diff --git a/api/src/org/labkey/api/data/NameGeneratorState.java b/api/src/org/labkey/api/data/NameGeneratorState.java
index fd0083024ec..d82896a0af5 100644
--- a/api/src/org/labkey/api/data/NameGeneratorState.java
+++ b/api/src/org/labkey/api/data/NameGeneratorState.java
@@ -50,9 +50,9 @@
 import java.util.stream.Collectors;
 
 import static org.labkey.api.data.NameGenerator.getParentImportAliasFieldKeys;
-import static org.labkey.api.exp.api.ExpMaterial.ALIQUOTED_FROM_INPUT;
 import static org.labkey.api.exp.api.ExpRunItem.INPUT_PARENT;
 import static org.labkey.api.exp.api.ExpRunItem.PARENT_IMPORT_ALIAS_MAP_PROP;
+import static org.labkey.api.exp.api.ExperimentService.isAliquotedFromColumn;
 
 public class NameGeneratorState implements AutoCloseable
 {
@@ -362,7 +362,7 @@ private void addParentLookupValues(String parentTypeName,
                                        boolean isMaterialParent,
                                        @Nullable Map<String, FieldKey> parentImportAliases,
                                        ExpObject parentObject,
-                                       Map<FieldKey, ArrayList<Object>> inputLookupValues,
+                                       Map<FieldKey, LinkedHashSet<Object>> inputLookupValues,
                                        @Nullable NameGenerator altNameGenerator)
     {
         String inputType = isMaterialParent ? ExpMaterial.MATERIAL_INPUT_PARENT : ExpData.DATA_INPUT_PARENT;
@@ -384,7 +384,7 @@ private void addParentLookupValues(String parentTypeName,
                 continue;
 
             // add to Input/<LookupField>
-            inputLookupValues.computeIfAbsent(FieldKey.fromParts(INPUT_PARENT, fieldName), (s) -> new ArrayList<>()).add(lookupValue);
+            inputLookupValues.computeIfAbsent(FieldKey.fromParts(INPUT_PARENT, fieldName), (s) -> new LinkedHashSet<>()).add(lookupValue);
 
             // add to importAlias/<LookupField>
             if (parentImportAliases != null)
@@ -393,19 +393,19 @@ private void addParentLookupValues(String parentTypeName,
                         .entrySet()
                         .stream()
                         .filter(entry -> inputFK.equals(entry.getValue()))
-                        .forEach(entry -> inputLookupValues.computeIfAbsent(FieldKey.fromParts(entry.getKey(), fieldName), (s) -> new ArrayList<>()).add(lookupValue));
+                        .forEach(entry -> inputLookupValues.computeIfAbsent(FieldKey.fromParts(entry.getKey(), fieldName), (s) -> new LinkedHashSet<>()).add(lookupValue));
             }
 
             // add to <Type>Inputs/<LookupField>
-            inputLookupValues.computeIfAbsent(FieldKey.fromParts(inputType, fieldName), (s) -> new ArrayList<>()).add(lookupValue);
+            inputLookupValues.computeIfAbsent(FieldKey.fromParts(inputType, fieldName), (s) -> new LinkedHashSet<>()).add(lookupValue);
             // add to <Type>Inputs/<TypeName>/<LookupField>
-            inputLookupValues.computeIfAbsent(FieldKey.fromParts(inputType, parentTypeName, fieldName), (s) -> new ArrayList<>()).add(lookupValue);
+            inputLookupValues.computeIfAbsent(FieldKey.fromParts(inputType, parentTypeName, fieldName), (s) -> new LinkedHashSet<>()).add(lookupValue);
         }
     }
 
     private void addAncestorLookupValues(
             ExpRunItem parentObject,
-            Map<FieldKey, ArrayList<Object>> inputLookupValues,
+            Map<FieldKey, LinkedHashSet<Object>> inputLookupValues,
             @Nullable NameGenerator altNameGenerator)
     {
         String parentLsid = parentObject.getLSID();
@@ -481,8 +481,8 @@ else if (parentObject instanceof ExpData expData)
 
                 if (!ancestorLookupValues.isEmpty())
                 {
-                    inputLookupValues.putIfAbsent(ancestorFieldKey, new ArrayList<>());
-                    List<Object> lookupValues = inputLookupValues.get(ancestorFieldKey);
+                    inputLookupValues.putIfAbsent(ancestorFieldKey, new LinkedHashSet<>());
+                    Set<Object> lookupValues = inputLookupValues.get(ancestorFieldKey);
                     for (Object lookupVal : ancestorLookupValues)
                     {
                         if (!lookupValues.contains(lookupVal))
@@ -497,7 +497,7 @@ private void addParentLookupContext(String parentTypeName/* already decoded */,
                                         String parentName,
                                         boolean isMaterialParent,
                                         @Nullable Map<String, FieldKey> parentImportAliases,
-                                        Map<FieldKey, ArrayList<Object>> inputLookupValues,
+                                        Map<FieldKey, LinkedHashSet<Object>> inputLookupValues,
                                         @Nullable NameGenerator altNameGenerator)
     {
         NameGenerator.ExpressionSummary expressionSummary = getExpressionSummary(altNameGenerator);
@@ -591,7 +591,7 @@ private Map<FieldKey, Object> additionalContext(@NotNull Map<String, Object> row
         if (expressionSummary.hasParentLookup() || expressionSummary.hasParentInputs())
         {
             Map<FieldKey, Set<String>> inputs = new HashMap<>();
-            Map<FieldKey, ArrayList<Object>> inputLookupValues = new HashMap<>();
+            Map<FieldKey, LinkedHashSet<Object>> inputLookupValues = new HashMap<>();
 
             inputs.put(FieldKey.fromParts(INPUT_PARENT), new LinkedHashSet<>());
             inputs.put(FieldKey.fromParts(ExpData.DATA_INPUT_PARENT), new LinkedHashSet<>());
@@ -663,7 +663,7 @@ else if (value.isEmpty())
             ctx.putAll(inputValues);
 
             Map<FieldKey, Object> lookupValues = new HashMap<>();
-            inputLookupValues.forEach((key, value) -> lookupValues.put(key, value.size() > 1 ? value : (value.size() == 1 ? value.get(0) : null)));
+            inputLookupValues.forEach((key, value) -> lookupValues.put(key, value.size() > 1 ? value : (value.size() == 1 ? value.iterator().next() : null)));
             ctx.putAll(lookupValues);
         }
 
@@ -740,12 +740,12 @@ else if (value.isEmpty())
     private void addParentLookupInput(String colName,
                                       Object value,
                                       @Nullable Map<String, FieldKey> parentImportAliases,
-                                      Map<FieldKey, ArrayList<Object>> inputLookupValues,
+                                      Map<FieldKey, LinkedHashSet<Object>> inputLookupValues,
                                       @Nullable NameGenerator altNameGenerator)
     {
         String prefix = null;
         String dataType = null;
-        if (ALIQUOTED_FROM_INPUT.equalsIgnoreCase(colName))
+        if (isAliquotedFromColumn(colName))
         {
             prefix = ExpMaterial.MATERIAL_INPUT_PARENT;
             dataType = getParentTable() != null ? getParentTable().getName() : null;
@@ -791,7 +791,7 @@ private void addInputs(String colName,
         String[] parts = colName.split("/", 2);
         String prefix = null;
         String decodedDataType = null;
-        if (ALIQUOTED_FROM_INPUT.equalsIgnoreCase(colName))
+        if (isAliquotedFromColumn(colName))
         {
             prefix = ExpMaterial.MATERIAL_INPUT_PARENT;
             decodedDataType = getParentTable() != null ? getParentTable().getName() : null;
diff --git a/api/src/org/labkey/api/exp/api/ExpMaterial.java b/api/src/org/labkey/api/exp/api/ExpMaterial.java
index 95bde41b9f7..c1b9b829fdb 100644
--- a/api/src/org/labkey/api/exp/api/ExpMaterial.java
+++ b/api/src/org/labkey/api/exp/api/ExpMaterial.java
@@ -35,6 +35,7 @@ public interface ExpMaterial extends ExpRunItem
     String MATERIAL_INPUTS_PREFIX_LC = MATERIAL_INPUTS_PREFIX.toLowerCase();
     String MATERIAL_OUTPUT_CHILD = "MaterialOutputs";
     String ALIQUOTED_FROM_INPUT = "AliquotedFrom";
+    String ALIQUOTED_FROM_INPUT_LABEL = "Aliquoted From";
 
     @Nullable
     ExpSampleType getSampleType();
diff --git a/api/src/org/labkey/api/exp/api/ExpSampleType.java b/api/src/org/labkey/api/exp/api/ExpSampleType.java
index 496afe9e2c8..7560e159d8f 100644
--- a/api/src/org/labkey/api/exp/api/ExpSampleType.java
+++ b/api/src/org/labkey/api/exp/api/ExpSampleType.java
@@ -18,6 +18,7 @@
 
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
+import org.labkey.api.collections.CaseInsensitiveHashMap;
 import org.labkey.api.data.Container;
 import org.labkey.api.data.ContainerFilter;
 import org.labkey.api.exp.ExperimentException;
@@ -242,6 +243,15 @@ String createSampleName(@NotNull Map<String, Object> rowMap,
 
     @NotNull Map<String, String> getImportAliases() throws IOException;
 
+    // Issue 53063: support "Aliquoted From"
+    @NotNull
+    default Map<String, String> getImportAliasesIncludingAliquot() throws IOException
+    {
+        Map<String, String> aliases = new CaseInsensitiveHashMap<>(getImportAliases());
+        aliases.put(ExpMaterial.ALIQUOTED_FROM_INPUT_LABEL, ExpMaterial.ALIQUOTED_FROM_INPUT);
+        return aliases;
+    }
+
     @NotNull Map<String, String> getRequiredImportAliases() throws IOException;
 
     @NotNull Map<String, Map<String, Object>> getImportAliasMap() throws IOException;
diff --git a/api/src/org/labkey/api/exp/api/ExperimentService.java b/api/src/org/labkey/api/exp/api/ExperimentService.java
index 40d9651fd26..cc3c1cca948 100644
--- a/api/src/org/labkey/api/exp/api/ExperimentService.java
+++ b/api/src/org/labkey/api/exp/api/ExperimentService.java
@@ -506,6 +506,12 @@ static boolean isInputOutputColumn(String columnName)
                ExpMaterial.MATERIAL_OUTPUT_CHILD.equalsIgnoreCase(prefix);
     }
 
+    static boolean isAliquotedFromColumn(String columnName)
+    {
+        return ExpMaterial.ALIQUOTED_FROM_INPUT.equalsIgnoreCase(columnName) ||
+               ExpMaterial.ALIQUOTED_FROM_INPUT_LABEL.equalsIgnoreCase(columnName);
+    }
+
     // convert MaterialInputs/Blood/Type to MaterialInputs/Blood$SType
     static @Nullable String getEncodedLineageKey(String inputColumn /*not encoded*/)
     {
diff --git a/api/src/org/labkey/api/query/QueryUpdateService.java b/api/src/org/labkey/api/query/QueryUpdateService.java
index 78723b7d7ac..53925404dec 100644
--- a/api/src/org/labkey/api/query/QueryUpdateService.java
+++ b/api/src/org/labkey/api/query/QueryUpdateService.java
@@ -109,6 +109,7 @@ enum ConfigParameters
         SkipRequiredFieldValidation,        // (Bool) skip validation of required fields, used during import when the import of data happens in two hitches (e.g., samples in one file and sample statuses in a second)
         BulkLoad,                // (Bool) skips detailed auditing
         CheckForCrossProjectData,                // (Bool) Check if data belong to other projects
+        ProcessingPartition,                // (Bool) Importing a partitioned file from original file
         SkipInsertOptionValidation,  // (Bool) Skip assert(supportsInsertOption(context.getInsertOption())) for special scenarios (e.g., folder import uses merge action that's otherwise not supported for a table),
         PreferPKOverObjectUriAsKey,    // (Bool) Prefer getPkColumnNames instead of getObjectURIColumnName to use as keys
         SkipReselectRows, // (Bool) If true, skip qus.getRows and use raw returned rows. Applicable for CommandType.insert/insertWithKeys/update/updateChangingKeys
diff --git a/experiment/src/org/labkey/experiment/ExpDataIterators.java b/experiment/src/org/labkey/experiment/ExpDataIterators.java
index 264733d0a42..e0a9723ecad 100644
--- a/experiment/src/org/labkey/experiment/ExpDataIterators.java
+++ b/experiment/src/org/labkey/experiment/ExpDataIterators.java
@@ -162,6 +162,7 @@
 import static org.labkey.api.exp.api.ExpData.DATA_INPUTS_PREFIX_LC;
 import static org.labkey.api.exp.api.ExpData.DATA_INPUT_PARENT;
 import static org.labkey.api.exp.api.ExpMaterial.ALIQUOTED_FROM_INPUT;
+import static org.labkey.api.exp.api.ExpMaterial.ALIQUOTED_FROM_INPUT_LABEL;
 import static org.labkey.api.exp.api.ExpMaterial.MATERIAL_INPUTS_PREFIX_LC;
 import static org.labkey.api.exp.api.ExpMaterial.MATERIAL_INPUT_PARENT;
 import static org.labkey.api.exp.api.ExpRunItem.INPUTS_PREFIX_LC;
@@ -2591,6 +2592,7 @@ public boolean next() throws BatchValidationException
                 {
                     _context.setCrossTypeImport(false);
                     _context.setCrossFolderImport(false);
+                    _context.putConfigParameter(QueryUpdateService.ConfigParameters.ProcessingPartition, true);
 
                     boolean hasCrossFolderImport = false;
 
@@ -2610,6 +2612,7 @@ public boolean next() throws BatchValidationException
                     if (_isCrossFolder && !_context.getInsertOption().updateOnly && hasCrossFolderImport) // all updates are cross-folder due to lack of Container column
                         SimpleMetricsService.get().increment(ExperimentService.MODULE_NAME, _isSamples ? "sampleImport" : "dataClassImport", "multiFolderImport");
 
+                    _context.putConfigParameter(QueryUpdateService.ConfigParameters.ProcessingPartition, false);
                     _context.setCrossTypeImport(_isCrossType);
                     _context.setCrossFolderImport(_isCrossFolder);
                 }
@@ -2861,6 +2864,7 @@ private TypeData createSampleHeaderRow(ExpSampleTypeImpl sampleType, Container c
             Map<String, String> aliasMap = sampleType.getImportAliases();
             validFields.addAll(aliasMap.keySet());
             validFields.add(ALIQUOTED_FROM_INPUT);
+            validFields.add(ALIQUOTED_FROM_INPUT_LABEL);
             validFields.add("StorageUnit");
             validFields.add("Storage Unit");
             validFields.add("StorageUnitLabel");
diff --git a/experiment/src/org/labkey/experiment/api/ExpDataClassDataTableImpl.java b/experiment/src/org/labkey/experiment/api/ExpDataClassDataTableImpl.java
index 01899ea6430..9b3bd485f40 100644
--- a/experiment/src/org/labkey/experiment/api/ExpDataClassDataTableImpl.java
+++ b/experiment/src/org/labkey/experiment/api/ExpDataClassDataTableImpl.java
@@ -1370,6 +1370,32 @@ else if (name != null)
             return dataRow;
         }
 
+
+        @Override
+        protected Map<String, Object> updateRow(User user, Container container, Map<String, Object> row, @NotNull Map<String, Object> oldRow, boolean allowOwner, boolean retainCreation)
+                throws InvalidKeyException, ValidationException, QueryUpdateServiceException, SQLException
+        {
+            Map<String, Object> result = super.updateRow(user, container, row, oldRow, allowOwner, retainCreation);
+
+            // add MaterialInput/DataInputs field from parent alias
+            try
+            {
+                Map<String, String> parentAliases = _dataClass.getImportAliases();
+                for (String alias : parentAliases.keySet())
+                {
+                    if (row.containsKey(alias))
+                        result.put(parentAliases.get(alias), result.get(alias));
+                }
+            }
+            catch (IOException e)
+            {
+                throw new RuntimeException(e);
+            }
+
+            return result;
+
+        }
+
         @Override
         protected Map<String, Object> _update(User user, Container c, Map<String, Object> row, Map<String, Object> oldRow, Object[] keys) throws SQLException, ValidationException
         {
diff --git a/experiment/src/org/labkey/experiment/api/ExpMaterialTableImpl.java b/experiment/src/org/labkey/experiment/api/ExpMaterialTableImpl.java
index 2356cc65f8b..80393dc07d5 100644
--- a/experiment/src/org/labkey/experiment/api/ExpMaterialTableImpl.java
+++ b/experiment/src/org/labkey/experiment/api/ExpMaterialTableImpl.java
@@ -1725,7 +1725,7 @@ public DataIteratorBuilder persistRows(DataIteratorBuilder data, DataIteratorCon
         // TODO: subclass PersistDataIteratorBuilder to index Materials! not DataClass!
         try
         {
-            var persist = new ExpDataIterators.PersistDataIteratorBuilder(data, this, propertiesTable, _ss, getUserSchema().getContainer(), getUserSchema().getUser(), _ss.getImportAliases(), sampleTypeObjectId)
+            var persist = new ExpDataIterators.PersistDataIteratorBuilder(data, this, propertiesTable, _ss, getUserSchema().getContainer(), getUserSchema().getUser(), _ss.getImportAliasesIncludingAliquot(), sampleTypeObjectId)
                     .setFileLinkDirectory(SAMPLETYPE_FILE_DIRECTORY);
             ExperimentServiceImpl experimentServiceImpl = ExperimentServiceImpl.get();
             SearchService.TaskIndexingQueue queue = SearchService.get().defaultTask().getQueue(getContainer(), SearchService.PRIORITY.modified);
diff --git a/experiment/src/org/labkey/experiment/api/ExpSampleTypeTestCase.jsp b/experiment/src/org/labkey/experiment/api/ExpSampleTypeTestCase.jsp
index ff3606d9a6b..c3fc1591d95 100644
--- a/experiment/src/org/labkey/experiment/api/ExpSampleTypeTestCase.jsp
+++ b/experiment/src/org/labkey/experiment/api/ExpSampleTypeTestCase.jsp
@@ -468,23 +468,80 @@ public void testNameExpression() throws Exception
 
     List<Map<String, Object>> aliquotRows = new ArrayList<>();
     aliquotRows.add(CaseInsensitiveHashMap.of("aliquotedFrom", expectedName1, "AliquotCount", 10));
-    aliquotRows.add(CaseInsensitiveHashMap.of("Aliquotedfrom", expectedName2, "aliquotCount", 5));
-    aliquotRows.add(CaseInsensitiveHashMap.of("ALIQUOTEDFROM", expectedName1, "Aliquotcount", 15));
-    aliquotRows.add(CaseInsensitiveHashMap.of("AliquotedFrom", expectedName3, "ALIQUOTCOUNT", 2));
-
     List<Map<String, Object>> aliquots = insertSampleRows(sampleTypeName, aliquotRows);
-
     assertExpectedName(st, expectedName1 + "-ALI-0004");
     assertEquals(expectedName1, aliquots.get(0).get("AliquotedFrom"));
 
+    aliquotRows = new ArrayList<>();
+    aliquotRows.add(CaseInsensitiveHashMap.of("Aliquotedfrom", expectedName2, "aliquotCount", 5));
+    aliquots = insertSampleRows(sampleTypeName, aliquotRows);
     assertExpectedName(st, expectedName2 + "-ALI-0005");
-    assertEquals(expectedName2, aliquots.get(1).get("aliquotedFrom"));
+    assertEquals(expectedName2, aliquots.get(0).get("aliquotedFrom"));
 
+    aliquotRows = new ArrayList<>();
+    aliquotRows.add(CaseInsensitiveHashMap.of("ALIQUOTEDFROM", expectedName1, "Aliquotcount", 15));
+    aliquots = insertSampleRows(sampleTypeName, aliquotRows);
     assertExpectedName(st, expectedName1 + "-ALI-0006");
-    assertEquals(expectedName1, aliquots.get(2).get("aliquotedfrom"));
+    assertEquals(expectedName1, aliquots.get(0).get("aliquotedfrom"));
 
+    aliquotRows = new ArrayList<>();
+    aliquotRows.add(CaseInsensitiveHashMap.of("AliquotedFrom", expectedName3, "ALIQUOTCOUNT", 2));
+    aliquots = insertSampleRows(sampleTypeName, aliquotRows);
     assertExpectedName(st, expectedName3 + "-ALI-0007");
-    assertEquals(expectedName3, aliquots.get(3).get("ALIQUOTEDFROM"));
+    assertEquals(expectedName3, aliquots.get(0).get("ALIQUOTEDFROM"));
+
+    // Issue 53063: Support "Aliquoted From"
+    aliquotRows = new ArrayList<>();
+    aliquotRows.add(CaseInsensitiveHashMap.of("Aliquoted From", expectedName2, "ALIQUOTCOUNT", 2));
+    aliquots = insertSampleRows(sampleTypeName, aliquotRows);
+    assertExpectedName(st, expectedName2 + "-ALI-0008");
+    assertEquals(expectedName2, aliquots.get(0).get("ALIQUOTEDFROM"));
+
+    aliquotRows = new ArrayList<>();
+    aliquotRows.add(CaseInsensitiveHashMap.of("aliquoted from", expectedName3, "ALIQUOTCOUNT", 3));
+    aliquots = insertSampleRows(sampleTypeName, aliquotRows);
+    assertExpectedName(st, expectedName3 + "-ALI-0009");
+    assertEquals(expectedName3, aliquots.get(0).get("aliquotedFrom"));
+
+    // test the default aliquot naming pattern (${${AliquotedFrom}-:withCounter}
+    st.setAliquotNameExpression("");
+    st.save(user);
+
+    aliquotRows = new ArrayList<>();
+    aliquotRows.add(CaseInsensitiveHashMap.of("aliquotedFrom", expectedName1));
+    aliquots = insertSampleRows(sampleTypeName, aliquotRows);
+    assertExpectedName(st, expectedName1 + "-1");
+    assertEquals(expectedName1, aliquots.get(0).get("AliquotedFrom"));
+
+    aliquotRows = new ArrayList<>();
+    aliquotRows.add(CaseInsensitiveHashMap.of("Aliquotedfrom", expectedName1));
+    aliquots = insertSampleRows(sampleTypeName, aliquotRows);
+    assertExpectedName(st, expectedName1 + "-2");
+    assertEquals(expectedName1, aliquots.get(0).get("aliquotedFrom"));
+
+    aliquotRows = new ArrayList<>();
+    aliquotRows.add(CaseInsensitiveHashMap.of("ALIQUOTEDFROM", expectedName1));
+    aliquots = insertSampleRows(sampleTypeName, aliquotRows);
+    assertExpectedName(st, expectedName1 + "-3");
+    assertEquals(expectedName1, aliquots.get(0).get("aliquotedfrom"));
+
+    aliquotRows = new ArrayList<>();
+    aliquotRows.add(CaseInsensitiveHashMap.of("AliquotedFrom", expectedName1));
+    aliquots = insertSampleRows(sampleTypeName, aliquotRows);
+    assertExpectedName(st, expectedName1 + "-4");
+    assertEquals(expectedName1, aliquots.get(0).get("ALIQUOTEDFROM"));
+
+    aliquotRows = new ArrayList<>();
+    aliquotRows.add(CaseInsensitiveHashMap.of("Aliquoted From", expectedName1));
+    aliquots = insertSampleRows(sampleTypeName, aliquotRows);
+    assertExpectedName(st, expectedName1 + "-5");
+    assertEquals(expectedName1, aliquots.get(0).get("ALIQUOTEDFROM"));
+
+    aliquotRows = new ArrayList<>();
+    aliquotRows.add(CaseInsensitiveHashMap.of("aliquoted from", expectedName1));
+    aliquots = insertSampleRows(sampleTypeName, aliquotRows);
+    assertExpectedName(st, expectedName1 + "-6");
+    assertEquals(expectedName1, aliquots.get(0).get("aliquotedFrom"));
 }
 
 @Test
diff --git a/experiment/src/org/labkey/experiment/api/ExperimentServiceImpl.java b/experiment/src/org/labkey/experiment/api/ExperimentServiceImpl.java
index 5d2e5f94876..1f1908e175b 100644
--- a/experiment/src/org/labkey/experiment/api/ExperimentServiceImpl.java
+++ b/experiment/src/org/labkey/experiment/api/ExperimentServiceImpl.java
@@ -10252,6 +10252,7 @@ else if (inputColumns != null)
             allColumns.addAll(inputColumns);
 
         Map<String, String> parentAliasColumnMap = new CaseInsensitiveHashMap<>();
+        parentAliasColumnMap.put(ExpMaterial.ALIQUOTED_FROM_INPUT_LABEL, ExpMaterial.ALIQUOTED_FROM_INPUT);
         try
         {
             if (currentDataType instanceof ExpDataClass dataClass)
@@ -10270,7 +10271,7 @@ else if (currentDataType instanceof ExpSampleType sampleType)
             String columnName = inputColName;
             if (parentAliasColumnMap.containsKey(columnName))
                 columnName = parentAliasColumnMap.get(columnName);
-            if (ExperimentService.isInputOutputColumn(columnName) || "parent".equalsIgnoreCase(columnName))
+            if (ExperimentService.isInputOutputColumn(columnName) || ExperimentService.isAliquotedFromColumn(columnName) || "parent".equalsIgnoreCase(columnName))
             {
                 if (seenColumns.contains(columnName))
                     throw new ApiUsageException(String.format(DUPLICATE_COLUMN_IN_DATA_ERROR, columnName));
diff --git a/experiment/src/org/labkey/experiment/api/SampleTypeUpdateServiceDI.java b/experiment/src/org/labkey/experiment/api/SampleTypeUpdateServiceDI.java
index 461eb6f64fe..8417fd01071 100644
--- a/experiment/src/org/labkey/experiment/api/SampleTypeUpdateServiceDI.java
+++ b/experiment/src/org/labkey/experiment/api/SampleTypeUpdateServiceDI.java
@@ -858,6 +858,31 @@ public static boolean isAliquotStatusChangeNeedRecalc(Collection<Long> available
         return false;
     }
 
+    @Override
+    protected Map<String, Object> updateRow(User user, Container container, Map<String, Object> row, @NotNull Map<String, Object> oldRow, boolean allowOwner, boolean retainCreation)
+            throws InvalidKeyException, ValidationException, QueryUpdateServiceException, SQLException
+    {
+        Map<String, Object> result = super.updateRow(user, container, row, oldRow, allowOwner, retainCreation);
+
+        // add MaterialInput/DataInputs field from parent alias
+        try
+        {
+            Map<String, String> parentAliases = _sampleType.getImportAliases();
+            for (String alias : parentAliases.keySet())
+            {
+                if (row.containsKey(alias))
+                    result.put(parentAliases.get(alias), result.get(alias));
+            }
+        }
+        catch (IOException e)
+        {
+            throw new RuntimeException(e);
+        }
+
+        return result;
+
+    }
+
     @Override
     protected Map<String, Object> _update(User user, Container c, Map<String, Object> row, Map<String, Object> oldRow, Object[] keys) throws SQLException, ValidationException
     {
@@ -1631,7 +1656,7 @@ public DataIterator getDataIterator(DataIteratorContext context)
             addColumns.addUniqueIdDbSequenceColumns(ContainerManager.getRoot(), materialTable);
 
             // recompute only add when AliquotedFrom column is not null
-            if (columnNameMap.containsKey(ExpMaterial.ALIQUOTED_FROM_INPUT))
+            if (columnNameMap.containsKey(ExpMaterial.ALIQUOTED_FROM_INPUT) || columnNameMap.containsKey(ExpMaterial.ALIQUOTED_FROM_INPUT_LABEL))
             {
                 addColumns.addNullColumn(ROOT_RECOMPUTE_ROWID_COL, JdbcType.INTEGER);
                 addColumns.addNullColumn(PARENT_RECOMPUTE_NAME_COL, JdbcType.VARCHAR);
@@ -1752,7 +1777,7 @@ static class _GenerateNamesDataIterator extends SimpleTranslator
 
             try
             {
-                Map<String, String> importAliasMap = sampleType.getImportAliases();
+                Map<String, String> importAliasMap = sampleType.getImportAliasesIncludingAliquot();
                 _extraPropsFns.add(() -> Map.of(PARENT_IMPORT_ALIAS_MAP_PROP, importAliasMap));
             }
             catch (IOException e)
@@ -1792,24 +1817,7 @@ protected void processNextInput()
         {
             Map<String, Object> map = new CaseInsensitiveHashMap<>(((MapDataIterator)getInput()).getMap());
 
-            String aliquotedFrom = null;
-            Object aliquotedFromObj = map.get(ExpMaterial.ALIQUOTED_FROM_INPUT);
-            if (aliquotedFromObj != null)
-            {
-                if (aliquotedFromObj instanceof String)
-                {
-                    // Issue 45563: We need the AliquotedFrom name to be quoted so we can properly find the parent,
-                    // but we don't want to include the quotes in the name we generate using AliquotedFrom
-                    aliquotedFrom = StringUtilsLabKey.unquoteString((String) aliquotedFromObj).trim();
-                    map.put(ExpMaterial.ALIQUOTED_FROM_INPUT, aliquotedFrom);
-                }
-                else if (aliquotedFromObj instanceof Number)
-                {
-                    aliquotedFrom = aliquotedFromObj.toString();
-                }
-            }
-
-            boolean isAliquot = !StringUtils.isEmpty(aliquotedFrom);
+            boolean isAliquot = isAliquotRow(map);
 
             try
             {
@@ -1840,7 +1848,8 @@ else if (aliquotedFromObj instanceof Number)
             catch (NameGenerator.NameGenerationException e)
             {
                 // Failed to generate a name due to some part of the expression not in the row
-                String rowText = _context.isCrossFolderImport() || _context.isCrossTypeImport() ? "" : " on row " + e.getRowNumber();
+                // Issue 53963: Cross-sample-type import gives incorrect row number in message
+                String rowText = _context.getConfigParameterBoolean(QueryUpdateService.ConfigParameters.ProcessingPartition) ? "" : " on row " + e.getRowNumber();
                 if (isAliquot)
                     addRowError("Failed to generate name for aliquot" + rowText + " using aliquot naming pattern " + _sampleType.getAliquotNameExpression() + ". Check the syntax of the aliquot naming pattern and the data values for the aliquot.");
                 else if (_sampleType.hasNameExpression())
@@ -1926,7 +1935,7 @@ void init(TableInfo target, boolean useImportAliases, boolean initRollupCounts)
                 ColumnInfo from = di.getColumnInfo(i);
                 if (from != null)
                 {
-                    if (getAliquotedFromColName().equalsIgnoreCase(from.getName()))
+                    if (isAliquotedFromColName(from.getName()))
                         aliquotedFromDataColInd = i;
                     else if (unitsImportAliasSet.contains(from.getName()))
                         unitDataColInd = i;
@@ -2011,10 +2020,12 @@ else if (StoredAmount.name().equalsIgnoreCase(name))
             }
         }
 
-        private String getAliquotedFromColName()
+        private boolean isAliquotedFromColName(String fromCol)
         {
-            // for update, AliquotedFromLSID is reselected from existing row. For other actions, "AliquotedFrom" needs to be provided
-            return _context.getInsertOption().updateOnly ? AliquotedFromLSID.name() : ExpMaterial.ALIQUOTED_FROM_INPUT;
+            if (_context.getInsertOption().updateOnly)
+                return AliquotedFromLSID.name().equalsIgnoreCase(fromCol);
+
+            return ExperimentService.isAliquotedFromColumn(fromCol);
         }
 
         private void _addConvertColumn(String name, int fromIndex, JdbcType toType, ForeignKey toFk, int derivationDataColInd, boolean isAliquotField)
@@ -2175,6 +2186,36 @@ else if (aliquotedFrom instanceof Number)
         }
     }
 
+    private static boolean isAliquotRow(Map<String, Object> map, String aliquotedFromColName)
+    {
+        String aliquotedFrom = null;
+        Object aliquotedFromObj = map.get(aliquotedFromColName);
+        if (aliquotedFromObj == null && map.containsKey(ColumnInfo.labelFromName(ExpMaterial.ALIQUOTED_FROM_INPUT)))
+            aliquotedFromObj = map.get(ColumnInfo.labelFromName(ExpMaterial.ALIQUOTED_FROM_INPUT));
+        if (aliquotedFromObj != null)
+        {
+            if (aliquotedFromObj instanceof String)
+            {
+                // Issue 45563: We need the AliquotedFrom name to be quoted so we can properly find the parent,
+                // but we don't want to include the quotes in the name we generate using AliquotedFrom
+                aliquotedFrom = StringUtilsLabKey.unquoteString((String) aliquotedFromObj).trim();
+                if (!StringUtils.isEmpty(aliquotedFrom))
+                    map.put(ExpMaterial.ALIQUOTED_FROM_INPUT, aliquotedFrom);
+            }
+            else if (aliquotedFromObj instanceof Number)
+            {
+                aliquotedFrom = aliquotedFromObj.toString();
+            }
+        }
+
+        return !StringUtils.isEmpty(aliquotedFrom);
+    }
+
+    private static boolean isAliquotRow(Map<String, Object> map)
+    {
+        return isAliquotRow(map, ExpMaterial.ALIQUOTED_FROM_INPUT) || isAliquotRow(map, ExpMaterial.ALIQUOTED_FROM_INPUT_LABEL);
+    }
+
     public static class SampleNameGeneratorState extends NameGeneratorState
     {
         private final NameGenerator aliquotNameGenerator;
@@ -2195,24 +2236,7 @@ public String nextName(Map<String, Object> map,
                                @Nullable Set<ExpMaterial> parentSamples,
                                @Nullable List<Supplier<Map<String, Object>>> _extraPropsFns) throws NameGenerator.NameGenerationException
         {
-            String aliquotedFrom = null;
-            Object aliquotedFromObj = map.get(ExpMaterial.ALIQUOTED_FROM_INPUT);
-            if (aliquotedFromObj != null)
-            {
-                if (aliquotedFromObj instanceof String)
-                {
-                    // Issue 45563: We need the AliquotedFrom name to be quoted so we can properly find the parent,
-                    // but we don't want to include the quotes in the name we generate using AliquotedFrom
-                    aliquotedFrom = StringUtilsLabKey.unquoteString((String) aliquotedFromObj).trim();
-                    map.put(ExpMaterial.ALIQUOTED_FROM_INPUT, aliquotedFrom);
-                }
-                else if (aliquotedFromObj instanceof Number)
-                {
-                    aliquotedFrom = aliquotedFromObj.toString();
-                }
-            }
-
-            boolean isAliquot = !StringUtils.isEmpty(aliquotedFrom);
+            boolean isAliquot = isAliquotRow(map);
 
             String generatedName = null;
             if (isAliquot && aliquotNameGenerator != null)
diff --git a/experiment/src/org/labkey/experiment/controllers/exp/ExperimentController.java b/experiment/src/org/labkey/experiment/controllers/exp/ExperimentController.java
index 49d87a94d84..255b762d8ab 100644
--- a/experiment/src/org/labkey/experiment/controllers/exp/ExperimentController.java
+++ b/experiment/src/org/labkey/experiment/controllers/exp/ExperimentController.java
@@ -4422,6 +4422,7 @@ protected Map<String, String> getRenamedColumns()
             Set<String> aliases = new CaseInsensitiveHashSet();
             // Issue 53419: Aliquot parent with number like names that starts with leading zeroes aren't resolved during import
             aliases.add(ExpMaterial.ALIQUOTED_FROM_INPUT);
+            aliases.add(ExpMaterial.ALIQUOTED_FROM_INPUT_LABEL);
             boolean crossTypeImport = getOptionParamValue(AbstractQueryImportAction.Params.crossTypeImport);
             // Issue 51894: We need to stop conversion to numbers for alias fields for all type
             // If there are aliases defined for one type that are number fields in another type, this will prevent