diff --git a/src/azul/plugins/metadata/hca/aggregate.py b/src/azul/plugins/metadata/hca/aggregate.py
index 91dcf5504..9263e6780 100644
--- a/src/azul/plugins/metadata/hca/aggregate.py
+++ b/src/azul/plugins/metadata/hca/aggregate.py
@@ -71,7 +71,7 @@ def _transform_entity(self, entity: JSON) -> JSON:
                     is_intermediate=entity['is_intermediate'],
                     count=(fqid, 1),
                     content_description=entity['content_description'],
-                    matrix_cell_count=(fqid, entity['matrix_cell_count']))
+                    matrix_cell_count=(fqid, entity.get('matrix_cell_count')))
 
     def _group_keys(self, entity) -> Tuple[Any]:
         return entity['file_format'], entity['is_intermediate']
diff --git a/src/azul/plugins/metadata/hca/transform.py b/src/azul/plugins/metadata/hca/transform.py
index 7b2d5e01e..23a042194 100644
--- a/src/azul/plugins/metadata/hca/transform.py
+++ b/src/azul/plugins/metadata/hca/transform.py
@@ -767,7 +767,12 @@ def _file(self, file: api.File, related_files: Iterable[api.File] = ()) -> Mutab
                 } if isinstance(file, api.SequenceFile) else {
                 }
             ),
-            'matrix_cell_count': getattr(file, 'matrix_cell_count', None),
+            **(
+                {
+                    'matrix_cell_count': file.matrix_cell_count
+                } if isinstance(file, api.AnalysisFile) else {
+                }
+            ),
         }
 
     @classmethod
diff --git a/test/indexer/data/aaa96233-bf27-44c7-82df-b4dc15ad4d9d.2018-11-02T113344.698028Z.results.json b/test/indexer/data/aaa96233-bf27-44c7-82df-b4dc15ad4d9d.2018-11-02T113344.698028Z.results.json
index d1c7404ba..66750d912 100644
--- a/test/indexer/data/aaa96233-bf27-44c7-82df-b4dc15ad4d9d.2018-11-02T113344.698028Z.results.json
+++ b/test/indexer/data/aaa96233-bf27-44c7-82df-b4dc15ad4d9d.2018-11-02T113344.698028Z.results.json
@@ -137,9 +137,7 @@
                         "_type": "file",
                         "read_index": "read2",
                         "lane_index": 9223372036854774784,
-                        "lane_index_": null,
-                        "matrix_cell_count": 9223372036854774784,
-                        "matrix_cell_count_": null
+                        "lane_index_": null
                     },
                     {
                         "related_files": [],
@@ -164,9 +162,7 @@
                         "_type": "file",
                         "read_index": "read1",
                         "lane_index": 9223372036854774784,
-                        "lane_index_": null,
-                        "matrix_cell_count": 9223372036854774784,
-                        "matrix_cell_count_": null
+                        "lane_index_": null
                     }
                 ],
                 "analysis_protocols": [],
@@ -601,9 +597,7 @@
                         "_type": "file",
                         "read_index": "read1",
                         "lane_index": 9223372036854774784,
-                        "lane_index_": null,
-                        "matrix_cell_count": 9223372036854774784,
-                        "matrix_cell_count_": null
+                        "lane_index_": null
                     }
                 ],
                 "analysis_protocols": [],
@@ -837,9 +831,7 @@
                         "_type": "file",
                         "read_index": "read2",
                         "lane_index": 9223372036854774784,
-                        "lane_index_": null,
-                        "matrix_cell_count": 9223372036854774784,
-                        "matrix_cell_count_": null
+                        "lane_index_": null
                     }
                 ],
                 "analysis_protocols": [],
@@ -1073,9 +1065,7 @@
                         "_type": "file",
                         "read_index": "read2",
                         "lane_index": 9223372036854774784,
-                        "lane_index_": null,
-                        "matrix_cell_count": 9223372036854774784,
-                        "matrix_cell_count_": null
+                        "lane_index_": null
                     },
                     {
                         "related_files": [],
@@ -1100,9 +1090,7 @@
                         "_type": "file",
                         "read_index": "read1",
                         "lane_index": 9223372036854774784,
-                        "lane_index_": null,
-                        "matrix_cell_count": 9223372036854774784,
-                        "matrix_cell_count_": null
+                        "lane_index_": null
                     }
                 ],
                 "analysis_protocols": [],
@@ -1336,9 +1324,7 @@
                         "_type": "file",
                         "read_index": "read2",
                         "lane_index": 9223372036854774784,
-                        "lane_index_": null,
-                        "matrix_cell_count": 9223372036854774784,
-                        "matrix_cell_count_": null
+                        "lane_index_": null
                     },
                     {
                         "related_files": [],
@@ -1363,9 +1349,7 @@
                         "_type": "file",
                         "read_index": "read1",
                         "lane_index": 9223372036854774784,
-                        "lane_index_": null,
-                        "matrix_cell_count": 9223372036854774784,
-                        "matrix_cell_count_": null
+                        "lane_index_": null
                     }
                 ],
                 "analysis_protocols": [],
@@ -1676,9 +1660,7 @@
                         "_type": "file",
                         "read_index": "read2",
                         "lane_index": 9223372036854774784,
-                        "lane_index_": null,
-                        "matrix_cell_count": 9223372036854774784,
-                        "matrix_cell_count_": null
+                        "lane_index_": null
                     },
                     {
                         "related_files": [],
@@ -1703,9 +1685,7 @@
                         "_type": "file",
                         "read_index": "read1",
                         "lane_index": 9223372036854774784,
-                        "lane_index_": null,
-                        "matrix_cell_count": 9223372036854774784,
-                        "matrix_cell_count_": null
+                        "lane_index_": null
                     }
                 ],
                 "analysis_protocols": [],
@@ -2196,9 +2176,7 @@
                         "_type": "file",
                         "read_index": "read1",
                         "lane_index": 9223372036854774784,
-                        "lane_index_": null,
-                        "matrix_cell_count": 9223372036854774784,
-                        "matrix_cell_count_": null
+                        "lane_index_": null
                     }
                 ],
                 "analysis_protocols": [],
@@ -2491,9 +2469,7 @@
                         "_type": "file",
                         "read_index": "read2",
                         "lane_index": 9223372036854774784,
-                        "lane_index_": null,
-                        "matrix_cell_count": 9223372036854774784,
-                        "matrix_cell_count_": null
+                        "lane_index_": null
                     }
                 ],
                 "analysis_protocols": [],
@@ -3276,9 +3252,7 @@
                         "_type": "file",
                         "read_index": "read2",
                         "lane_index": 9223372036854774784,
-                        "lane_index_": null,
-                        "matrix_cell_count": 9223372036854774784,
-                        "matrix_cell_count_": null
+                        "lane_index_": null
                     },
                     {
                         "related_files": [],
@@ -3303,9 +3277,7 @@
                         "_type": "file",
                         "read_index": "read1",
                         "lane_index": 9223372036854774784,
-                        "lane_index_": null,
-                        "matrix_cell_count": 9223372036854774784,
-                        "matrix_cell_count_": null
+                        "lane_index_": null
                     }
                 ],
                 "analysis_protocols": [],