diff --git a/notebooks/pancreatic_endocrinogenesis/11_screening_neurod2_targets.ipynb b/notebooks/pancreatic_endocrinogenesis/11_screening_neurod2_targets.ipynb
index b441cb0..3727bff 100644
--- a/notebooks/pancreatic_endocrinogenesis/11_screening_neurod2_targets.ipynb
+++ b/notebooks/pancreatic_endocrinogenesis/11_screening_neurod2_targets.ipynb
@@ -157,7 +157,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "adata = sc.read_h5ad(DATA_DIR / DATASET / \"processed\" / \"adata_preprocessed_filtered.h5ad\")"
+    "adata = sc.read_h5ad(DATA_DIR / DATASET / \"processed\" / \"adata_preprocessed.h5ad\")"
    ]
   },
   {
diff --git a/notebooks/pancreatic_endocrinogenesis/2_scvelo.ipynb b/notebooks/pancreatic_endocrinogenesis/2_scvelo.ipynb
index 55842ed..2058d1a 100644
--- a/notebooks/pancreatic_endocrinogenesis/2_scvelo.ipynb
+++ b/notebooks/pancreatic_endocrinogenesis/2_scvelo.ipynb
@@ -99,7 +99,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "adata = sc.read_h5ad(DATA_DIR / DATASET / \"processed\" / \"adata_preprocessed_filtered.h5ad\")"
+    "adata = sc.read_h5ad(DATA_DIR / DATASET / \"processed\" / \"adata_preprocessed.h5ad\")"
    ]
   },
   {
diff --git a/notebooks/pancreatic_endocrinogenesis/2_veloVI.ipynb b/notebooks/pancreatic_endocrinogenesis/2_veloVI.ipynb
index 5ec11c5..4afa72b 100644
--- a/notebooks/pancreatic_endocrinogenesis/2_veloVI.ipynb
+++ b/notebooks/pancreatic_endocrinogenesis/2_veloVI.ipynb
@@ -139,7 +139,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "adata = sc.read_h5ad(DATA_DIR / DATASET / \"processed\" / \"adata_preprocessed_filtered.h5ad\")"
+    "adata = sc.read_h5ad(DATA_DIR / DATASET / \"processed\" / \"adata_preprocessed.h5ad\")"
    ]
   },
   {
diff --git a/notebooks/pancreatic_endocrinogenesis/4_test_gene_regulation.ipynb b/notebooks/pancreatic_endocrinogenesis/4_test_gene_regulation.ipynb
index 6630623..9710348 100644
--- a/notebooks/pancreatic_endocrinogenesis/4_test_gene_regulation.ipynb
+++ b/notebooks/pancreatic_endocrinogenesis/4_test_gene_regulation.ipynb
@@ -152,7 +152,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "adata = sc.read_h5ad(DATA_DIR / DATASET / \"processed\" / \"adata_preprocessed_filtered.h5ad\")"
+    "adata = sc.read_h5ad(DATA_DIR / DATASET / \"processed\" / \"adata_preprocessed.h5ad\")"
    ]
   },
   {
diff --git a/notebooks/pancreatic_endocrinogenesis/7_repeat_regvelo.ipynb b/notebooks/pancreatic_endocrinogenesis/7_repeat_regvelo.ipynb
index 4f0b7f2..c36cf54 100644
--- a/notebooks/pancreatic_endocrinogenesis/7_repeat_regvelo.ipynb
+++ b/notebooks/pancreatic_endocrinogenesis/7_repeat_regvelo.ipynb
@@ -138,7 +138,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "adata = sc.read_h5ad(DATA_DIR / DATASET / \"processed\" / \"adata_preprocessed_filtered.h5ad\")\n",
+    "adata = sc.read_h5ad(DATA_DIR / DATASET / \"processed\" / \"adata_preprocessed.h5ad\")\n",
     "TF = adata.var_names[adata.var[\"tf\"]]\n",
     "\n",
     "# Prepare skeleton\n",
diff --git a/scripts/pancreatic_endocrinogenesis/11_screening_neurod2_targets.py b/scripts/pancreatic_endocrinogenesis/11_screening_neurod2_targets.py
index c44d59d..979e34e 100644
--- a/scripts/pancreatic_endocrinogenesis/11_screening_neurod2_targets.py
+++ b/scripts/pancreatic_endocrinogenesis/11_screening_neurod2_targets.py
@@ -61,7 +61,7 @@
 # ## Data loading
 
 # %%
-adata = sc.read_h5ad(DATA_DIR / DATASET / "processed" / "adata_preprocessed_filtered.h5ad")
+adata = sc.read_h5ad(DATA_DIR / DATASET / "processed" / "adata_preprocessed.h5ad")
 
 # %%
 palette = dict(zip(adata.obs["clusters"].cat.categories, adata.uns["clusters_colors"]))
diff --git a/scripts/pancreatic_endocrinogenesis/2_scvelo.py b/scripts/pancreatic_endocrinogenesis/2_scvelo.py
index ad4b0eb..efdec1a 100644
--- a/scripts/pancreatic_endocrinogenesis/2_scvelo.py
+++ b/scripts/pancreatic_endocrinogenesis/2_scvelo.py
@@ -29,7 +29,7 @@
 # ## Data loading
 
 # %%
-adata = sc.read_h5ad(DATA_DIR / DATASET / "processed" / "adata_preprocessed_filtered.h5ad")
+adata = sc.read_h5ad(DATA_DIR / DATASET / "processed" / "adata_preprocessed.h5ad")
 
 # %% [markdown]
 # ## Velocity pipeline
diff --git a/scripts/pancreatic_endocrinogenesis/2_veloVI.py b/scripts/pancreatic_endocrinogenesis/2_veloVI.py
index f36531b..8f9b8ef 100644
--- a/scripts/pancreatic_endocrinogenesis/2_veloVI.py
+++ b/scripts/pancreatic_endocrinogenesis/2_veloVI.py
@@ -35,7 +35,7 @@
 # ## Data loading
 
 # %%
-adata = sc.read_h5ad(DATA_DIR / DATASET / "processed" / "adata_preprocessed_filtered.h5ad")
+adata = sc.read_h5ad(DATA_DIR / DATASET / "processed" / "adata_preprocessed.h5ad")
 
 # %% [markdown]
 # ## Velocity pipeline
diff --git a/scripts/pancreatic_endocrinogenesis/4_test_gene_regulation.py b/scripts/pancreatic_endocrinogenesis/4_test_gene_regulation.py
index 6af5ba3..ea42823 100644
--- a/scripts/pancreatic_endocrinogenesis/4_test_gene_regulation.py
+++ b/scripts/pancreatic_endocrinogenesis/4_test_gene_regulation.py
@@ -54,7 +54,7 @@
 # ## Data loading
 
 # %%
-adata = sc.read_h5ad(DATA_DIR / DATASET / "processed" / "adata_preprocessed_filtered.h5ad")
+adata = sc.read_h5ad(DATA_DIR / DATASET / "processed" / "adata_preprocessed.h5ad")
 
 # %% [markdown]
 # ## Model loading
diff --git a/scripts/pancreatic_endocrinogenesis/7_repeat_regvelo.py b/scripts/pancreatic_endocrinogenesis/7_repeat_regvelo.py
index 0747e1d..bbbbb24 100644
--- a/scripts/pancreatic_endocrinogenesis/7_repeat_regvelo.py
+++ b/scripts/pancreatic_endocrinogenesis/7_repeat_regvelo.py
@@ -49,7 +49,7 @@
 # ## Data loading
 
 # %%
-adata = sc.read_h5ad(DATA_DIR / DATASET / "processed" / "adata_preprocessed_filtered.h5ad")
+adata = sc.read_h5ad(DATA_DIR / DATASET / "processed" / "adata_preprocessed.h5ad")
 TF = adata.var_names[adata.var["tf"]]
 
 # Prepare skeleton