diff --git a/.agents/skills/protocol-migration/SKILL.md b/.agents/skills/protocol-migration/SKILL.md
index fc2d684..975ef47 100644
--- a/.agents/skills/protocol-migration/SKILL.md
+++ b/.agents/skills/protocol-migration/SKILL.md
@@ -57,24 +57,18 @@ When migrating:
 You may normalize formatting only when the meaning is unchanged and unambiguous:
 
 - Add a space between numbers and units.
-- Standardize temperature formatting to `37 °C`.
-- Standardize volume units to `µL`, `mL`, `L`, using the micro sign `µ` consistently.
-- Standardize concentration units to `mM`, `µM`, `nM`, `% (w/v)`, etc., using the micro sign `µ` consistently.
-- Standardize time units to full words: `seconds`, `minutes`, `hours`.
-- Standardize chemical names to match the source but with consistent formatting (e.g. `Tris-HCl` instead of `Tris HCl`).
+- Use full-word time units: `seconds`, `minutes`, `hours`.
+- Use standard units and spacing, for example `37 °C`, `10 µL`, `1 mM`, `100 nM`.
 - Standardize pH formatting to `pH 7.4`.
-- Standardize chemical formulas with HTML subscripts, for example H2O to H<sub>2</sub>O. Similarly for other chemical formulas (e.g. MgCl2 to MgCl<sub>2</sub>).
+- Standardize chemical names without changing meaning, for example `Tris-HCl` instead of `Tris HCl`.
+- Standardize chemical formulas with HTML subscripts, for example H2O to H<sub>2</sub>O and MgCl2 to MgCl<sub>2</sub>.
 - Do not use Unicode subscript characters such as `₂`.
-- Standardize `RNAseq` or `RNA-Seq` to `RNA-seq`. Same for `ChIP-seq`, `ATAC-seq`, etc.
-- Use numbered lists for procedural actions in sequence. For other non-procedural content, bullets are better. Note-like text such as Note, NB, Optional, Recommended, and Warning should use blockquote style such as `> **Note**`.
-- Normalize bullet formatting and markdown table formatting.
-- Normalize heading structure to match the repository template.
-- For reaction mixes and anything tabular, place them inside a table as in template.
-- For image-based tables, convert to Markdown tables wherever this is legible and unambiguous; otherwise retain the image at the correct protocol location with `CHECK:` explaining why it could not be safely converted.
-- Normalize markdown headings, bullets, and tables.
-- "Note" or "NOTE" or "NB" or "Optional" or "Recommended" or "Warning" are normalized to start with `>` (example `> **Note**`) and are placed immediately after the step they refer to, or at the end of the protocol if they clearly refer to the whole protocol.
+- Standardize names such as `RNAseq` or `RNA-Seq` to `RNA-seq`, and similarly for `ChIP-seq`, `ATAC-seq`, and related names.
+- Use numbered lists for procedural actions in sequence, bullets for non-procedural lists, and tables for reaction mixes or other tabular content.
+- Normalize note-like labels such as Note, NB, Optional, Recommended, and Warning to blockquote style, for example `> **Note:**`.
+- Normalize headings, bullets, Markdown tables, and `Contents` links to match the repository template.
+- Convert image-based tables to Markdown tables when legible and unambiguous; otherwise retain the image with `CHECK:`.
 - Remove empty columns from tables.
-- Synchronize `Contents` with actual headings in the protocol.
 
 ## Disallowed changes
 - Do not infer omitted concentrations, times, temperatures, or volumes.
@@ -92,30 +86,23 @@ You may normalize formatting only when the meaning is unchanged and unambiguous:
 - Do not omit protocol-relevant images, image-based tables, figures, diagrams, or visual instructions.
 
 ## Output requirements
-- edit `README.md`
-- use the template headings exactly
-- use the template headings in `README.md`
-- keep all source content
-- add `CHECK:` markers for uncertainty
-- use `CHECK:` only for genuine unresolved uncertainty. If no uncertainty remains, do not mention `CHECK:` at all
-- add `# Migration notes`
-- after drafting, add a short summary in `# Migration notes` covering:
+- Only edit `README.md`.
+- Use the template headings exactly.
+- Keep all source content.
+- Keep the Ule Lab Protocol Template attribution badge at the top of the file, but do not add or preserve a template release-version badge.
+- Remove the template instruction note and the "Template repository: Click `Use this template`..." note.
+- Add `CHECK:` markers only for genuine unresolved uncertainty.
+- Add an `# Migration notes` section covering:
+  - imported protocol metadata from `source-metadata.yml`, using only non-blank lines
+  - `template_version` from `template-metadata.yml`
   - formatting normalizations performed
   - ambiguities and uncertainty flagged
   - content placed in `## Unplaced content`
-- add `# Migration notes` including:
-  - imported protocol metadata from `source-metadata.yml`, using only the non-blank lines
-  - template_version from `template-metadata.yml`
-  - ambiguous mappings
-  - normalized formatting changes
   - extracted images converted to Markdown tables
   - extracted images retained in `README.md`
   - extracted images omitted because they were decorative or duplicated non-protocol content
-  - extracted images that could not be confidently classified or converted, marked with `CHECK:`
+  - extracted images that could not be confidently classified or converted
   - content copied verbatim but not confidently placed
-- keep `[![Created with Ule Lab Protocol Template](https://img.shields.io/badge/created%20with-Ule%20Lab%20Protocol%20Template-blue)](https://github.com/ulelab/protocol-template)` at the top of the file
-- remove the template instruction note
-- delete the "Template repository: Click `Use this template` to create a new protocol repo..." note
 
 ## Verification
 After drafting, verify the migration against the source:
diff --git a/.claude/skills/protocol-migration/SKILL.md b/.claude/skills/protocol-migration/SKILL.md
index fc2d684..975ef47 100644
--- a/.claude/skills/protocol-migration/SKILL.md
+++ b/.claude/skills/protocol-migration/SKILL.md
@@ -57,24 +57,18 @@ When migrating:
 You may normalize formatting only when the meaning is unchanged and unambiguous:
 
 - Add a space between numbers and units.
-- Standardize temperature formatting to `37 °C`.
-- Standardize volume units to `µL`, `mL`, `L`, using the micro sign `µ` consistently.
-- Standardize concentration units to `mM`, `µM`, `nM`, `% (w/v)`, etc., using the micro sign `µ` consistently.
-- Standardize time units to full words: `seconds`, `minutes`, `hours`.
-- Standardize chemical names to match the source but with consistent formatting (e.g. `Tris-HCl` instead of `Tris HCl`).
+- Use full-word time units: `seconds`, `minutes`, `hours`.
+- Use standard units and spacing, for example `37 °C`, `10 µL`, `1 mM`, `100 nM`.
 - Standardize pH formatting to `pH 7.4`.
-- Standardize chemical formulas with HTML subscripts, for example H2O to H<sub>2</sub>O. Similarly for other chemical formulas (e.g. MgCl2 to MgCl<sub>2</sub>).
+- Standardize chemical names without changing meaning, for example `Tris-HCl` instead of `Tris HCl`.
+- Standardize chemical formulas with HTML subscripts, for example H2O to H<sub>2</sub>O and MgCl2 to MgCl<sub>2</sub>.
 - Do not use Unicode subscript characters such as `₂`.
-- Standardize `RNAseq` or `RNA-Seq` to `RNA-seq`. Same for `ChIP-seq`, `ATAC-seq`, etc.
-- Use numbered lists for procedural actions in sequence. For other non-procedural content, bullets are better. Note-like text such as Note, NB, Optional, Recommended, and Warning should use blockquote style such as `> **Note**`.
-- Normalize bullet formatting and markdown table formatting.
-- Normalize heading structure to match the repository template.
-- For reaction mixes and anything tabular, place them inside a table as in template.
-- For image-based tables, convert to Markdown tables wherever this is legible and unambiguous; otherwise retain the image at the correct protocol location with `CHECK:` explaining why it could not be safely converted.
-- Normalize markdown headings, bullets, and tables.
-- "Note" or "NOTE" or "NB" or "Optional" or "Recommended" or "Warning" are normalized to start with `>` (example `> **Note**`) and are placed immediately after the step they refer to, or at the end of the protocol if they clearly refer to the whole protocol.
+- Standardize names such as `RNAseq` or `RNA-Seq` to `RNA-seq`, and similarly for `ChIP-seq`, `ATAC-seq`, and related names.
+- Use numbered lists for procedural actions in sequence, bullets for non-procedural lists, and tables for reaction mixes or other tabular content.
+- Normalize note-like labels such as Note, NB, Optional, Recommended, and Warning to blockquote style, for example `> **Note:**`.
+- Normalize headings, bullets, Markdown tables, and `Contents` links to match the repository template.
+- Convert image-based tables to Markdown tables when legible and unambiguous; otherwise retain the image with `CHECK:`.
 - Remove empty columns from tables.
-- Synchronize `Contents` with actual headings in the protocol.
 
 ## Disallowed changes
 - Do not infer omitted concentrations, times, temperatures, or volumes.
@@ -92,30 +86,23 @@ You may normalize formatting only when the meaning is unchanged and unambiguous:
 - Do not omit protocol-relevant images, image-based tables, figures, diagrams, or visual instructions.
 
 ## Output requirements
-- edit `README.md`
-- use the template headings exactly
-- use the template headings in `README.md`
-- keep all source content
-- add `CHECK:` markers for uncertainty
-- use `CHECK:` only for genuine unresolved uncertainty. If no uncertainty remains, do not mention `CHECK:` at all
-- add `# Migration notes`
-- after drafting, add a short summary in `# Migration notes` covering:
+- Only edit `README.md`.
+- Use the template headings exactly.
+- Keep all source content.
+- Keep the Ule Lab Protocol Template attribution badge at the top of the file, but do not add or preserve a template release-version badge.
+- Remove the template instruction note and the "Template repository: Click `Use this template`..." note.
+- Add `CHECK:` markers only for genuine unresolved uncertainty.
+- Add an `# Migration notes` section covering:
+  - imported protocol metadata from `source-metadata.yml`, using only non-blank lines
+  - `template_version` from `template-metadata.yml`
   - formatting normalizations performed
   - ambiguities and uncertainty flagged
   - content placed in `## Unplaced content`
-- add `# Migration notes` including:
-  - imported protocol metadata from `source-metadata.yml`, using only the non-blank lines
-  - template_version from `template-metadata.yml`
-  - ambiguous mappings
-  - normalized formatting changes
   - extracted images converted to Markdown tables
   - extracted images retained in `README.md`
   - extracted images omitted because they were decorative or duplicated non-protocol content
-  - extracted images that could not be confidently classified or converted, marked with `CHECK:`
+  - extracted images that could not be confidently classified or converted
   - content copied verbatim but not confidently placed
-- keep `[![Created with Ule Lab Protocol Template](https://img.shields.io/badge/created%20with-Ule%20Lab%20Protocol%20Template-blue)](https://github.com/ulelab/protocol-template)` at the top of the file
-- remove the template instruction note
-- delete the "Template repository: Click `Use this template` to create a new protocol repo..." note
 
 ## Verification
 After drafting, verify the migration against the source:
diff --git a/.github/copilot-instructions.md b/.github/copilot-instructions.md
index 2bf6589..d84b620 100644
--- a/.github/copilot-instructions.md
+++ b/.github/copilot-instructions.md
@@ -49,24 +49,18 @@ When migrating:
 ## Allowed formatting normalization
 You may normalize formatting only when the meaning is unchanged and unambiguous:
 - Add a space between numbers and units.
-- Standardize temperature formatting to `37 °C`.
-- Standardize volume units to `µL`, `mL`, `L`, using the micro sign `µ` consistently.
-- Standardize concentration units to `mM`, `µM`, `nM`, `% (w/v)`, etc., using the micro sign `µ` consistently.
-- Standardize time units to full words: `seconds`, `minutes`, `hours`.
-- Standardize chemical names to match the source but with consistent formatting (e.g. `Tris-HCl` instead of `Tris HCl`).
+- Use full-word time units: `seconds`, `minutes`, `hours`.
+- Use standard units and spacing, for example `37 °C`, `10 µL`, `1 mM`, `100 nM`.
 - Standardize pH formatting to `pH 7.4`.
-- Standardize chemical formulas with HTML subscripts, for example H2O to H<sub>2</sub>O. Similarly for other chemical formulas (e.g. MgCl2 to MgCl<sub>2</sub>).
+- Standardize chemical names without changing meaning, for example `Tris-HCl` instead of `Tris HCl`.
+- Standardize chemical formulas with HTML subscripts, for example H2O to H<sub>2</sub>O and MgCl2 to MgCl<sub>2</sub>.
 - Do not use Unicode subscript characters such as `₂`.
-- Standardize `RNAseq` or `RNA-Seq` to `RNA-seq`. Same for `ChIP-seq`, `ATAC-seq`, etc.
-- Use numbered lists for procedural actions in sequence. For other non-procedural content, bullets are better. Note-like text such as Note, NB, Optional, Recommended, and Warning should use blockquote style such as `> **Note**`.
-- Normalize bullet formatting and markdown table formatting.
-- Normalize heading structure to match the repository template.
-- For reaction mixes and anything tabular, place them inside a table as in template.
-- For image-based tables, convert to Markdown tables wherever this is legible and unambiguous; otherwise retain the image at the correct protocol location with `CHECK:` explaining why it could not be safely converted.
-- Normalize markdown headings, bullets, and tables.
-- "Note" or "NOTE" or "NB" or "Optional" or "Recommended" or "Warning" are normalized to start with `>` (example `> **Note**`) and are placed immediately after the step they refer to, or at the end of the protocol if they clearly refer to the whole protocol.
+- Standardize names such as `RNAseq` or `RNA-Seq` to `RNA-seq`, and similarly for `ChIP-seq`, `ATAC-seq`, and related names.
+- Use numbered lists for procedural actions in sequence, bullets for non-procedural lists, and tables for reaction mixes or other tabular content.
+- Normalize note-like labels such as Note, NB, Optional, Recommended, and Warning to blockquote style, for example `> **Note:**`.
+- Normalize headings, bullets, Markdown tables, and `Contents` links to match the repository template.
+- Convert image-based tables to Markdown tables when legible and unambiguous; otherwise retain the image with `CHECK:`.
 - Remove empty columns from tables.
-- Synchronize `Contents` with actual headings in the protocol.
 
 ## Disallowed changes
 - Do not infer omitted concentrations, times, temperatures, or volumes.
@@ -85,27 +79,23 @@ You may normalize formatting only when the meaning is unchanged and unambiguous:
 
 ## Output requirements
 When drafting a migrated protocol:
+- Only edit `README.md`.
 - Use the template headings exactly.
-- Use the template headings in `README.md`.
 - Keep all source content.
-- Add `CHECK:` markers for uncertainty.
-- Use `CHECK:` only for genuine unresolved uncertainty. If no uncertainty remains, do not mention `CHECK:` at all.
-- Add an `# Migration notes` section listing:
+- Keep the Ule Lab Protocol Template attribution badge at the top of the file, but do not add or preserve a template release-version badge.
+- Remove the template instruction note and the "Template repository: Click `Use this template`..." note.
+- Add `CHECK:` markers only for genuine unresolved uncertainty.
+- Add an `# Migration notes` section covering:
+  - imported protocol metadata from `source-metadata.yml`, using only non-blank lines
+  - `template_version` from `template-metadata.yml`
   - formatting normalizations performed
   - ambiguities and uncertainty flagged
   - content placed in `## Unplaced content`
-  - Imported protocol metadata from `source-metadata.yml`, using only the non-blank lines.
-  - template_version from `template-metadata.yml`.
-  - ambiguous mappings.
-  - normalized formatting changes.
-  - extracted images converted to Markdown tables.
-  - extracted images retained in `README.md`.
-  - extracted images omitted because they were decorative or duplicated non-protocol content.
-  - extracted images that could not be confidently classified or converted, marked with `CHECK:`.
-  - content copied verbatim but not confidently placed.
-- Keep `[![Created with Ule Lab Protocol Template](https://img.shields.io/badge/created%20with-Ule%20Lab%20Protocol%20Template-blue)](https://github.com/ulelab/protocol-template)` at the top of the file.
-- Delete the "Template repository: Click `Use this template` to create a new protocol repo..." note.
-- Remove the template instruction note.
+  - extracted images converted to Markdown tables
+  - extracted images retained in `README.md`
+  - extracted images omitted because they were decorative or duplicated non-protocol content
+  - extracted images that could not be confidently classified or converted
+  - content copied verbatim but not confidently placed
 
 ## Verification
 After drafting, verify the migration against the source:
diff --git a/.github/workflows/pdf_header.tex b/.github/workflows/pdf_header.tex
index 43fea5c..864636c 100644
--- a/.github/workflows/pdf_header.tex
+++ b/.github/workflows/pdf_header.tex
@@ -30,11 +30,20 @@
 
 \pagestyle{fancy}
 \fancyhf{}
+\setlength{\headheight}{14pt}
 
-\fancyhead[L]{\small\href{\repoURL}{\nolinkurl{\repoURL}}}
-\fancyhead[R]{\small\textbf{Commit:} \href{\commitURL}{\githash}\ \textbar\ \texttt{\gitactor}}
+\fancyhead[L]{%
+  \begin{minipage}[t]{0.54\textwidth}
+    \raggedright\scriptsize\href{\repoURL}{\nolinkurl{\repoURL}}
+  \end{minipage}%
+}
+\fancyhead[R]{%
+  \begin{minipage}[t]{0.44\textwidth}
+    \raggedleft\scriptsize\textbf{Commit:} \href{\commitURL}{\githash}\ \textbar\ \texttt{\gitactor}
+  \end{minipage}%
+}
 
 \fancyfoot[C]{\thepage}
 
 \renewcommand{\headrulewidth}{0.4pt}
-\renewcommand{\footrulewidth}{0pt}
\ No newline at end of file
+\renewcommand{\footrulewidth}{0pt}
diff --git a/.github/workflows/readme-to-pdf.yml b/.github/workflows/readme-to-pdf.yml
index 5e6b89f..905c6fb 100644
--- a/.github/workflows/readme-to-pdf.yml
+++ b/.github/workflows/readme-to-pdf.yml
@@ -113,6 +113,11 @@ jobs:
             -e 's/`\[X\]`/\\FAILstatus{}/g' \
             README._pdf.md > README._pdf.tmp && mv README._pdf.tmp README._pdf.md
 
+      - name: Render HTML subscripts for PDF only
+        run: |
+          set -euo pipefail
+          sed -E 's|<sub>([^<]+)</sub>|\\textsubscript{\1}|g' README._pdf.md > README._pdf.tmp && mv README._pdf.tmp README._pdf.md
+
       - name: Create PDF metadata definitions
         run: |
           set -euo pipefail
diff --git a/.github/workflows/validate-protocol.yml b/.github/workflows/validate-protocol.yml
index 2406a3d..a45b745 100644
--- a/.github/workflows/validate-protocol.yml
+++ b/.github/workflows/validate-protocol.yml
@@ -74,11 +74,23 @@ jobs:
           python -m unittest discover -s tests -p 'test_*.py'
 
       - name: Run content validation
+        id: content_validation
         if: steps.validation_gate.outputs.should_validate == 'true'
+        continue-on-error: true
         run: |
           python scripts/validate_protocol_content.py README.md
 
       - name: Run style validation
+        id: style_validation
         if: steps.validation_gate.outputs.should_validate == 'true'
+        continue-on-error: true
         run: |
           python scripts/validate_protocol_style.py README.md
+
+      - name: Fail if README validation failed
+        if: ${{ steps.validation_gate.outputs.should_validate == 'true' && (steps.content_validation.outcome != 'success' || steps.style_validation.outcome != 'success') }}
+        run: |
+          echo "README validation failed."
+          echo "Content validation outcome: ${{ steps.content_validation.outcome }}"
+          echo "Style validation outcome: ${{ steps.style_validation.outcome }}"
+          exit 1
diff --git a/README.md b/README.md
index f3fe486..f2d3e8f 100644
--- a/README.md
+++ b/README.md
@@ -1,5 +1,4 @@
 [![Created with Ule Lab Protocol Template](https://img.shields.io/badge/created%20with-Ule%20Lab%20Protocol%20Template-blue)](https://github.com/ulelab/protocol-template)
-[![Template version](https://img.shields.io/github/v/release/ulelab/protocol-template)](https://github.com/ulelab/protocol-template/releases)
 
 > Template repository: Click `Use this template` to create a new protocol repo. Template docs are in [docs/USING_THIS_TEMPLATE.md](https://github.com/ulelab/protocol-template/blob/main/docs/USING_THIS_TEMPLATE.md)
 # TODO: Protocol title
diff --git a/docs/PROMPT.md b/docs/PROMPT.md
index 50eee0a..015ce6d 100644
--- a/docs/PROMPT.md
+++ b/docs/PROMPT.md
@@ -9,7 +9,7 @@ Apply those instructions even if you are not GitHub Copilot.
 Do not change protocol meaning.
 Use `legacy/source.md` as the primary source when rewriting `README.md`.
 Use `legacy/source.txt` only as a fallback when `legacy/source.md` looks malformed, incomplete, or unclear.
-Use the PDF file in `legacy/` as the final reference source of truth for tables, figures, layout-dependent content, and anything still ambiguous after checking the generated text sources.
+Use the PDF file in `legacy/` as the final reference source of truth for tables, figures, layout-dependent content, and anything still ambiguous.
 Treat image references in `legacy/source.md` and files in `legacy/images/` as extracted protocol content, not decorative artifacts, until they have been reviewed.
 If `legacy/source.md` and `legacy/source.txt` disagree, prefer `legacy/source.md` for general structure and prose, but use the original PDF as the final tie-breaker.
 
@@ -51,26 +51,21 @@ When migrating:
 - mention in `# Migration notes` which extracted images were converted to Markdown tables, which were retained as images, which were omitted as non-protocol/decorative, and which require `CHECK:`
 
 ## Allowed formatting normalization
-Normalize formatting only when the meaning is unchanged and unambiguous:
-
-- add a space between numbers and units
-- use `seconds`, `minutes`, `hours`
-- use `µL`, `mL`, `L`
-- use `37 °C` style temperature formatting
-- standardize concentration units to `mM`, `µM`, `nM`, `% (w/v)`, etc., using the micro sign `µ` consistently
-- standardize pH formatting to `pH 7.4`
-- standardize chemical names to match the source but with consistent formatting, for example `Tris-HCl` instead of `Tris HCl`
-- standardize chemical formulas with HTML subscripts, for example H2O to H<sub>2</sub>O and MgCl2 to MgCl<sub>2</sub>
-- do not use Unicode subscript characters such as `₂`
-- standardize `RNAseq` or `RNA-Seq` to `RNA-seq`, and similarly for `ChIP-seq`, `ATAC-seq`, and related names
-- Use numbered lists for procedural actions in sequence. For other non-procedural content, bullets are better. Note-like text such as Note, NB, Optional, Recommended, and Warning should use blockquote style such as `> **Note**`.
-- normalize bullets, headings, and markdown tables to match the repository template
-- use tables for reaction mixes and other tabular content
-- convert image-based tables to Markdown tables wherever this is legible and unambiguous; otherwise retain the image at the correct protocol location with `CHECK:` explaining why it could not be safely converted
-- normalize note-like text such as Note, NB, Optional, Recommended, and Warning to blockquote style, for example `> **Note**`
-- place note-like text immediately after the step it refers to, or at the end of the protocol if it clearly refers to the whole protocol
-- remove empty columns from tables
-- synchronize `Contents` with the actual headings in the protocol
+You may normalize formatting only when the meaning is unchanged and unambiguous:
+
+- Add a space between numbers and units.
+- Use full-word time units: `seconds`, `minutes`, `hours`.
+- Use standard units and spacing, for example `37 °C`, `10 µL`, `1 mM`, `100 nM`.
+- Standardize pH formatting to `pH 7.4`.
+- Standardize chemical names without changing meaning, for example `Tris-HCl` instead of `Tris HCl`.
+- Standardize chemical formulas with HTML subscripts, for example H2O to H<sub>2</sub>O and MgCl2 to MgCl<sub>2</sub>.
+- Do not use Unicode subscript characters such as `₂`.
+- Standardize names such as `RNAseq` or `RNA-Seq` to `RNA-seq`, and similarly for `ChIP-seq`, `ATAC-seq`, and related names.
+- Use numbered lists for procedural actions in sequence, bullets for non-procedural lists, and tables for reaction mixes or other tabular content.
+- Normalize note-like labels such as Note, NB, Optional, Recommended, and Warning to blockquote style, for example `> **Note:**`.
+- Normalize headings, bullets, Markdown tables, and `Contents` links to match the repository template.
+- Convert image-based tables to Markdown tables when legible and unambiguous; otherwise retain the image with `CHECK:`.
+- Remove empty columns from tables.
 
 ## Disallowed changes
 - do not infer omitted concentrations, times, temperatures, or volumes
@@ -90,28 +85,21 @@ Normalize formatting only when the meaning is unchanged and unambiguous:
 ## Output requirements
 - Only edit `README.md`.
 - Use the template headings exactly.
-- Use the template headings in `README.md`.
 - Keep all source content.
-- Add `CHECK:` markers for uncertainty.
-- Use `CHECK:` only for genuine unresolved uncertainty. If no uncertainty remains, do not mention `CHECK:` at all.
-- Add an `# Migration notes` section.
-- After drafting, add a short summary in `# Migration notes` covering:
+- Keep the Ule Lab Protocol Template attribution badge at the top of the file, but do not add or preserve a template release-version badge.
+- Remove the template instruction note and the "Template repository: Click `Use this template`..." note.
+- Add `CHECK:` markers only for genuine unresolved uncertainty.
+- Add an `# Migration notes` section covering:
+  - imported protocol metadata from `source-metadata.yml`, using only non-blank lines
+  - `template_version` from `template-metadata.yml`
   - formatting normalizations performed
   - ambiguities and uncertainty flagged
   - content placed in `## Unplaced content`
-- Include the following in `# Migration notes`:
-  - imported protocol metadata from `source-metadata.yml`, using only the non-blank lines
-  - template_version from `template-metadata.yml`
-  - ambiguous mappings
-  - normalized formatting changes
   - extracted images converted to Markdown tables
   - extracted images retained in `README.md`
   - extracted images omitted because they were decorative or duplicated non-protocol content
-  - extracted images that could not be confidently classified or converted, marked with `CHECK:`
+  - extracted images that could not be confidently classified or converted
   - content copied verbatim but not confidently placed
-- Keep `[![Created with Ule Lab Protocol Template](https://img.shields.io/badge/created%20with-Ule%20Lab%20Protocol%20Template-blue)](https://github.com/ulelab/protocol-template)` at the top of the file.
-- Remove the template instruction note.
-- Delete the "Template repository: Click `Use this template` to create a new protocol repo..." note.
 
 ## Verification
 After drafting, verify the migration against the source:
diff --git a/docs/USING_THIS_TEMPLATE.md b/docs/USING_THIS_TEMPLATE.md
index b7ab309..8949e5d 100644
--- a/docs/USING_THIS_TEMPLATE.md
+++ b/docs/USING_THIS_TEMPLATE.md
@@ -32,7 +32,10 @@ If you are new to GitHub, start with this short [GitHub Hello World tutorial](ht
 - [Make changes to an existing protocol](#make-changes-to-an-existing-protocol)
 - [Use the protocol in the lab](#use-the-protocol-in-the-lab)
 - [Release a protocol](#release-a-protocol)
+- [Tips for making the most of the template](#tips-for-making-the-most-of-the-template)
 - [Citation information](#citation-information)
+- [Maintainer and contributor notes (template maintainers only)](#maintainer-and-contributor-notes)
+
 ---
 
 # Create a new protocol repository
@@ -51,6 +54,10 @@ You now have your own copy of the template.
 The structure of the template is:
 ```md
 .
+├── .agents
+│   └── skills/protocol-migration/ # Codex migration skill
+├── .claude
+│   └── skills/protocol-migration/ # Claude Code migration skill
 ├── .github
 │   ├── workflows/              # Automation for validations and PDF generation
 │   └── copilot-instructions.md # AI-assisted migration instructions
@@ -99,7 +106,7 @@ The main file you must edit for protocol content is `README.md`. **Do not rename
 10. The validation GitHub Actions workflow (`validate-protocol-README`) will automatically run on that pull request when `README.md` has changed. It runs a content check for the required title, status line, status legend, key headings, unresolved placeholders, and placeholder step names, plus a style check for unit formatting. If checks fail, fix them before merging into `main`.
 11. Ask for a reviewer where possible.
 
-> **Review scope**: Before opening the pull request, check the changed files. For a routine protocol edit, only `README.md` or `CODEOWNERS` should change. This does not apply to the one-time legacy PDF import workflow, where files in `legacy/` may also be created or updated. If any other files changed, remove those changes or explain clearly why they are needed.
+> **Review scope**: Before opening the pull request, check the changed files. For a routine protocol edit, expected changes are `README.md`, `CODEOWNERS`, and optionally `legacy/source-metadata.yml` when provenance is updated. This does not apply to the one-time legacy PDF import workflow, where files in `legacy/` may also be created or updated. If any other files changed, remove those changes or explain clearly why they are needed.
 
 > **Note**: Always check accuracy and make sure required sections, such as protocol status and the status legend, are present.
 
@@ -175,7 +182,7 @@ At minimum, make sure your protocol includes:
 - a status legend row containing `[OK]`, `[?]`, and `[X]`
 - a short description (`# About`)
 - contents (`## Contents`)
-- a materials section (`# ... Materials`)
+- a top-level materials section, optionally numbered, for example `# Materials` or `# 7. Materials`
 
 > **Note**: These are mandatory items for validation.
 
@@ -283,15 +290,10 @@ If you want to adapt or improve an existing protocol on GitHub:
 10. If the PDF is not generated within a few minutes (you may need to refresh the page), go to the GitHub **Actions** tab, manually run the `README-to-pdf` workflow, and select your working branch in the **Use workflow from** branch menu.
 11. PDF generation creates another commit, usually with a message like `Update <repo-name>.pdf`.
 12. Before making any further local changes after pushing, run `git pull`. GitHub Actions may have added a new commit on your branch.
-13. If you have questions about a protocol, or want to propose a change, open a GitHub Issue using the `Protocol issues` template and assign relevant people.
-14. If you are developing a protocol as a team, you can use a GitHub Project.
-15. Use Issues to track optimisation ideas or questions.
-16. Add images, gels, notes or links to code or data to the relevant Issue.
-17. Close the Issue when the question is resolved.
-18. This helps keep a record of what has already been tried.
-19. If your change should become part of the main protocol, open a pull request to `main` and request review from relevant people.
-20. Before requesting review, check the changed files. For a routine protocol edit, only `README.md` or `CODEOWNERS` should change. For a legacy PDF import, files in `legacy/` may also be created or updated. If any other files changed, remove those changes or explain clearly why they are needed.
-21. Do not merge into `main` without review, unless you are the only person using that protocol.
+13. For issue tracking, Projects, branches, commits, pull requests, and Slack notifications, follow [Tips for making the most of the template](#tips-for-making-the-most-of-the-template).
+14. If your change should become part of the main protocol, open a pull request to `main` and request review from relevant people.
+15. Before requesting review, check the changed files. For a routine protocol edit, expected changes are `README.md`, `CODEOWNERS`, and optionally `legacy/source-metadata.yml` when provenance is updated. For a legacy PDF import, files in `legacy/` may also be created or updated. If any other files changed, remove those changes or explain clearly why they are needed.
+16. Do not merge into `main` without review, unless you are the only person using that protocol.
 
 ---
 
@@ -329,10 +331,62 @@ Before using a protocol in the lab, check all of the following:
 
 # Release a protocol
 
-Once a protocol has been added and confirmed to be working — that is, its status is 🟢 `[OK]` and this is clearly marked at the top of the file, create the first release: `1.0.0`.
-> **Recommended**: Link releases to Zenodo if you want each protocol version to have a citable DOI.
+Once a protocol has been added and confirmed to be working, create the first release: `1.0.0`.
+
+Before releasing:
+
+1. Confirm the protocol status is 🟢 `[OK]`.
+2. Confirm validation passes on `main`.
+3. Confirm the generated PDF is current and the PDF header commit SHA matches the protocol commit you intend to release.
+4. Create a GitHub release and tag, starting with `1.0.0`.
+5. Link the release to Zenodo if you want a citable DOI.
+6. Tell maintainers listed in `CODEOWNERS` and relevant protocol users when a new version is released.
+
+Further changes can then be released using semantic versioning.
+
+---
+
+# Tips for making the most of the template
+
+Use the repository as both the current protocol and the record of how the protocol changed.
+
+### Issues and Projects
+
+- Open one GitHub Issue per problem, optimisation, question, or protocol aspect. Use the `Protocol issues` template.
+- Keep issues modular: if the discussion splits into a separate problem, open a separate issue and link it. If an issue is complex, open sub-issues.
+- Link issues to a GitHub Project when work is shared, ongoing, or has multiple follow-up steps.
+- Add useful evidence directly to the issue: images, gels, follow-up results, notes, links to analysis repositories, database records, sample sheets, or source data.
+- Close the issue when the result is incorporated into `README.md`, rejected with a clear reason, or moved to a new issue. Add comments to explain the reason and to discuss an issue.
+
+### Branches, commits, and pull requests
+
+- Create a branch for each meaningful feature, fix, or experimental optimisation round. Use the appropriate base branch; it does not always need to be `main`.
+- Keep commits small and descriptive.
+- Mention related issues in commit messages or pull requests, for example `refs #12` while investigating or `closes #12` when the change resolves the issue.
+- In pull requests, request reviewers, tag relevant people, and invite discussion before merging changes that affect how people run or interpret the protocol.
+
+### Slack integration
+
+If your team uses Slack, you can connect a protocol repository to a Slack channel with the [GitHub integration for Slack](https://github.com/integrations/slack). In the relevant Slack channel:
+
+```text
+/invite @github
+/github signin
+/github subscribe owner/repo
+```
+
+Replace `owner/repo` with the protocol repository, for example `ulelab/protocol-rnaseq`.
+
+You can set what type of notifications you want updates for on Slack by specifying the type of subscription:
+
+Examples:
+```text
+/github subscribe owner/repo issues pulls reviews comments
+/github subscribe owner/repo workflows
+/github unsubscribe owner/repo commits
+```
 
-Further changes can then be released using semantic versioning. Ensure maintainers listed in `CODEOWNERS` and other protocol developers and users are involved or aware if a new version release is planned.
+Use Slack notifications to keep the channel aware of issues, pull requests, reviews, and workflow status. Tune subscriptions if the channel becomes noisy.
 
 ---
 
@@ -356,3 +410,54 @@ Template citation:
 Ira A. Iosub. `protocol-template`, DOI: https://doi.org/10.5281/zenodo.20148013
 
 The template citation metadata is stored in `docs/template-metadata.yml`.
+
+---
+
+# Maintainer and contributor notes
+
+> **Template maintainers only:** This section is for people maintaining `ulelab/protocol-template` itself. It is not part of the normal protocol-author workflow; most users can stop at [Citation information](#citation-information).
+
+> **Note:** The template `README.md` intentionally contains placeholders, so content validation may fail in this template repository. Protocol repositories created from the template should pass content validation after the placeholders are replaced.
+
+## When to change this template
+
+Change this repository only when the change should apply to future protocol repositories or to the shared template machinery.
+
+> **Important:** Existing protocol repositories do not automatically inherit changes made here after they were created from the template. If a template change is important for existing protocol repositories, communicate it separately or apply it to those repositories directly.
+
+Good reasons to change the template include:
+
+- improving the default protocol structure in `README.md`
+- clarifying the user guide
+- changing validation or style-fix rules
+- improving legacy PDF migration support
+- adjusting PDF rendering
+- updating shared issue, pull request, or ownership defaults
+- updating template metadata, licensing, notices, or release information
+
+For a one-off correction to a single protocol, change that protocol repository instead.
+
+## Keep the user experience lightweight
+
+The template should make the common path obvious: create a repository, edit `README.md`, validate, review, and use the generated PDF.
+
+- Do not add new required user steps unless they prevent a real recurring failure.
+- Prefer improving existing workflows, scripts, or docs over adding new files.
+- Keep maintainer rationale out of the main protocol-author path.
+- Keep generated or temporary files out of the template unless users need them as examples or defaults.
+- Avoid broad rewrites when a small, tested change fixes the problem.
+
+## Change checklist
+
+Before merging template changes:
+
+1. For Markdown-only documentation changes, at least inspect the rendered Markdown or diff carefully.
+2. For PDF rendering changes, generate or inspect the PDF produced by the `README-to-pdf` workflow.
+3. For workflow changes, check triggers, permissions, branch behavior, generated commits, and whether users need to run `git pull` afterwards.
+4. For migration behavior changes, keep `docs/PROMPT.md`, `.github/copilot-instructions.md`, `.agents/skills/protocol-migration/SKILL.md`, and `.claude/skills/protocol-migration/SKILL.md` consistent.
+5. For validator or fixer changes, add or update exact regression tests for the intended behavior and important false positives.
+6. Update this guide if applicable.
+
+## Releases
+
+Use template releases for meaningful template changes. Update `docs/template-metadata.yml` when the template version, citation metadata, or release metadata changes.
diff --git a/protocol-template.pdf b/protocol-template.pdf
index c46ee2e..50efa19 100644
Binary files a/protocol-template.pdf and b/protocol-template.pdf differ
diff --git a/scripts/fix_protocol_style.py b/scripts/fix_protocol_style.py
index fd4beb8..35a50c8 100644
--- a/scripts/fix_protocol_style.py
+++ b/scripts/fix_protocol_style.py
@@ -19,11 +19,10 @@
     rf"\b(?P<value>{NUMBER_RE})(?P<space>\s*)(?P<unit>uL|ul|UL|uM|UM|ug|μL|μM|μg)\b"
 )
 UNIT_RE = re.compile(
-    rf"\b(?P<value>{NUMBER_RE})(?P<space>\s*)(?P<unit>µL|mL|ml|ML|L|l|µg|mg|g|kg|ng|mM|µM|nM|M|μL|μM|μg)\b"
+    rf"\b(?P<value>{NUMBER_RE})(?P<space>\s*)(?P<unit>µL|mL|ml|ML|L|l|µg|mg|g|kg|ng|mM|µM|nM|M)\b"
 )
 TIME_RE = re.compile(
-    rf"\b(?P<value>{NUMBER_RE})(?P<space>\s*)(?P<unit>seconds?|second|minutes?|minute|hours?|hour|secs?|sec|mins?|min|hrs?|hr|s|h)\b",
-    re.IGNORECASE,
+    rf"\b(?P<value>{NUMBER_RE})(?P<space>\s*)(?P<unit>(?i:seconds?|minutes?|hours?|secs?|mins?|hrs?)|s|h)\b",
 )
 CHEMICAL_FORMULA_RE = re.compile(r"\b(?P<formula>(?:[A-Z][a-z]?\d*){2,})\b")
 UNICODE_SUBSCRIPT_RE = re.compile(r"\b(?P<formula>[A-Za-z₀₁₂₃₄₅₆₇₈₉]+)\b")
@@ -70,6 +69,9 @@
     "hours": "hour",
 }
 UNICODE_SUBSCRIPT_MAP = str.maketrans("₀₁₂₃₄₅₆₇₈₉", "0123456789")
+LITERAL_CHEMICAL_FORMULAS = {
+    "ddH2O": "ddH<sub>2</sub>O",
+}
 NOTE_LABEL_RE = re.compile(
     r"^(?P<indent>\s*)(?P<label>Note|NOTE|NB|Optional|Recommended|Warning):\s*(?P<body>.*)$",
     re.MULTILINE,
@@ -86,6 +88,41 @@ def html_subscript_formula(formula: str) -> str:
     return re.sub(r"(\d+)", r"<sub>\1</sub>", formula)
 
 
+def is_word_char(char: str) -> bool:
+    return char.isalnum() or char == "_"
+
+
+def replace_literal_token(text: str, token: str, replacement: str) -> str:
+    fixed = []
+    start = 0
+
+    while True:
+        index = text.find(token, start)
+        if index == -1:
+            fixed.append(text[start:])
+            return "".join(fixed)
+
+        before = text[index - 1] if index > 0 else ""
+        after_index = index + len(token)
+        after = text[after_index] if after_index < len(text) else ""
+        if (not before or not is_word_char(before)) and (
+            not after or not is_word_char(after)
+        ):
+            fixed.append(text[start:index])
+            fixed.append(replacement)
+        else:
+            fixed.append(text[start:after_index])
+
+        start = after_index
+
+
+def normalize_literal_chemical_formulas(text: str) -> str:
+    fixed = text
+    for found, preferred in LITERAL_CHEMICAL_FORMULAS.items():
+        fixed = replace_literal_token(fixed, found, preferred)
+    return fixed
+
+
 def apply_regex_substitution(
     text: str,
     pattern: re.Pattern,
@@ -134,6 +171,7 @@ def normalize_plain_chemical_formula(match: Match[str]) -> str:
 def fix_readme_style(readme: str) -> str:
     fixed = readme
 
+    fixed = normalize_literal_chemical_formulas(fixed)
     fixed = apply_regex_substitution(
         fixed,
         PH_RE,
diff --git a/scripts/validate_protocol_style.py b/scripts/validate_protocol_style.py
index 9fa8261..6f8c63d 100644
--- a/scripts/validate_protocol_style.py
+++ b/scripts/validate_protocol_style.py
@@ -14,11 +14,10 @@
     rf"\b(?P<value>{NUMBER_RE})(?P<space>\s*)(?P<unit>uL|ul|UL|uM|UM|ug|μL|μM|μg)\b"
 )
 UNIT_RE = re.compile(
-    rf"\b(?P<value>{NUMBER_RE})(?P<space>\s*)(?P<unit>µL|mL|ml|ML|L|l|µg|mg|g|kg|ng|mM|µM|nM|M|μL|μM|μg)\b"
+    rf"\b(?P<value>{NUMBER_RE})(?P<space>\s*)(?P<unit>µL|mL|ml|ML|L|l|µg|mg|g|kg|ng|mM|µM|nM|M)\b"
 )
 TIME_RE = re.compile(
-    rf"\b(?P<value>{NUMBER_RE})(?P<space>\s*)(?P<unit>seconds?|second|minutes?|minute|hours?|hour|secs?|sec|mins?|min|hrs?|hr|s|h)\b",
-    re.IGNORECASE,
+    rf"\b(?P<value>{NUMBER_RE})(?P<space>\s*)(?P<unit>(?i:seconds?|minutes?|hours?|secs?|mins?|hrs?)|s|h)\b",
 )
 CHEMICAL_FORMULA_RE = re.compile(
     r"\b(?P<formula>(?:[A-Z][a-z]?\d*){2,})\b"
@@ -189,6 +188,9 @@
     "hours": "hour",
 }
 UNICODE_SUBSCRIPT_MAP = str.maketrans("₀₁₂₃₄₅₆₇₈₉", "0123456789")
+LITERAL_CHEMICAL_FORMULAS = {
+    "ddH2O": "ddH<sub>2</sub>O",
+}
 
 
 def preferred_time_token(value: str, unit: str) -> str:
@@ -201,6 +203,41 @@ def html_subscript_formula(formula: str) -> str:
     return re.sub(r"(\d+)", r"<sub>\1</sub>", formula)
 
 
+def is_word_char(char: str) -> bool:
+    return char.isalnum() or char == "_"
+
+
+def contains_literal_token(text: str, token: str) -> bool:
+    start = 0
+    while True:
+        index = text.find(token, start)
+        if index == -1:
+            return False
+
+        before = text[index - 1] if index > 0 else ""
+        after_index = index + len(token)
+        after = text[after_index] if after_index < len(text) else ""
+        if (not before or not is_word_char(before)) and (
+            not after or not is_word_char(after)
+        ):
+            return True
+
+        start = index + len(token)
+
+
+def is_acronym_like_formula(formula: str, token_matches: List[re.Match]) -> bool:
+    if any(char.islower() for char in formula) or len(token_matches) < 3:
+        return False
+
+    if not token_matches[-1].group(2):
+        return False
+
+    uncounted_prefix_tokens = [
+        token_match for token_match in token_matches[:-1] if not token_match.group(2)
+    ]
+    return len(uncounted_prefix_tokens) >= 2
+
+
 def is_supported_chemical_formula(formula: str) -> bool:
     if not any(char.isdigit() for char in formula):
         return False
@@ -209,18 +246,25 @@ def is_supported_chemical_formula(formula: str) -> bool:
     if not tokens or "".join(tokens) != formula:
         return False
 
-    return all(
-        re.match(r"([A-Z][a-z]?)(\d*)$", token) is not None
-        and re.match(r"([A-Z][a-z]?)(\d*)$", token).group(1) in PERIODIC_TABLE_SYMBOLS
-        for token in tokens
-    )
+    token_matches = []
+    for token in tokens:
+        token_match = re.match(r"([A-Z][a-z]?)(\d*)$", token)
+        if token_match is None or token_match.group(1) not in PERIODIC_TABLE_SYMBOLS:
+            return False
+        token_matches.append(token_match)
+
+    if is_acronym_like_formula(formula, token_matches):
+        return False
+
+    return True
 
 
 def format_unit_failure(line_number: int, found: str, preferred: str) -> str:
     if "μ" in found:
         return (
-            f"Line {line_number}: unit uses Greek mu `μ`; use the micro sign `µ` "
-            f"in `{preferred}` instead of `{found}`."
+            f"Line {line_number}: unit uses Greek letter mu `μ` (U+03BC); "
+            f"copy/paste the micro sign `µ` (U+00B5) in `{preferred}` "
+            f"instead of `{found}`."
         )
 
     return f"Line {line_number}: unit should use `{preferred}` style, found `{found}`."
@@ -263,6 +307,12 @@ def validate_readme_style(readme: str) -> List[str]:
                     f"Line {line_number}: pH should use `{preferred}` style, found `{match.group(0)}`."
                 )
 
+        for found, preferred in LITERAL_CHEMICAL_FORMULAS.items():
+            if contains_literal_token(line, found):
+                failures.append(
+                    f"Line {line_number}: chemical formula should use `{preferred}` style, found `{found}`."
+                )
+
         for match in CHEMICAL_FORMULA_RE.finditer(line):
             formula = match.group("formula")
             if "<sub>" in formula or not is_supported_chemical_formula(formula):
diff --git a/tests/test_fix_protocol_style.py b/tests/test_fix_protocol_style.py
index 717fb29..921885d 100644
--- a/tests/test_fix_protocol_style.py
+++ b/tests/test_fix_protocol_style.py
@@ -16,6 +16,20 @@ def test_fixer_normalizes_supported_style_issues(self) -> None:
 
 Add 10 µL lysis buffer and incubate for 5 minutes at 20 °C.
 Adjust to pH 7.4 with 1 µM primer in H<sub>2</sub>O and MgCl<sub>2</sub>.
+"""
+
+        self.assertEqual(fix_readme_style(original), expected)
+
+    def test_fixer_normalizes_literal_ddh2o(self) -> None:
+        original = """# Wash
+
+Rinse with ddH2O before storage.
+Keep the addH2O helper label unchanged.
+"""
+        expected = """# Wash
+
+Rinse with ddH<sub>2</sub>O before storage.
+Keep the addH2O helper label unchanged.
 """
 
         self.assertEqual(fix_readme_style(original), expected)
@@ -30,12 +44,29 @@ def test_fixer_normalizes_greek_mu_and_note_labels(self) -> None:
 
         self.assertEqual(fix_readme_style(original), expected)
 
+    def test_fixer_does_not_rewrite_uppercase_biology_and_figure_labels(self) -> None:
+        readme = """# Notes
+
+Measure 25S rRNA and 3S RNA.
+See Supplementary Figure 1S, Figure 2H, and Table 2H.
+"""
+
+        self.assertEqual(fix_readme_style(readme), readme)
+
     def test_fixer_does_not_subscript_non_chemical_product_codes(self) -> None:
         readme = """# Reagents
 
 - Totalpure NGS/Ampure XP beads
 - 20 µM Cas9 Nuclease, S. pyogenes (M0386T)
 - 20 µM Cas9 Nuclease, S. pyogenes (M₀₃₈₆T)
+"""
+
+        self.assertEqual(fix_readme_style(readme), readme)
+
+    def test_fixer_does_not_subscript_bioinformatics_acronyms(self) -> None:
+        readme = """# Notes
+
+Compare CHIP3, FISH3, and NGS2 annotations before ChIP-seq.
 """
 
         self.assertEqual(fix_readme_style(readme), readme)
diff --git a/tests/test_validate_protocol_style.py b/tests/test_validate_protocol_style.py
index 7fbd448..0ba252b 100644
--- a/tests/test_validate_protocol_style.py
+++ b/tests/test_validate_protocol_style.py
@@ -62,6 +62,20 @@ def test_volume_and_time_formatting_are_reported(self) -> None:
             )
         )
 
+    def test_uppercase_biology_and_figure_labels_are_not_time_units(self) -> None:
+        readme = (
+            VALID_README
+            + "\nMeasure 25S rRNA and 3S RNA.\n"
+            + "See Supplementary Figure 1S, Figure 2H, and Table 2H.\n"
+        )
+
+        failures = validate_readme_style(readme)
+
+        self.assertFalse(any("25 seconds" in failure for failure in failures))
+        self.assertFalse(any("3 seconds" in failure for failure in failures))
+        self.assertFalse(any("1 second" in failure for failure in failures))
+        self.assertFalse(any("2 hours" in failure for failure in failures))
+
     def test_temperature_formatting_is_reported(self) -> None:
         readme = VALID_README.replace("20 °C", "20C", 1)
 
@@ -88,11 +102,32 @@ def test_greek_mu_is_reported_and_normalized_to_micro_sign(self) -> None:
 
         self.assertTrue(
             any(
-                "unit uses Greek mu `μ`; use the micro sign `µ`" in failure
+                "unit uses Greek letter mu `μ` (U+03BC); copy/paste the micro sign `µ` (U+00B5)"
+                in failure
                 for failure in failures
             )
         )
 
+    def test_greek_mu_unit_reports_one_copyable_message_per_token(self) -> None:
+        cases = [
+            ("10 μL lysis buffer", "10 µL", "10 μL"),
+            ("1 μM primer", "1 µM", "1 μM"),
+            ("2 μg enzyme", "2 µg", "2 μg"),
+        ]
+
+        for readme, preferred, found in cases:
+            with self.subTest(found=found):
+                failures = validate_readme_style(readme)
+
+                self.assertEqual(
+                    failures,
+                    [
+                        "Line 1: unit uses Greek letter mu `μ` (U+03BC); "
+                        "copy/paste the micro sign `µ` (U+00B5) in "
+                        f"`{preferred}` instead of `{found}`."
+                    ],
+                )
+
     def test_ph_spacing_and_case_are_reported(self) -> None:
         readme = VALID_README.replace("pH 7.4", "PH7.4", 1)
 
@@ -114,6 +149,26 @@ def test_plain_chemical_formula_uses_html_subscripts(self) -> None:
             )
         )
 
+    def test_ddh2o_uses_html_subscript(self) -> None:
+        readme = VALID_README + "\nRinse with ddH2O before storage.\n"
+
+        failures = validate_readme_style(readme)
+
+        self.assertTrue(
+            any(
+                "chemical formula should use `ddH<sub>2</sub>O` style"
+                in failure
+                for failure in failures
+            )
+        )
+
+    def test_ddh2o_substring_is_not_reported(self) -> None:
+        readme = VALID_README + "\nKeep the addH2O helper label unchanged.\n"
+
+        failures = validate_readme_style(readme)
+
+        self.assertFalse(any("ddH<sub>2</sub>O" in failure for failure in failures))
+
     def test_unicode_subscript_formula_is_reported(self) -> None:
         readme = VALID_README.replace("MgCl<sub>2</sub>", "MgCl₂", 1)
 
@@ -133,6 +188,18 @@ def test_non_chemical_abbreviation_with_digits_is_not_reported(self) -> None:
 
         self.assertFalse(any("RT<sub>1</sub>" in failure for failure in failures))
 
+    def test_bioinformatics_acronyms_with_digits_are_not_chemical_formulas(self) -> None:
+        readme = (
+            VALID_README
+            + "\nCompare CHIP3, FISH3, and NGS2 annotations before ChIP-seq.\n"
+        )
+
+        failures = validate_readme_style(readme)
+
+        self.assertFalse(any("CHIP<sub>3</sub>" in failure for failure in failures))
+        self.assertFalse(any("FISH<sub>3</sub>" in failure for failure in failures))
+        self.assertFalse(any("NGS<sub>2</sub>" in failure for failure in failures))
+
 
 if __name__ == "__main__":
     unittest.main()