dd6958bf3e8dfeb13dad8906a5c471293c471152
mspeir
  Wed Jul 22 07:56:17 2026 -0700
Update Gateway, Table Browser, and Custom Track tutorials for the new assembly search box

Replaced the old Clade/Genome/Assembly drop-down wording and screenshots with
the current genome search box, re-recorded the step GIFs, and expanded the
guided walkthroughs (Table Browser filter/intersection and output fields,
Custom Track track line, Gateway GenArk/recent-genomes and species tree).

refs #37355

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

diff --git docs/tutorials/tableBrowserTutorial.md docs/tutorials/tableBrowserTutorial.md
index 3d1d786c2c4..8cd87921fa9 100644
--- docs/tutorials/tableBrowserTutorial.md
+++ docs/tutorials/tableBrowserTutorial.md
@@ -52,35 +52,33 @@
 
 ``` image
 src=/images/tableBrowserAnnotated.png
 width=65%
 ```
 
 ---
 
 ## Guided Walkthrough
 
 
 <div class="row">
   <div class="col-md-6">
 ### Step 1: Select Your Assembly
 
-  Use the **Clade**, **Genome**, and **Assembly** menus to choose your reference genome.
-  
-  - *Clade*: Major organism group (e.g., Mammal, Vertebrate)
-  - *Genome*: Species (e.g., Human, Mouse)
-  - *Assembly*: Specific genome version (e.g., hg38)
+  Use the **Genome** search box to choose your reference genome. Start typing a species name,
+  common name, or assembly ID and pick a match from the list that drops down. The Table Browser
+  reloads on that assembly, and **Assembly** shows which one you are using.
   </div>
 
   <div class="col-md-6">
   ```image
   src=/images/assemblySelection.gif
   width=80%
   ```
 </div>
 </div>
 
 ---
 
 
 <div class="row">
   <div class="col-md-6">
@@ -135,46 +133,67 @@
   src=/images/defineRegions.gif
   width=80%
   ```
   </div>
 
   <div class="col-md-6">
 ### Step 4: Define a Genomic Region
   You can limit the output to a specific region or get data genome-wide.
   Whole-genome output may be unavailable for some tracks due to the large amount of data. 
   
   Options include:
   
   - Entering a position (e.g., `chr7:117199645-117356025`)
   - Typing a gene name and clicking <button>Lookup</button>
   - Using <button>Define regions</button> to upload/paste multiple coordinates
+  - Pasting or uploading a list of identifiers, such as gene names or accessions, with
+    <button>Paste list</button> or <button>Upload list</button> to return only those items
   
   </div>
 </div>
 
 ---
 
+### Optional: filter, subset, or combine tracks
+
+The **Filter** and **Intersection** tools, in the *Subset, combine, compare with another
+track* section, let you narrow down or combine data before you get output.
+
+Click <button>Create</button> next to **Filter** to keep only the rows that match conditions
+you set, for example genes on the plus strand or items above a score cutoff. A filter stays
+in place until you clear it, so you can switch tracks or regions and rerun the same query.
+
+Click <button>Create</button> next to **Intersection** to combine the current track with a
+second one. This answers questions like which SNPs fall inside RefSeq coding exons, or which
+of your regions overlap a peak track. You pick the second track and whether to keep the rows
+that overlap or the ones that don't.
+
+---
+
 <div class="row">
   <div class="col-md-6">
 ### Step 5: Select Output Format
   Use the **Output format** dropdown to choose what type of file or fields you want returned.
   
   Options include:
   
-  - All fields from the table
-  - Selected fields only
-  - File formats like BED, GTF, or custom tracks
+  - **All fields from selected table** returns the table as it is stored.
+  - **Selected fields from primary and related tables** lets you pick just the columns you
+    want, and pull in columns from related tables in the same query. This is the easiest way
+    to get something like gene names next to coordinates without downloading the whole table.
+  - File formats like **BED**, **GTF**, or a **custom track** you can load back into the browser.
+  - **Sequence** returns the DNA, or protein for some tracks, covered by your table.
   </div>
   <div class="col-md-6">
   ``` image
   src=/images/tutorialImages/tableBrowserOutputDropDown.png
   width=80%
   ```
   </div>
 </div>
 
 
 ---
 
 <div class="row">
   <div class="col-md-6">
   ``` image