diff --git a/.github/workflows/multi-omics-submission-test.yaml b/.github/workflows/multi-omics-submission-test.yaml
index 886686d..3f3f4c8 100644
--- a/.github/workflows/multi-omics-submission-test.yaml
+++ b/.github/workflows/multi-omics-submission-test.yaml
@@ -15,9 +15,10 @@ jobs:
       # Where mars-cli will put .mars/
       MARS_SETTINGS_DIR: ${{ github.workspace }}/mars_settings
 
-      # Paths for MARS repo and ISA template
+      # Paths for MARS repo and ISA templates
       REPOSITORY_SERVICES_PATH: ${{ github.workspace }}/MARS/repository-services
-      ISA_TEMPLATE_PATH: ${{ github.workspace }}/MARS/test-data/biosamples-input-isa.json
+      ISA_TEMPLATE_PATH: ${{ github.workspace }}/MARS/test-data/biosamples-input-isa-multi.json
+      HOLOFOOD_ISA_TEMPLATE_PATH: ${{ github.workspace }}/MARS/test-data/HoloFoodinISA_v1.0.json
 
       # Credentials from GitHub secrets
       WEBIN_USERNAME: ${{ secrets.WEBIN_USERNAME }}
@@ -73,30 +74,43 @@ jobs:
           echo "Services did not become healthy in time ❌"
           exit 1
 
-      - name: Prepare PoC - settings, ISA JSON, credentials, dataFiles
+      - name: Prepare PoC - settings, ISA JSONs, credentials, dataFiles
         run: |
           python scripts/prepare_poc_submission.py
 
-      - name: Run mars-cli submit
+      - name: Submit multi-omics ISA JSON
         run: |
           set -euo pipefail
 
-          # Build list of --data-files arguments from generated .fastq.gz files
           DATA_ARGS=()
-          for f in poc_work/data/*.fastq.gz; do
-            echo "Using data file: ./$f"
-            DATA_ARGS+=( --data-files "./$f" )
+          for data_file in poc_work/multi-omics/data/*; do
+            DATA_ARGS+=( --data-files "$data_file" )
           done
 
-          echo "Running mars-cli with data args: $DATA_ARGS"
+          mars-cli --development submit \
+            --submit-to-metabolights False \
+            --file-transfer ftp \
+            --output "output_multi_omics_${{ github.run_id }}_${{ github.run_attempt }}" \
+            "${DATA_ARGS[@]}" \
+            --credentials-file ./poc_work/credentials.json \
+            poc_work/multi-omics/isa.json
+
+      - name: Submit HoloFood ISA JSON
+        run: |
+          set -euo pipefail
+
+          DATA_ARGS=()
+          for data_file in poc_work/holofood/data/*; do
+            DATA_ARGS+=( --data-files "$data_file" )
+          done
 
           mars-cli --development submit \
             --submit-to-metabolights False \
             --file-transfer ftp \
-            --output "output_${{ github.run_id }}_${{ github.run_attempt }}.json" \
+            --output "output_holofood_${{ github.run_id }}_${{ github.run_attempt }}" \
             "${DATA_ARGS[@]}" \
             --credentials-file ./poc_work/credentials.json \
-            ./poc_work/isa.json
+            poc_work/holofood/isa.json
 
       - name: Collect repository-service logs
         if: always()
diff --git a/MARS b/MARS
index 8d9763e..f92a39e 160000
--- a/MARS
+++ b/MARS
@@ -1 +1 @@
-Subproject commit 8d9763e3501c3243ea5772b1d070e264494200c1
+Subproject commit f92a39e38e32d0334f12af1aae158bfa97cce950
diff --git a/README.md b/README.md
index 9378a67..cfffc94 100644
--- a/README.md
+++ b/README.md
@@ -404,5 +404,3 @@ python mars_cli.py --credential-service-name metabolights  --username-credential
 
 [To set up and run the MARS tool locally using Docker, follow these steps](../repository-services/README.md)
 
-
-
diff --git a/mars_lib/isa_json.py b/mars_lib/isa_json.py
index 793376b..53695f5 100644
--- a/mars_lib/isa_json.py
+++ b/mars_lib/isa_json.py
@@ -484,29 +484,26 @@ def update_isa_json(isa_json: IsaJson, repo_response: RepositoryResponse) -> Isa
 
             add_accession_to_data_file_node(updated_node, accession.value)
         else:
-            # Add study accession to study comments
             updated_study = apply_filter(study_filter, investigation.studies)
-
-            study_accession_comment: Comment = Comment(
+            accession_comment = Comment(
                 name=f"{target_repository}_{target_level}_accession",
                 value=accession.value,
             )
-            updated_study.comments.append(study_accession_comment)
-
-            # Add study accession to assay comments
-            updated_assay = next(
-                filter(
-                    lambda assay: is_assay_for_target_repo(assay, target_repository),
-                    updated_study.assays,
-                ),
-                None,
-            )
-            if updated_assay:
-                assay_accession_comment: Comment = Comment(
-                    name=f"{target_repository}_{target_level}_accession",
-                    value=accession.value,
+
+            if target_level == "study":
+                updated_study.comments.append(accession_comment)
+            else:
+                updated_assay = next(
+                    filter(
+                        lambda assay: is_assay_for_target_repo(
+                            assay, target_repository
+                        ),
+                        updated_study.assays,
+                    ),
+                    None,
                 )
-                updated_assay.comments.append(assay_accession_comment)
+                if updated_assay:
+                    updated_assay.comments.append(accession_comment)
     isa_json.investigation = investigation
     return isa_json
 
@@ -525,10 +522,13 @@ def map_data_files_to_repositories(
     for assay in assays:
         target_repo_comment: Comment = detect_target_repo_comment(assay.comments)
         # This is an effect of everything being optional in the Comment model.
-        # Should we decide to make the value mandatory, this guard clause would not be necessary anymore.
+        # Should we decide to make the value mandatory, this guard clause
+        # would not be necessary anymore.
         if target_repo_comment.value is None:
             raise ValueError(
-                f"At least one assay in the ISA-JSON has no '{TARGET_REPO_KEY}' comment. Mapping not possible. Make sure all assays in the ISA-JSON have this comment!"
+                f"At least one assay in the ISA-JSON has no "
+                f"'{TARGET_REPO_KEY}' comment. Mapping not possible. "
+                f"Make sure all assays in the ISA-JSON have this comment!"
             )
         assay_data_files = [df.name for df in assay.dataFiles]
 
@@ -555,7 +555,11 @@ def map_data_files_to_repositories(
 
     [
         print_and_log(
-            msg=f"File '{rf['short_name']}' could not be mapped to any data file in the ISA-JSON. For this reason, it will be skipped during submission!",
+            msg=(
+                f"File '{rf['short_name']}' could not be mapped to any data "
+                f"file in the ISA-JSON. For this reason, it will be skipped "
+                f"during submission!"
+            ),
             level="warning",
         )
         for rf in remaining_files
diff --git a/scripts/isa_generator.py b/scripts/isa_generator.py
index 555a79b..77f64dc 100644
--- a/scripts/isa_generator.py
+++ b/scripts/isa_generator.py
@@ -14,19 +14,29 @@ def _timestamp_suffix() -> str:
     return datetime.now(UTC).strftime("%Y%m%d%H%M%S") + "_" + uuid.uuid4().hex[:6]
 
 
-def _write_dummy_fastq_gz(path: Path) -> None:
-    """
-    Write a tiny dummy FASTQ dataset into a .fastq.gz file.
-    Content doesn't matter, as long as it's valid-ish FASTQ text.
-    """
+def _write_dummy_data_file(path: Path) -> None:
+    """Write a tiny dummy file, using gzip for compressed FASTQ extensions."""
     path.parent.mkdir(parents=True, exist_ok=True)
-    with gzip.open(path, "wt") as fh:
-        fh.write(
-            "@read1\n"
-            "ACGTACGTACGTACGT\n"
-            "+\n"
-            "FFFFFFFFFFFFFFFF\n"
-        )
+    content = "@read1\nACGTACGTACGTACGT\n+\nFFFFFFFFFFFFFFFF\n"
+    if path.name.lower().endswith((".fastq.gz", ".fq.gz")):
+        with gzip.open(path, "wt") as fh:
+            fh.write(content)
+    else:
+        path.write_text(content)
+
+
+def _add_suffix_before_extension(file_name: str, suffix: str) -> str:
+    """Insert a unique suffix while preserving the original file extension."""
+    lower_name = file_name.lower()
+    for compound_extension in (".fastq.gz", ".fq.gz"):
+        if lower_name.endswith(compound_extension):
+            extension = file_name[-len(compound_extension) :]
+            return f"{file_name[:-len(compound_extension)]}_{suffix}{extension}"
+
+    extension = Path(file_name).suffix
+    if extension:
+        return f"{file_name[:-len(extension)]}_{suffix}{extension}"
+    return f"{file_name}_{suffix}"
 
 
 def _md5_of_file(path: Path) -> str:
@@ -40,34 +50,33 @@ def _md5_of_file(path: Path) -> str:
     return h.hexdigest()
 
 
-def _get_first_assay(isa_obj: dict[str, Any]) -> dict[str, Any] | None:
+def _get_all_assays(isa_obj: dict[str, Any]) -> List[dict[str, Any]]:
     """
-    Navigate to investigation.studies[0].assays[0] (if present).
+    Return all assays found under investigation.studies[*].assays[*].
     """
     inv = isa_obj.get("investigation")
     if inv is None:
         inv = isa_obj
 
     if not isinstance(inv, dict):
-        return None
+        return []
 
     studies = inv.get("studies") or []
-    if not isinstance(studies, list) or not studies:
-        return None
+    if not isinstance(studies, list):
+        return []
 
-    first_study = studies[0]
-    if not isinstance(first_study, dict):
-        return None
+    assays: List[dict[str, Any]] = []
+    for study in studies:
+        if not isinstance(study, dict):
+            continue
 
-    assays = first_study.get("assays") or []
-    if not isinstance(assays, list) or not assays:
-        return None
+        study_assays = study.get("assays") or []
+        if not isinstance(study_assays, list):
+            continue
 
-    first_assay = assays[0]
-    if not isinstance(first_assay, dict):
-        return None
+        assays.extend(assay for assay in study_assays if isinstance(assay, dict))
 
-    return first_assay
+    return assays
 
 
 def _ensure_comment(comments: List[dict[str, Any]], name: str, value: str) -> None:
@@ -83,74 +92,80 @@ def _ensure_comment(comments: List[dict[str, Any]], name: str, value: str) -> No
 
 
 def _update_datafiles_with_generated_files(
-    assay: dict[str, Any],
+    assays: List[dict[str, Any]],
     data_dir: Path,
-    n_files: int,
+    n_files: int | None,
 ) -> List[Path]:
     """
-    For the first assay, update its dataFiles entries with newly generated .fastq.gz files.
+    Update assay dataFiles entries with newly generated files.
 
-    Behaviour per dataFiles[i] (for i < n_files):
+    Behaviour per touched data file:
 
-      - Generate a unique .fastq.gz file based on the existing 'name':
-          e.g. ENA_TEST2.R2.fastq.gz -> ENA_TEST2.R2_<suffix>.fastq.gz
-        (if name doesn't end with .fastq.gz, just append _<suffix>.fastq.gz)
+      - Generate a unique file based on the existing 'name' while preserving
+        its extension, for example:
+          ENA_TEST2.R2.fastq.gz -> ENA_TEST2.R2_<suffix>.fastq.gz
+          reads.R1.fq.gz         -> reads.R1_<suffix>.fq.gz
 
       - Write a dummy FASTQ into that file and compute its MD5.
 
-      - Update the dataFiles[i] object:
+      - Update the dataFiles entry:
           * "name" = new file name
           * in "comments":
               - "file name"       -> new file name
-              - "file type"       -> "fastq"
-              - "file checksum"   -> MD5 of the .fastq.gz
+              - "file type"       -> the preserved extension
+              - "file checksum"   -> MD5 of the generated file
               - "checksum_method" -> "MD5"
             (existing "accession", "submission date", etc. are kept as-is)
     """
-    data_files_json = assay.get("dataFiles") or []
-    if not isinstance(data_files_json, list):
-        return []
-
     generated_paths: List[Path] = []
     suffix = _timestamp_suffix()
+    updated_count = 0
 
-    # We only touch up to n_files entries, and only those that look like objects
-    for i, df_json in enumerate(data_files_json):
-        if i >= n_files:
-            break
-        if not isinstance(df_json, dict):
+    for assay in assays:
+        data_files_json = assay.get("dataFiles") or []
+        if not isinstance(data_files_json, list):
             continue
 
-        original_name = df_json.get("name")
-        if not isinstance(original_name, str) or not original_name:
-            continue
+        for df_json in data_files_json:
+            if n_files is not None and updated_count >= n_files:
+                return generated_paths
+            if not isinstance(df_json, dict):
+                continue
+
+            original_name = df_json.get("name")
+            if not isinstance(original_name, str) or not original_name:
+                continue
+
+            # ISA data file names can include a relative directory (HoloFood uses
+            # FILES/RAW_FILES/...). Upload mapping is filename-based, so generated
+            # PoC files and their ISA names must use only the basename.
+            original_basename = original_name.replace("\\", "/").rsplit("/", 1)[-1]
 
-        # Build unique .fastq.gz name
-        if original_name.endswith(".fastq.gz"):
-            base = original_name[:-len(".fastq.gz")]
-            new_name = f"{base}_{suffix}.fastq.gz"
-        else:
-            new_name = f"{original_name}_{suffix}.fastq.gz"
+            new_name = _add_suffix_before_extension(original_basename, suffix)
 
-        file_path = data_dir / new_name
-        _write_dummy_fastq_gz(file_path)
-        md5 = _md5_of_file(file_path)
+            file_path = data_dir / new_name
+            _write_dummy_data_file(file_path)
+            md5 = _md5_of_file(file_path)
 
-        # Update the JSON entry
-        df_json["name"] = new_name
+            df_json["name"] = new_name
 
-        comments = df_json.get("comments")
-        if not isinstance(comments, list):
-            comments = []
-            df_json["comments"] = comments
+            comments = df_json.get("comments")
+            if not isinstance(comments, list):
+                comments = []
+                df_json["comments"] = comments
 
-        _ensure_comment(comments, "file name", new_name)
-        _ensure_comment(comments, "file type", "fastq")
-        _ensure_comment(comments, "file checksum", md5)
-        _ensure_comment(comments, "checksum_method", "MD5")
-        # DO NOT touch 'accession' or 'submission date' if present
+            _ensure_comment(comments, "file name", new_name)
+            file_type = (
+                "fastq"
+                if new_name.lower().endswith((".fastq.gz", ".fq.gz"))
+                else Path(new_name).suffix.lstrip(".") or "data"
+            )
+            _ensure_comment(comments, "file type", file_type)
+            _ensure_comment(comments, "file checksum", md5)
+            _ensure_comment(comments, "checksum_method", "MD5")
 
-        generated_paths.append(file_path)
+            generated_paths.append(file_path)
+            updated_count += 1
 
     return generated_paths
 
@@ -158,15 +173,15 @@ def _update_datafiles_with_generated_files(
 def generate_isa_json_with_data(
     work_dir: Path,
     template_path: Path,
-    n_files: int = 2,
+    n_files: int | None = None,
 ) -> Tuple[Path, List[Path]]:
     """
     PoC behaviour:
 
       1. Load ISA-JSON template from template_path.
-      2. Find investigation.studies[0].assays[0].dataFiles.
-      3. For up to n_files entries in dataFiles, generate UNIQUE .fastq.gz files
-         and update:
+      2. Find all investigation.studies[*].assays[*].dataFiles.
+      3. For each data file (or the first n_files when limited), generate UNIQUE
+         files with preserved extensions and update:
            - dataFiles[i]["name"]
            - dataFiles[i]["comments"] entries for file name, type, checksum, method.
       4. Write the resulting ISA-JSON to work_dir / 'isa.json'.
@@ -177,12 +192,12 @@ def generate_isa_json_with_data(
 
     isa_obj = json.loads(template_path.read_text())
 
-    assay = _get_first_assay(isa_obj)
+    assays = _get_all_assays(isa_obj)
     generated_paths: List[Path] = []
-    if assay is not None:
+    if assays:
         data_dir = work_dir / "data"
         generated_paths = _update_datafiles_with_generated_files(
-            assay=assay,
+            assays=assays,
             data_dir=data_dir,
             n_files=n_files,
         )
diff --git a/scripts/prepare_poc_submission.py b/scripts/prepare_poc_submission.py
index c47456b..df188ae 100644
--- a/scripts/prepare_poc_submission.py
+++ b/scripts/prepare_poc_submission.py
@@ -1,21 +1,23 @@
 #!/usr/bin/env python
 """
-Prepare a PoC environment for MARS-CLI (no pytest, no run script):
+Prepare the PoC environments for MARS-CLI (no pytest, no run script):
 
 - Ensure settings.ini exists in $MARS_SETTINGS_DIR/.mars, or ~/.mars
-- Generate an ISA-JSON from a template, where:
-    * dataFiles entries in the first assay are updated to point to
-      UNIQUE .fastq.gz files
+- Generate an ISA-JSON from each configured template, where:
+    * dataFiles entries are updated to point to UNIQUE generated files while
+      preserving their original extensions
     * 'file name', 'file type', 'file checksum', 'checksum_method'
       comments are updated accordingly (MD5 over the .fastq.gz)
 - Create poc_work/credentials.json from environment variables
 
-The GitHub Action (or you, locally) will then call mars_cli.py directly using:
+Set ``HOLOFOOD_ISA_TEMPLATE_PATH`` to prepare the additional HoloFood
+submission alongside ``ISA_TEMPLATE_PATH``.
 
-  ISA JSON:        poc_work/isa.json
+The GitHub Action (or you, locally) will then call mars-cli using:
+
+  ISA JSON:        poc_work/<submission>/isa.json
   Credentials:     poc_work/credentials.json
-  Data files:      whatever generate_isa_json_with_data() returned
-                   (typically poc_work/data/*.fastq.gz)
+  Data files:      poc_work/<submission>/data/*.fastq.gz
 """
 
 
@@ -120,23 +122,34 @@ def main() -> None:
     work_dir = PROJECT_ROOT / "poc_work"
     work_dir.mkdir(parents=True, exist_ok=True)
 
-    isa_template = resolve_isa_template()
-
-    isa_path, data_files = generate_isa_json_with_data(
-        work_dir=work_dir,
-        template_path=isa_template,
-        n_files=2,
-    )
+    isa_templates = {"multi-omics": resolve_isa_template()}
+    holofood_template = os.environ.get("HOLOFOOD_ISA_TEMPLATE_PATH")
+    if holofood_template:
+        holofood_path = Path(holofood_template)
+        if not holofood_path.exists():
+            raise FileNotFoundError(f"HoloFood ISA template not found at {holofood_path}")
+        isa_templates["holofood"] = holofood_path
+
+    prepared_submissions = []
+    for submission_name, isa_template in isa_templates.items():
+        submission_dir = work_dir / submission_name
+        isa_path, data_files = generate_isa_json_with_data(
+            work_dir=submission_dir,
+            template_path=isa_template,
+        )
+        prepared_submissions.append((isa_template, isa_path, data_files))
 
     cred_path = write_credentials_json(work_dir)
 
     print(f"[MARS-POC] settings.ini:    {settings_path}")
     print(f"[MARS-POC] work dir:        {work_dir}")
-    print(f"[MARS-POC] ISA JSON file:   {isa_path}")
     print(f"[MARS-POC] credentials:     {cred_path}")
-    print(f"[MARS-POC] data files:")
-    for df in data_files:
-        print(f"  - {df}")
+    for isa_template, isa_path, data_files in prepared_submissions:
+        print(f"[MARS-POC] template:        {isa_template}")
+        print(f"[MARS-POC] ISA JSON file:   {isa_path}")
+        print("[MARS-POC] data files:")
+        for data_file in data_files:
+            print(f"  - {data_file}")
 
 
 if __name__ == "__main__":
diff --git a/tests/fixtures/isa_jsons/0_Initial_ISA_JSON_in_model.json b/tests/fixtures/isa_jsons/0_Initial_ISA_JSON_in_model.json
index 0cf74fc..5e553a5 100644
--- a/tests/fixtures/isa_jsons/0_Initial_ISA_JSON_in_model.json
+++ b/tests/fixtures/isa_jsons/0_Initial_ISA_JSON_in_model.json
@@ -82,33 +82,6 @@
                   "termAccession": "",
                   "termSource": ""
                 }
-              },
-              {
-                "@id": "#characteristic_category/submission_date_358",
-                "characteristicType": {
-                  "comments": [],
-                  "annotationValue": "submission date",
-                  "termAccession": "",
-                  "termSource": ""
-                }
-              },
-              {
-                "@id": "#characteristic_category/status_359",
-                "characteristicType": {
-                  "comments": [],
-                  "annotationValue": "status",
-                  "termAccession": "",
-                  "termSource": ""
-                }
-              },
-              {
-                "@id": "#characteristic_category/accession_360",
-                "characteristicType": {
-                  "comments": [],
-                  "annotationValue": "accession",
-                  "termAccession": "",
-                  "termSource": ""
-                }
               }
             ],
             "dataFiles": [
@@ -158,7 +131,18 @@
                 {
                   "comments": [],
                   "@id": "#other_material/332",
-                  "characteristics": [],
+                  "characteristics": [
+                    {
+                      "category": {
+                        "@id": "#characteristic_category/Title_350"
+                      },
+                      "value": {
+                        "annotationValue": "Arabidopsis leaf amplicon sequencing experiment",
+                        "termAccession": "",
+                        "termSource": ""
+                      }
+                    }
+                  ],
                   "name": "extract 1",
                   "type": "library name",
                   "derivesFrom": [
@@ -173,56 +157,7 @@
                 {
                   "comments": [],
                   "@id": "#other_material/333",
-                  "characteristics": [
-                    {
-                      "comments": [],
-                      "category": {
-                        "@id": "#characteristic_category/Title_350"
-                      },
-                      "value": {
-                        "comments": [],
-                        "annotationValue": "library 1",
-                        "termAccession": "",
-                        "termSource": ""
-                      }
-                    },
-                    {
-                      "comments": [],
-                      "category": {
-                        "@id": "#characteristic_category/submission_date_358"
-                      },
-                      "value": {
-                        "comments": [],
-                        "annotationValue": "",
-                        "termAccession": "",
-                        "termSource": ""
-                      }
-                    },
-                    {
-                      "comments": [],
-                      "category": {
-                        "@id": "#characteristic_category/status_359"
-                      },
-                      "value": {
-                        "comments": [],
-                        "annotationValue": "",
-                        "termAccession": "",
-                        "termSource": ""
-                      }
-                    },
-                    {
-                      "comments": [],
-                      "category": {
-                        "@id": "#characteristic_category/accession_360"
-                      },
-                      "value": {
-                        "comments": [],
-                        "annotationValue": "",
-                        "termAccession": "",
-                        "termSource": ""
-                      }
-                    }
-                  ],
+                  "characteristics": [],
                   "name": "library 1",
                   "type": "library name",
                   "derivesFrom": [
@@ -524,15 +459,6 @@
               "termSource": ""
             }
           },
-          {
-            "@id": "#characteristic_category/cell_type_321",
-            "characteristicType": {
-              "comments": [],
-              "annotationValue": "cell_type",
-              "termAccession": "",
-              "termSource": ""
-            }
-          },
           {
             "@id": "#characteristic_category/dev_stage_322",
             "characteristicType": {
@@ -604,6 +530,38 @@
               "termAccession": "",
               "termSource": ""
             }
+          },
+          {
+            "@id": "#characteristic_category/genotype_330",
+            "characteristicType": {
+              "annotationValue": "genotype",
+              "termAccession": "",
+              "termSource": ""
+            }
+          },
+          {
+            "@id": "#characteristic_category/growth_condition_331",
+            "characteristicType": {
+              "annotationValue": "growth condition",
+              "termAccession": "",
+              "termSource": ""
+            }
+          },
+          {
+            "@id": "#characteristic_category/organism_part_332",
+            "characteristicType": {
+              "annotationValue": "organism part",
+              "termAccession": "",
+              "termSource": ""
+            }
+          },
+          {
+            "@id": "#characteristic_category/sample_description_333",
+            "characteristicType": {
+              "annotationValue": "sample description",
+              "termAccession": "",
+              "termSource": ""
+            }
           }
         ],
         "description": "Nucleic acid sequencing and metabolomics and proteomics of Arabidopsis thaliana in specific experimental conditions to test a specific hypothesis.\r\n",
@@ -664,18 +622,6 @@
                     "termSource": ""
                   }
                 },
-                {
-                  "comments": [],
-                  "category": {
-                    "@id": "#characteristic_category/cell_type_321"
-                  },
-                  "value": {
-                    "comments": [],
-                    "annotationValue": "na",
-                    "termAccession": "",
-                    "termSource": ""
-                  }
-                },
                 {
                   "comments": [],
                   "category": {
@@ -683,7 +629,7 @@
                   },
                   "value": {
                     "comments": [],
-                    "annotationValue": "budding",
+                    "annotationValue": "vegetative rosette stage",
                     "termAccession": "",
                     "termSource": ""
                   }
@@ -695,7 +641,7 @@
                   },
                   "value": {
                     "comments": [],
-                    "annotationValue": "01/01/2022",
+                    "annotationValue": "2022-01-01",
                     "termAccession": "",
                     "termSource": ""
                   }
@@ -707,7 +653,7 @@
                   },
                   "value": {
                     "comments": [],
-                    "annotationValue": "seed",
+                    "annotationValue": "whole plant",
                     "termAccession": "",
                     "termSource": ""
                   }
@@ -760,6 +706,26 @@
                     "termSource": ""
                   }
                 },
+                {
+                  "category": {
+                    "@id": "#characteristic_category/genotype_330"
+                  },
+                  "value": {
+                    "annotationValue": "Col-0",
+                    "termAccession": "",
+                    "termSource": ""
+                  }
+                },
+                {
+                  "category": {
+                    "@id": "#characteristic_category/growth_condition_331"
+                  },
+                  "value": {
+                    "annotationValue": "16 h light / 8 h dark growth chamber",
+                    "termAccession": "",
+                    "termSource": ""
+                  }
+                },
                 {
                   "comments": [],
                   "category": {
@@ -787,7 +753,28 @@
               "comments": [],
               "@id": "#sample/331",
               "name": "leaf 1",
-              "characteristics": [],
+              "characteristics": [
+                {
+                  "category": {
+                    "@id": "#characteristic_category/organism_part_332"
+                  },
+                  "value": {
+                    "annotationValue": "leaf",
+                    "termAccession": "",
+                    "termSource": ""
+                  }
+                },
+                {
+                  "category": {
+                    "@id": "#characteristic_category/sample_description_333"
+                  },
+                  "value": {
+                    "annotationValue": "young rosette leaf collected for DNA extraction",
+                    "termAccession": "",
+                    "termSource": ""
+                  }
+                }
+              ],
               "factorValues": [],
               "derivesFrom": [
                 {
@@ -861,7 +848,38 @@
                 "derivesFrom": []
               }
             ],
-            "parameterValues": [],
+            "parameterValues": [
+              {
+                "category": {
+                  "@id": "#parameter/sample_collection_isolation_source"
+                },
+                "value": {
+                  "annotationValue": "leaf tissue",
+                  "termAccession": "",
+                  "termSource": ""
+                }
+              },
+              {
+                "category": {
+                  "@id": "#parameter/sample_collection_method"
+                },
+                "value": {
+                  "annotationValue": "sterile scalpel excision",
+                  "termAccession": "",
+                  "termSource": ""
+                }
+              },
+              {
+                "category": {
+                  "@id": "#parameter/sample_collection_preservation"
+                },
+                "value": {
+                  "annotationValue": "flash frozen in liquid nitrogen",
+                  "termAccession": "",
+                  "termSource": ""
+                }
+              }
+            ],
             "performer": "",
             "previousProcess": {
               "comments": [],
@@ -888,7 +906,32 @@
             ],
             "description": "",
             "name": "sample collection",
-            "parameters": [],
+            "parameters": [
+              {
+                "@id": "#parameter/sample_collection_isolation_source",
+                "parameterName": {
+                  "annotationValue": "isolation_source",
+                  "termAccession": "",
+                  "termSource": ""
+                }
+              },
+              {
+                "@id": "#parameter/sample_collection_method",
+                "parameterName": {
+                  "annotationValue": "collection method",
+                  "termAccession": "",
+                  "termSource": ""
+                }
+              },
+              {
+                "@id": "#parameter/sample_collection_preservation",
+                "parameterName": {
+                  "annotationValue": "sample preservation",
+                  "termAccession": "",
+                  "termSource": ""
+                }
+              }
+            ],
             "protocolType": {
               "comments": [],
               "annotationValue": "sample collection",
@@ -1062,4 +1105,4 @@
     "submissionDate": "",
     "title": "Bob's investigation"
   }
-}
\ No newline at end of file
+}
diff --git a/tests/fixtures/isa_jsons/1_after_biosamples.json b/tests/fixtures/isa_jsons/1_after_biosamples.json
index e6d713c..fb25781 100644
--- a/tests/fixtures/isa_jsons/1_after_biosamples.json
+++ b/tests/fixtures/isa_jsons/1_after_biosamples.json
@@ -82,33 +82,6 @@
                   "termAccession": "",
                   "termSource": ""
                 }
-              },
-              {
-                "@id": "#characteristic_category/submission_date_358",
-                "characteristicType": {
-                  "comments": [],
-                  "annotationValue": "submission date",
-                  "termAccession": "",
-                  "termSource": ""
-                }
-              },
-              {
-                "@id": "#characteristic_category/status_359",
-                "characteristicType": {
-                  "comments": [],
-                  "annotationValue": "status",
-                  "termAccession": "",
-                  "termSource": ""
-                }
-              },
-              {
-                "@id": "#characteristic_category/accession_360",
-                "characteristicType": {
-                  "comments": [],
-                  "annotationValue": "accession",
-                  "termAccession": "",
-                  "termSource": ""
-                }
               }
             ],
             "dataFiles": [
@@ -158,7 +131,18 @@
                 {
                   "comments": [],
                   "@id": "#other_material/332",
-                  "characteristics": [],
+                  "characteristics": [
+                    {
+                      "category": {
+                        "@id": "#characteristic_category/Title_350"
+                      },
+                      "value": {
+                        "annotationValue": "Arabidopsis leaf amplicon sequencing experiment",
+                        "termAccession": "",
+                        "termSource": ""
+                      }
+                    }
+                  ],
                   "name": "extract 1",
                   "type": "library name",
                   "derivesFrom": [
@@ -173,56 +157,7 @@
                 {
                   "comments": [],
                   "@id": "#other_material/333",
-                  "characteristics": [
-                    {
-                      "comments": [],
-                      "category": {
-                        "@id": "#characteristic_category/Title_350"
-                      },
-                      "value": {
-                        "comments": [],
-                        "annotationValue": "library 1",
-                        "termAccession": "",
-                        "termSource": ""
-                      }
-                    },
-                    {
-                      "comments": [],
-                      "category": {
-                        "@id": "#characteristic_category/submission_date_358"
-                      },
-                      "value": {
-                        "comments": [],
-                        "annotationValue": "",
-                        "termAccession": "",
-                        "termSource": ""
-                      }
-                    },
-                    {
-                      "comments": [],
-                      "category": {
-                        "@id": "#characteristic_category/status_359"
-                      },
-                      "value": {
-                        "comments": [],
-                        "annotationValue": "",
-                        "termAccession": "",
-                        "termSource": ""
-                      }
-                    },
-                    {
-                      "comments": [],
-                      "category": {
-                        "@id": "#characteristic_category/accession_360"
-                      },
-                      "value": {
-                        "comments": [],
-                        "annotationValue": "",
-                        "termAccession": "",
-                        "termSource": ""
-                      }
-                    }
-                  ],
+                  "characteristics": [],
                   "name": "library 1",
                   "type": "library name",
                   "derivesFrom": [
@@ -524,15 +459,6 @@
               "termSource": ""
             }
           },
-          {
-            "@id": "#characteristic_category/cell_type_321",
-            "characteristicType": {
-              "comments": [],
-              "annotationValue": "cell_type",
-              "termAccession": "",
-              "termSource": ""
-            }
-          },
           {
             "@id": "#characteristic_category/dev_stage_322",
             "characteristicType": {
@@ -604,6 +530,38 @@
               "termAccession": "",
               "termSource": ""
             }
+          },
+          {
+            "@id": "#characteristic_category/genotype_330",
+            "characteristicType": {
+              "annotationValue": "genotype",
+              "termAccession": "",
+              "termSource": ""
+            }
+          },
+          {
+            "@id": "#characteristic_category/growth_condition_331",
+            "characteristicType": {
+              "annotationValue": "growth condition",
+              "termAccession": "",
+              "termSource": ""
+            }
+          },
+          {
+            "@id": "#characteristic_category/organism_part_332",
+            "characteristicType": {
+              "annotationValue": "organism part",
+              "termAccession": "",
+              "termSource": ""
+            }
+          },
+          {
+            "@id": "#characteristic_category/sample_description_333",
+            "characteristicType": {
+              "annotationValue": "sample description",
+              "termAccession": "",
+              "termSource": ""
+            }
           }
         ],
         "description": "Nucleic acid sequencing and metabolomics and proteomics of Arabidopsis thaliana in specific experimental conditions to test a specific hypothesis.\r\n",
@@ -664,18 +622,6 @@
                     "termSource": ""
                   }
                 },
-                {
-                  "comments": [],
-                  "category": {
-                    "@id": "#characteristic_category/cell_type_321"
-                  },
-                  "value": {
-                    "comments": [],
-                    "annotationValue": "na",
-                    "termAccession": "",
-                    "termSource": ""
-                  }
-                },
                 {
                   "comments": [],
                   "category": {
@@ -683,7 +629,7 @@
                   },
                   "value": {
                     "comments": [],
-                    "annotationValue": "budding",
+                    "annotationValue": "vegetative rosette stage",
                     "termAccession": "",
                     "termSource": ""
                   }
@@ -695,7 +641,7 @@
                   },
                   "value": {
                     "comments": [],
-                    "annotationValue": "01/01/2022",
+                    "annotationValue": "2022-01-01",
                     "termAccession": "",
                     "termSource": ""
                   }
@@ -707,7 +653,7 @@
                   },
                   "value": {
                     "comments": [],
-                    "annotationValue": "seed",
+                    "annotationValue": "whole plant",
                     "termAccession": "",
                     "termSource": ""
                   }
@@ -760,6 +706,26 @@
                     "termSource": ""
                   }
                 },
+                {
+                  "category": {
+                    "@id": "#characteristic_category/genotype_330"
+                  },
+                  "value": {
+                    "annotationValue": "Col-0",
+                    "termAccession": "",
+                    "termSource": ""
+                  }
+                },
+                {
+                  "category": {
+                    "@id": "#characteristic_category/growth_condition_331"
+                  },
+                  "value": {
+                    "annotationValue": "16 h light / 8 h dark growth chamber",
+                    "termAccession": "",
+                    "termSource": ""
+                  }
+                },
                 {
                   "comments": [],
                   "category": {
@@ -804,6 +770,26 @@
                     "@id": "#ontology_annotation/accession_#sample/331",
                     "annotationValue": "SAMEA131504584"
                   }
+                },
+                {
+                  "category": {
+                    "@id": "#characteristic_category/organism_part_332"
+                  },
+                  "value": {
+                    "annotationValue": "leaf",
+                    "termAccession": "",
+                    "termSource": ""
+                  }
+                },
+                {
+                  "category": {
+                    "@id": "#characteristic_category/sample_description_333"
+                  },
+                  "value": {
+                    "annotationValue": "young rosette leaf collected for DNA extraction",
+                    "termAccession": "",
+                    "termSource": ""
+                  }
                 }
               ],
               "factorValues": [],
@@ -879,7 +865,38 @@
                 "derivesFrom": []
               }
             ],
-            "parameterValues": [],
+            "parameterValues": [
+              {
+                "category": {
+                  "@id": "#parameter/sample_collection_isolation_source"
+                },
+                "value": {
+                  "annotationValue": "leaf tissue",
+                  "termAccession": "",
+                  "termSource": ""
+                }
+              },
+              {
+                "category": {
+                  "@id": "#parameter/sample_collection_method"
+                },
+                "value": {
+                  "annotationValue": "sterile scalpel excision",
+                  "termAccession": "",
+                  "termSource": ""
+                }
+              },
+              {
+                "category": {
+                  "@id": "#parameter/sample_collection_preservation"
+                },
+                "value": {
+                  "annotationValue": "flash frozen in liquid nitrogen",
+                  "termAccession": "",
+                  "termSource": ""
+                }
+              }
+            ],
             "performer": "",
             "previousProcess": {
               "comments": [],
@@ -906,7 +923,32 @@
             ],
             "description": "",
             "name": "sample collection",
-            "parameters": [],
+            "parameters": [
+              {
+                "@id": "#parameter/sample_collection_isolation_source",
+                "parameterName": {
+                  "annotationValue": "isolation_source",
+                  "termAccession": "",
+                  "termSource": ""
+                }
+              },
+              {
+                "@id": "#parameter/sample_collection_method",
+                "parameterName": {
+                  "annotationValue": "collection method",
+                  "termAccession": "",
+                  "termSource": ""
+                }
+              },
+              {
+                "@id": "#parameter/sample_collection_preservation",
+                "parameterName": {
+                  "annotationValue": "sample preservation",
+                  "termAccession": "",
+                  "termSource": ""
+                }
+              }
+            ],
             "protocolType": {
               "comments": [],
               "annotationValue": "sample collection",
@@ -1080,4 +1122,4 @@
     "submissionDate": "",
     "title": "Bob's investigation"
   }
-}
\ No newline at end of file
+}
diff --git a/tests/fixtures/isa_jsons/2_after_ena.json b/tests/fixtures/isa_jsons/2_after_ena.json
index db856ae..77669d1 100644
--- a/tests/fixtures/isa_jsons/2_after_ena.json
+++ b/tests/fixtures/isa_jsons/2_after_ena.json
@@ -87,24 +87,6 @@
                   "termSource": ""
                 }
               },
-              {
-                "@id": "#characteristic_category/submission_date_358",
-                "characteristicType": {
-                  "comments": [],
-                  "annotationValue": "submission date",
-                  "termAccession": "",
-                  "termSource": ""
-                }
-              },
-              {
-                "@id": "#characteristic_category/status_359",
-                "characteristicType": {
-                  "comments": [],
-                  "annotationValue": "status",
-                  "termAccession": "",
-                  "termSource": ""
-                }
-              },
               {
                 "@id": "#characteristic_category/accession_360",
                 "characteristicType": {
@@ -163,6 +145,18 @@
                   "comments": [],
                   "@id": "#other_material/332",
                   "characteristics": [
+                    {
+                      "category": {
+                        "@id": "#characteristic_category/Title_350"
+                      },
+                      "value": {
+                        "annotationValue": "Arabidopsis leaf amplicon sequencing experiment",
+                        "termAccession": "",
+                        "termSource": "",
+                        "comments": []
+                      },
+                      "comments": []
+                    },
                     {
                       "comments": [],
                       "@id": "#material_attribute_value/accession_360",
@@ -197,55 +191,6 @@
                   "comments": [],
                   "@id": "#other_material/333",
                   "characteristics": [
-                    {
-                      "comments": [],
-                      "category": {
-                        "@id": "#characteristic_category/Title_350"
-                      },
-                      "value": {
-                        "comments": [],
-                        "annotationValue": "library 1",
-                        "termAccession": "",
-                        "termSource": ""
-                      }
-                    },
-                    {
-                      "comments": [],
-                      "category": {
-                        "@id": "#characteristic_category/submission_date_358"
-                      },
-                      "value": {
-                        "comments": [],
-                        "annotationValue": "",
-                        "termAccession": "",
-                        "termSource": ""
-                      }
-                    },
-                    {
-                      "comments": [],
-                      "category": {
-                        "@id": "#characteristic_category/status_359"
-                      },
-                      "value": {
-                        "comments": [],
-                        "annotationValue": "",
-                        "termAccession": "",
-                        "termSource": ""
-                      }
-                    },
-                    {
-                      "comments": [],
-                      "@id": "#material_attribute_value/accession_360",
-                      "category": {
-                        "@id": "#characteristic_category/accession_360",
-                        "characteristicType": {
-                          "comments": [],
-                          "annotationValue": "accession",
-                          "termAccession": "",
-                          "termSource": ""
-                        }
-                      }
-                    },
                     {
                       "comments": [],
                       "category": {
@@ -559,15 +504,6 @@
               "termSource": ""
             }
           },
-          {
-            "@id": "#characteristic_category/cell_type_321",
-            "characteristicType": {
-              "comments": [],
-              "annotationValue": "cell_type",
-              "termAccession": "",
-              "termSource": ""
-            }
-          },
           {
             "@id": "#characteristic_category/dev_stage_322",
             "characteristicType": {
@@ -639,6 +575,38 @@
               "termAccession": "",
               "termSource": ""
             }
+          },
+          {
+            "@id": "#characteristic_category/genotype_330",
+            "characteristicType": {
+              "annotationValue": "genotype",
+              "termAccession": "",
+              "termSource": ""
+            }
+          },
+          {
+            "@id": "#characteristic_category/growth_condition_331",
+            "characteristicType": {
+              "annotationValue": "growth condition",
+              "termAccession": "",
+              "termSource": ""
+            }
+          },
+          {
+            "@id": "#characteristic_category/organism_part_332",
+            "characteristicType": {
+              "annotationValue": "organism part",
+              "termAccession": "",
+              "termSource": ""
+            }
+          },
+          {
+            "@id": "#characteristic_category/sample_description_333",
+            "characteristicType": {
+              "annotationValue": "sample description",
+              "termAccession": "",
+              "termSource": ""
+            }
           }
         ],
         "description": "Nucleic acid sequencing and metabolomics and proteomics of Arabidopsis thaliana in specific experimental conditions to test a specific hypothesis.\r\n",
@@ -699,18 +667,6 @@
                     "termSource": ""
                   }
                 },
-                {
-                  "comments": [],
-                  "category": {
-                    "@id": "#characteristic_category/cell_type_321"
-                  },
-                  "value": {
-                    "comments": [],
-                    "annotationValue": "na",
-                    "termAccession": "",
-                    "termSource": ""
-                  }
-                },
                 {
                   "comments": [],
                   "category": {
@@ -718,7 +674,7 @@
                   },
                   "value": {
                     "comments": [],
-                    "annotationValue": "budding",
+                    "annotationValue": "vegetative rosette stage",
                     "termAccession": "",
                     "termSource": ""
                   }
@@ -730,7 +686,7 @@
                   },
                   "value": {
                     "comments": [],
-                    "annotationValue": "01/01/2022",
+                    "annotationValue": "2022-01-01",
                     "termAccession": "",
                     "termSource": ""
                   }
@@ -742,7 +698,7 @@
                   },
                   "value": {
                     "comments": [],
-                    "annotationValue": "seed",
+                    "annotationValue": "whole plant",
                     "termAccession": "",
                     "termSource": ""
                   }
@@ -795,6 +751,26 @@
                     "termSource": ""
                   }
                 },
+                {
+                  "category": {
+                    "@id": "#characteristic_category/genotype_330"
+                  },
+                  "value": {
+                    "annotationValue": "Col-0",
+                    "termAccession": "",
+                    "termSource": ""
+                  }
+                },
+                {
+                  "category": {
+                    "@id": "#characteristic_category/growth_condition_331"
+                  },
+                  "value": {
+                    "annotationValue": "16 h light / 8 h dark growth chamber",
+                    "termAccession": "",
+                    "termSource": ""
+                  }
+                },
                 {
                   "comments": [],
                   "category": {
@@ -839,6 +815,26 @@
                     "@id": "#ontology_annotation/accession_#sample/331",
                     "annotationValue": "SAMEA131504584"
                   }
+                },
+                {
+                  "category": {
+                    "@id": "#characteristic_category/organism_part_332"
+                  },
+                  "value": {
+                    "annotationValue": "leaf",
+                    "termAccession": "",
+                    "termSource": ""
+                  }
+                },
+                {
+                  "category": {
+                    "@id": "#characteristic_category/sample_description_333"
+                  },
+                  "value": {
+                    "annotationValue": "young rosette leaf collected for DNA extraction",
+                    "termAccession": "",
+                    "termSource": ""
+                  }
                 }
               ],
               "factorValues": [],
@@ -914,7 +910,38 @@
                 "derivesFrom": []
               }
             ],
-            "parameterValues": [],
+            "parameterValues": [
+              {
+                "category": {
+                  "@id": "#parameter/sample_collection_isolation_source"
+                },
+                "value": {
+                  "annotationValue": "leaf tissue",
+                  "termAccession": "",
+                  "termSource": ""
+                }
+              },
+              {
+                "category": {
+                  "@id": "#parameter/sample_collection_method"
+                },
+                "value": {
+                  "annotationValue": "sterile scalpel excision",
+                  "termAccession": "",
+                  "termSource": ""
+                }
+              },
+              {
+                "category": {
+                  "@id": "#parameter/sample_collection_preservation"
+                },
+                "value": {
+                  "annotationValue": "flash frozen in liquid nitrogen",
+                  "termAccession": "",
+                  "termSource": ""
+                }
+              }
+            ],
             "performer": "",
             "previousProcess": {
               "comments": [],
@@ -941,7 +968,32 @@
             ],
             "description": "",
             "name": "sample collection",
-            "parameters": [],
+            "parameters": [
+              {
+                "@id": "#parameter/sample_collection_isolation_source",
+                "parameterName": {
+                  "annotationValue": "isolation_source",
+                  "termAccession": "",
+                  "termSource": ""
+                }
+              },
+              {
+                "@id": "#parameter/sample_collection_method",
+                "parameterName": {
+                  "annotationValue": "collection method",
+                  "termAccession": "",
+                  "termSource": ""
+                }
+              },
+              {
+                "@id": "#parameter/sample_collection_preservation",
+                "parameterName": {
+                  "annotationValue": "sample preservation",
+                  "termAccession": "",
+                  "termSource": ""
+                }
+              }
+            ],
             "protocolType": {
               "comments": [],
               "annotationValue": "sample collection",
@@ -1115,4 +1167,4 @@
     "submissionDate": "",
     "title": "Bob's investigation"
   }
-}
\ No newline at end of file
+}
diff --git a/tests/fixtures/mars_receipts/biosamples_success_response.json b/tests/fixtures/mars_receipts/biosamples_success_response.json
index 1fb4458..d7ef41a 100644
--- a/tests/fixtures/mars_receipts/biosamples_success_response.json
+++ b/tests/fixtures/mars_receipts/biosamples_success_response.json
@@ -13,7 +13,7 @@
                     "key": "studies",
                     "where": {
                         "key": "title",
-                        "value": "Arabidopsis thaliana"
+                        "value": "Integrated multi-omics profiling of Arabidopsis thaliana under controlled experimental conditions"
                     }
                 },
                 {
@@ -38,7 +38,7 @@
                     "key": "studies",
                     "where": {
                         "key": "title",
-                        "value": "Arabidopsis thaliana"
+                        "value": "Integrated multi-omics profiling of Arabidopsis thaliana under controlled experimental conditions"
                     }
                 },
                 {
diff --git a/tests/test_isa_json.py b/tests/test_isa_json.py
index b358c63..e1d6d38 100644
--- a/tests/test_isa_json.py
+++ b/tests/test_isa_json.py
@@ -35,7 +35,10 @@ def test_load_isa_json():
     # Should test the validation process of the ISA JSON file where root has 'investigation' as key.
     valid_isa_json02 = load_isa_json("MARS/test-data/biosamples-input-isa.json", False)
     assert len(valid_isa_json02.investigation.studies) == 1
-    assert valid_isa_json02.investigation.studies[0].title == "Arabidopsis thaliana"
+    assert (
+        valid_isa_json02.investigation.studies[0].title
+        == "Integrated multi-omics profiling of Arabidopsis thaliana under controlled experimental conditions"
+    )
 
     with pytest.raises(ValidationError):
         load_isa_json("./tests/fixtures/invalid_investigation.json", True)
@@ -245,7 +248,102 @@ def test_update_study_materials_with_accession_categories():
     )
 
 
-def test_update_study_and_assay_with_ena_study_accession_comment():
+def test_update_study_materials_multiple_samples_from_one_source():
+    json_path = "MARS/test-data/biosamples-input-isa-multi.json"
+    with open(json_path) as json_file:
+        json_data = json.load(json_file)
+
+    study = json_data["investigation"]["studies"][0]
+    root_sample = next(
+        sample for sample in study["materials"]["samples"] if sample["name"] == "root 1"
+    )
+    root_sample["derivesFrom"][0]["@id"] = "#source/330"
+    root_process = next(
+        process
+        for process in study["processSequence"]
+        if process["@id"] == "#process/sample_collection/431"
+    )
+    root_process["inputs"][0]["@id"] = "#source/330"
+
+    validated_isa_json = IsaJson.model_validate(json_data)
+    repo_response = RepositoryResponse.model_validate(
+        {
+            "targetRepository": "biosamples",
+            "errors": [],
+            "info": [],
+            "accessions": [
+                {
+                    "value": "SAMEA_SOURCE_1",
+                    "path": [
+                        {"key": "investigation"},
+                        {
+                            "key": "studies",
+                            "where": {
+                                "key": "title",
+                                "value": study["title"],
+                            },
+                        },
+                        {"key": "materials"},
+                        {
+                            "key": "sources",
+                            "where": {"key": "name", "value": "plant 1"},
+                        },
+                    ],
+                },
+                {
+                    "value": "SAMEA_LEAF_1",
+                    "path": [
+                        {"key": "investigation"},
+                        {
+                            "key": "studies",
+                            "where": {
+                                "key": "title",
+                                "value": study["title"],
+                            },
+                        },
+                        {"key": "materials"},
+                        {
+                            "key": "samples",
+                            "where": {"key": "name", "value": "leaf 1"},
+                        },
+                    ],
+                },
+                {
+                    "value": "SAMEA_ROOT_1",
+                    "path": [
+                        {"key": "investigation"},
+                        {
+                            "key": "studies",
+                            "where": {
+                                "key": "title",
+                                "value": study["title"],
+                            },
+                        },
+                        {"key": "materials"},
+                        {
+                            "key": "samples",
+                            "where": {"key": "name", "value": "root 1"},
+                        },
+                    ],
+                },
+            ],
+        }
+    )
+
+    updated_isa_json = update_isa_json(validated_isa_json, repo_response)
+    updated_study = updated_isa_json.investigation.studies[0]
+    updated_samples = updated_study.materials.samples
+
+    assert updated_study.materials.sources[0].characteristics[-1].value.annotationValue == (
+        "SAMEA_SOURCE_1"
+    )
+    assert updated_samples[0].derivesFrom[0].id == "#source/330"
+    assert updated_samples[0].characteristics[-1].value.annotationValue == "SAMEA_LEAF_1"
+    assert updated_samples[1].derivesFrom[0].id == "#source/330"
+    assert updated_samples[1].characteristics[-1].value.annotationValue == "SAMEA_ROOT_1"
+
+
+def test_update_study_only_with_ena_study_accession_comment():
     json_path = "tests/fixtures/isa_jsons/1_after_biosamples.json"
     isa_json = load_isa_json(json_path, False)
     response_file_path = "tests/fixtures/mars_receipts/ena_success_response.json"
@@ -267,10 +365,10 @@ def test_update_study_and_assay_with_ena_study_accession_comment():
         None,
     )
     assay_comments = ena_assay.comments
-    accession_comment = filter(
-        lambda x: x.name == "ena_study_accession", assay_comments
-    )
-    assert next(accession_comment).value == ena_study_accession_number
+    accession_comments = [
+        comment for comment in assay_comments if comment.name == "ena_study_accession"
+    ]
+    assert accession_comments == []
 
 
 def test_update_datafile_comment_with_accession_comment_present():