---
vault_clearance: KETER
halo:
  classification: RESTRICTED
  confidence: MEDIUM
  front: "12_Project_BloodyEchoes — BOOK"
  custodian: "Gemini"
  created: 2026-03-30
  updated: 2026-04-03
  wing: CONDITIONAL
  containment: "BOOK — bibliography + methods registry; not README / WORLDLINE / BOUNTY"
---

# Project BloodyEchoes — BOOK

Canonical bibliography and methods registry for **12_Project_BloodyEchoes** (genomic archaeology, TE / UHRF1, pre-publication). Convention: [`BOOK_Protocol.md`](../BOOK_Protocol.md). Orientation: [`README.md`](README.md). Open work: [`BOUNTY_BOARD.md`](BOUNTY_BOARD.md). Paradigm map: [`FORM.md`](FORM.md). **No `WORLDLINE.md` at project root.**


### Local registry slice (EYE / STAFF / STARS)

| Surface | Pointers |
|---------|----------|
| **EYEs** | Runs: [`README.md`](README.md) / [`WORLDLINE.md`](WORLDLINE.md) (if present). Registry: [`EYE_PROTOCOL.md`](../EYE_PROTOCOL.md) |
| **STAFF** | Runnable tools: [`STAFF_catalogue.json`](../STAFF_catalogue.json) — filter `project_dir` for this folder. |
| **STARS** | This file; rules: [`BOOK_Protocol.md`](../BOOK_Protocol.md). |
| **Audit sheet** | [`LOGGING_AND_REGISTRY_CHECKLIST.md`](../99_Archive/root_reports/2026-04/LOGGING_AND_REGISTRY_CHECKLIST.md) |


---

## 1. Transposons, epigenetic silencing, and paleogenomics (curate)

| ID | Kind | Note | Identifier |
|----|------|------|------------|
| BE-B1 | Stub | Primary literature for UHRF1, KRAB-ZFP, TE exaptation — add DOIs as coordinates and claims are frozen | *See BOUNTY_BOARD* |
| BE-B2 | Cross-ref | Temporal intervention framing (senescence / methylation maintenance) | [`../18_Project_LifeSong/BOOK.md`](../18_Project_LifeSong/BOOK.md) |

---

## 2. Databases and assemblies (curate)

| ID | Kind | Note | Identifier |
|----|------|------|------------|
| BE-T1 | Stub | Ensembl, UCSC, RepeatMasker — document build versions used in analysis | *TBD* |
| BE-T2 | GEO | Series referenced on project bounty material — curate cells/treatment from SOFT when used | [GSE302792](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE302792) |

---

## 3. Bounty → start here

| Workstream | Start with |
|------------|------------|
| Orthodox vs archaeology stack | [`FORM.md`](FORM.md) |
| Coordinates / TE maps | [`README.md`](README.md), [`BOUNTY_BOARD.md`](BOUNTY_BOARD.md) |

---

## STARS — US and international anchors

**Genome browsers and archives** — US NCBI/UCSC plus **UK Ensembl**.

### How to read STARS (context)

**STARS** here are **genome assembly, browser, and repeat-annotation** entry points. They **locate coordinates and features** (genes, TEs); **cell type or treatment** for expression data still requires **GEO/SRA** sample metadata.

| ID | What this STAR denotes | Typical use in this BOOK | Not / caveats |
|----|-------------------------|--------------------------|---------------|
| BE-S1 | NCBI (GenBank / assembly / SRA) | **Accession** lookup for assemblies and reads | Assembly patch level matters — match genome build to analysis. |
| BE-S2 | UCSC Genome Browser | **Visual** tracks and coordinates | Custom sessions are not persistent unless saved. |
| BE-S3 | Ensembl | **Gene models** and comparative genomics | Release version — pin for reproducibility. |
| BE-S4 | RepeatMasker / Dfam | **Repeat family** classification context | Library versions affect annotation calls. |

| ID | Region | Kind | Note | Identifier |
|----|--------|------|------|------------|
| BE-S1 | US | NCBI hub | GenBank / assembly / SRA entry points | [ncbi.nlm.nih.gov](https://www.ncbi.nlm.nih.gov/) |
| BE-S2 | US | Genome browser | UCSC Genome Browser | [genome.ucsc.edu](https://genome.ucsc.edu/) |
| BE-S3 | UK | Annotation / comparative | Ensembl | [ensembl.org](https://www.ensembl.org/) |
| BE-S4 | US | Repeat families | RepeatMasker / Dfam ecosystem | [repeatmasker.org](https://www.repeatmasker.org/) |
<!-- accession_scan:generated -->

## Accession gap index (automated scan)

**Generated:** 2026-03-30. **Policy:** Mentions found under this project (excluding `_archive/`, `u_os_dev/out/public_lab/`, `.git/`, `node_modules/`) outside root `BOOK.md`, that do **not** appear as a substring anywhere in **this** `BOOK.md` yet. **Curated sections above remain authoritative** — merge rows into them when ready.

| Kind | ID | Seen in |
|------|-----|---------|
| — | — | *GSE302792 promoted to §2 BE-T2; re-run `scan_project_accessions.py` to refresh.* |

<!-- /accession_scan -->

---

*BOOK revision: 2026-04-03 — GSE302792 promoted to §2; STARS context table.*