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diff --git a/docs/_static/tutorials/norman.png b/docs/_static/tutorials/norman.png
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diff --git a/docs/_static/tutorials/zhang.png b/docs/_static/tutorials/zhang.png
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diff --git a/docs/conf.py b/docs/conf.py
index 878b31f6..9e22f8f3 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -195,4 +195,7 @@
     "tutorials/notebooks/differential_gene_expression": "_static/tutorials/dge.png",
     "tutorials/notebooks/metadata_annotation": "_static/tutorials/metadata.png",
     "tutorials/notebooks/ontology_mapping": "_static/tutorials/ontology.png",
+    "tutorials/notebooks/norman_use_case": "_static/tutorials/norman.png",
+    "tutorials/notebooks/mcfarland_use_case": "_static/tutorials/mcfarland.png",
+    "tutorials/notebooks/zhang_use_case": "_static/tutorials/zhang.png",
 }
diff --git a/docs/tutorials/index.md b/docs/tutorials/index.md
index 22c4b24f..7960b8d2 100644
--- a/docs/tutorials/index.md
+++ b/docs/tutorials/index.md
@@ -11,13 +11,23 @@ Many are also designed to work seamlessly in Google colab.
 For questions about the usage of pertpy use the [scverse discourse](https://discourse.scverse.org/).
 :::
 
-## Quick start
+## Quick start: Tool specific tutorials
 
+### Data transformation
 ```{eval-rst}
 .. nbgallery::
 
    notebooks/guide_rna_assignment
    notebooks/mixscape
+   notebooks/perturbation_space
+   notebooks/metadata_annotation
+   notebooks/ontology_mapping
+```
+
+### Knowledge inference
+```{eval-rst}
+.. nbgallery::
+
    notebooks/augur
    notebooks/sccoda
    notebooks/sccoda_extended
@@ -29,13 +39,23 @@ For questions about the usage of pertpy use the [scverse discourse](https://disc
    notebooks/distance_tests
    notebooks/cinemaot
    notebooks/scgen_perturbation_prediction
-   notebooks/perturbation_space
    notebooks/differential_gene_expression
-   notebooks/metadata_annotation
-   notebooks/ontology_mapping
 ```
 
-### Glossary
+## Use cases
+Our use cases showcase a variety of pertpy tools applied to one dataset.
+They are designed to give you a sense of how to use pertpy in a real-world scenario.
+The use cases featured here are those we present in the pertpy [preprint](https://www.biorxiv.org/content/10.1101/2024.08.04.606516v1).
+
+```{eval-rst}
+.. nbgallery::
+
+   notebooks/norman_use_case
+   notebooks/mcfarland_use_case
+   notebooks/zhang_use_case
+```
+
+## Glossary
 
 ```{eval-rst}
 .. tab-set::
diff --git a/docs/tutorials/notebooks b/docs/tutorials/notebooks
index 55d33929..894e14e9 160000
--- a/docs/tutorials/notebooks
+++ b/docs/tutorials/notebooks
@@ -1 +1 @@
-Subproject commit 55d33929ce3ab5d4d38d5ae8b7684c822f720124
+Subproject commit 894e14e92b7901e218c435a908946dc016fc4412
diff --git a/pertpy/metadata/_cell_line.py b/pertpy/metadata/_cell_line.py
index ac89ae59..aad6ac79 100644
--- a/pertpy/metadata/_cell_line.py
+++ b/pertpy/metadata/_cell_line.py
@@ -341,8 +341,8 @@ def annotate_bulk_rna(
         # then we can compare these keys and fetch the corresponding metadata.
         if query_id not in adata.obs.columns:
             raise ValueError(
-                f"The specified `query_id` {query_id} can't be found in the `adata.obs`.\n"
-                "Ensure that you are using one of the available query IDs present in the adata.obs for the annotation.\n"
+                f"The specified `query_id` {query_id} can't be found in the `adata.obs`. \n"
+                "Ensure that you are using one of the available query IDs present in the adata.obs for the annotation."
                 "If the desired query ID is not available, you can fetch the cell line metadata "
                 "using the `annotate()` function before calling 'annotate_bulk_rna()'. "
                 "This ensures that the required query ID is included in your data, e.g. stripped_cell_line_name, DepMap ID."
@@ -359,9 +359,8 @@ def annotate_bulk_rna(
         else:
             reference_id = "DepMap_ID"
             logger.warning(
-                "To annotate bulk RNA data from Broad Institue, `DepMap_ID` is used as default reference and query identifier if no `reference_id` is given.\n"
-                "Ensure that `DepMap_ID` is available in 'adata.obs'.\n"
-                "Alternatively, use `annotate()` to annotate the cell line first "
+                "To annotate bulk RNA data from Broad Institue, `DepMap_ID` is used as default reference and query identifier if no `reference_id` is given."
+                "If `DepMap_ID` isn't available in 'adata.obs', use `annotate()` to annotate the cell line first."
             )
             if self.bulk_rna_broad is None:
                 self._download_bulk_rna(cell_line_source="broad")
diff --git a/pertpy/tools/_differential_gene_expression/_base.py b/pertpy/tools/_differential_gene_expression/_base.py
index c6c30293..4c86f02a 100644
--- a/pertpy/tools/_differential_gene_expression/_base.py
+++ b/pertpy/tools/_differential_gene_expression/_base.py
@@ -66,7 +66,7 @@ def data(self):
         if self.layer is None:
             return self.adata.X
         else:
-            return self.adata.layer[self.layer]
+            return self.adata.layers[self.layer]
 
     @classmethod
     @abstractmethod