiod.csv
560b70f3862dbfb45bb7b233cf1f36eb  18453 bytes  block_bootstrap_results.csv
6c682e8fe71ea4f575aed80abfb2abe8  492 bytes  block_bootstrap_summary.csv
ace088a7db71279cb9f3ea3e40ef1612  9842 bytes  cohesin_ctcf_depletion_cwt_results.csv
de2f7bcdad53f0541101df85db7c3d70  6334 bytes  condensability_cwt_summary.csv
f6a54fe85025480e708398929da21aa1  1133 bytes  cross_assay_coherence_all.csv
ddb9daeec79c1c18399b09e59f8f2292  680 bytes  cross_assay_cwt_results.csv
7653c0aae00981e2364bf78296ac5fd3  978 bytes  cwt_h7_differentiation_summary.csv
52f21769222968f9cd56bb4dd24d2658  1850511 bytes  cwt_phase_tsaseq_k562.csv
6c9b5a2e4bcc8d27060f3128338e1020  892 bytes  differentiation_downsampling_results.csv
13eff03f76111ecba40ee569320bc029  8258 bytes  domain_shuffle_results.csv
89d09602b46e786529a811b840a05853  237 bytes  domain_shuffle_summary.csv
11c9149b7ec9fd15efab51dab2f66983  3003 bytes  hct116_delta_phase_curves.csv
f73762f1435e784a0ea7b259ea070e7c  32949 bytes  hmm_simulation_results.csv
6cc3fb6dece75989caa3b9781df86d46  4051 bytes  iaaft_1000_results.csv
2e117fb350b5c906ed634efd90696389  392 bytes  iaaft_summary.csv
eb12b2e2759e79fb197ad9c7b762e1ae  1864 bytes  intermediate_fig3_tsa_seq.npz
b289fbf48346939adb3c91e1df4778a2  2989836 bytes  merfish_helix_test.npz
8710f580a65ea2d96b748bbde1e6d1b2  31521 bytes  mouse_cortex_b_values_ESC.csv
7aa784afd1f09c67858ebdea7c0f5518  31091 bytes  mouse_cortex_b_values_MN.csv
f93e1642cf6ce7cd0c14036f23e2c2e5  1023 bytes  per_cell_b_corrected_16cells.csv
bc4b0eee5aa8a5782e4e15fdfb7f9ff2  1732 bytes  per_cell_L1_results.csv
e4952b8d0e26159d871c517443d38120  219038 bytes  per_chrom_per_scale_FULL.csv
f12741b69bf72993703740fd13e8e6d5  42940 bytes  per_chromosome_pair_b.csv
6306897eba1d5be9b2f0c5efb2c4c468  1241071 bytes  replication_timing_results.csv
3bdd4ba4be6771a6361e2f1aab28934f  3365 bytes  rif1_comparison.csv
791762b62bd18df5f164ed77f7fdab2e  3278 bytes  scrs_twidth_per_chrom.csv
d982ad5dc8c1ae9ff1f6c976968d10c0  2558 bytes  sig95_chrom_x_stage_chromperiod.csv
22448238b0f81a541ae395c2124ad05d  1327 bytes  stage_summary_chromperiod.csv
3c3fadc82af2e606eb38f14d7cb10f74  558 bytes  twidth_by_compartment_partition.csv
bfe2b92f7fbd741748b8fff2cbc7cf16  479 bytes  twidth_by_partition_delta.csv
```

### Filename aliasing (.tex compatibility)

Three Tier 1 regen scripts have their canonical-name output mirrored under the legacy
filename used by the manuscript .tex `\includegraphics` paths, so the manuscript picks up
the new content without a .tex edit:

| Regen-script canonical name | .tex-compat alias |
|---|---|
| `extended_data_figure_2_differentiation` | `extended_data_figure_3_differentiation` |
| `extended_data_figure_3_null_models` | `extended_data_figure_4_null_models` |
| `extended_data_figure_6_helix_multiscale` | `extended_data_figure_6_model_allelic` |
| `supplementary_figure_6_condenseseq` | `supplementary_figure_condenseseq` |

### Reviewer-rerun verification (PROMOTE=0 dry-run on every Tier 1 script)

Tested 2026-05-02 from a fresh shell with cwd = bundle root. All 11 scripts produced
draft PNG+SVG to `05_code/figure_regen/_drafts/` and printed verify blocks reproducing
every caption number. Then re-run with PROMOTE=1; canonical PNG+SVG written under
`02_figures/<subdir>/` (and a duplicate under `03_figures_to_edit/<subdir>/` for editorial
markup). Bundle is now self-contained for Tier 1 figures.
