diff --git a/experiment/src/org/labkey/experiment/samples/UploadSamplesHelper.java b/experiment/src/org/labkey/experiment/samples/UploadSamplesHelper.java
index 0f2c9a3342d..1b04d42d422 100644
--- a/experiment/src/org/labkey/experiment/samples/UploadSamplesHelper.java
+++ b/experiment/src/org/labkey/experiment/samples/UploadSamplesHelper.java
@@ -305,8 +305,8 @@ public static Pair<RunInputOutputBean, RunInputOutputBean> resolveInputsAndOutpu
     {
         Map<ExpMaterial, String> parentMaterials = new HashMap<>();
         Map<ExpData, String> parentData = new HashMap<>();
-        Set<String> parentDataTypesToRemove = new HashSet<>();
-        Set<String> parentSampleTypesToRemove = new HashSet<>();
+        Set<String> parentDataTypesToRemove = new CaseInsensitiveHashSet();
+        Set<String> parentSampleTypesToRemove = new CaseInsensitiveHashSet();
 
         Map<ExpMaterial, String> childMaterials = new HashMap<>();
         Map<ExpData, String> childData = new HashMap<>();