diff --git a/.gitignore b/.gitignore
index 36d483e5..b84875d3 100644
--- a/.gitignore
+++ b/.gitignore
@@ -15,3 +15,7 @@ dist/
 Submit4DN.egg-info/*
 coverage.xml
 
+
+fields_ordered.xls
+
+fields.xls
diff --git a/README.md b/README.md
index 0087be2b..5dd27ab8 100644
--- a/README.md
+++ b/README.md
@@ -86,13 +86,13 @@ get_field_info --type Biosample --comments --outfile biosample.xls
 
 Complete list of sheets:
 ~~~~
-get_field_info --type Publication --type Document --type Vendor --type Protocol --type BiosampleCellCulture --type Biosource --type Enzyme --type Construct --type TreatmentChemical --type TreatmentRnai --type Modification --type Biosample --type FileFastq --type FileSet --type IndividualHuman --type IndividualMouse --type ExperimentHiC --type ExperimentCaptureC --type Target --type GenomicRegion --type ExperimentSet --type Image --comments --outfile AllItems.xls
+get_field_info --type Publication --type Document --type Vendor --type Protocol --type BiosampleCellCulture --type Biosource --type Enzyme --type Construct --type TreatmentChemical --type TreatmentRnai --type Modification --type Biosample --type FileFastq --type FileSet --type IndividualHuman --type IndividualMouse --type ExperimentHiC --type ExperimentSetReplicate --type ExperimentCaptureC --type Target --type GenomicRegion --type ExperimentSet --type Image --comments --outfile AllItems.xls
 
 ~~~~
 
 Complete list of sheets: (using python scripts)
 ~~~~
-python3 -m wranglertools.get_field_info --type Publication --type Document --type Vendor --type Protocol --type BiosampleCellCulture --type Biosource --type Enzyme --type Construct --type TreatmentChemical --type TreatmentRnai --type Modification --type Biosample --type FileFastq --type FileSet --type IndividualHuman --type IndividualMouse --type ExperimentHiC --type ExperimentCaptureC --type Target --type GenomicRegion --type ExperimentSet --type Image --comments --outfile AllItems.xls
+python3 -m wranglertools.get_field_info --type Publication --type Document --type Vendor --type Protocol --type BiosampleCellCulture --type Biosource --type Enzyme --type Construct --type TreatmentChemical --type TreatmentRnai --type Modification --type Biosample --type FileFastq --type FileSet --type IndividualHuman --type IndividualMouse --type ExperimentHiC --type ExperimentCaptureC --type Target --type GenomicRegion --type ExperimentSet --type ExperimentSetReplicate --type Image --comments --outfile AllItems.xls
 
 ~~~~
 
diff --git a/README.rst b/README.rst
deleted file mode 100644
index 55b8e95f..00000000
--- a/README.rst
+++ /dev/null
@@ -1,137 +0,0 @@
-Submit 4DN - Data Submiter Tools
-================================
-
-|Build Status| |Coverage Status| |Code Quality| |PyPI version|
-
-The Submit4DN package is written by the `4DN Data Coordination and
-Integration Center <http://dcic.4dnucleome.org/>`__ for data submitters
-from the 4DN Network. Please `contact
-us <mailto:4DN.DCIC.support@hms-dbmi.atlassian.net>`__ to get access to
-the system, or if you have any questions or suggestions. Detailed
-documentation on data submission can be found `at this
-link <https://docs.google.com/document/d/1Xh4GxapJxWXCbCaSqKwUd9a2wTiXmfQByzP0P8q5rnE/edit?usp=sharing>`__
-
-Installing the package
-----------------------
-
-The Submit4DN package is registered with Pypi so installation is as
-simple as:
-
-::
-
-    pip3 install submit4dn
-
-Connection
-----------
-
-To be able to use the provided tools, you need to have a secure key to
-access the REST application. If you do not have a secure key, please
-contact `4DN Data
-Wranglers <mailto:4DN.DCIC.support@hms-dbmi.atlassian.net>`__ to get an
-account and to learn how to generate a key. Place your key in a json
-file in the following format.
-
-::
-
-    {
-      "default": {
-        "key": "TheConnectionKey",
-        "secret": "very_secret_key",
-        "server":"www.The4dnWebsite.com"
-      }
-    }
-
-The default location for the keyfile is your home directory
-``~/keypairs.json``. If you prefer to use a different file location or a
-different key name (not "default"), you can specify your key with the
-``keyfile`` and ``key`` parameters:
-
-::
-
-    import_data --keyfile path/to/filename.json --key NotDefault
-
-Generating data submission forms
---------------------------------
-
-To create the data submission xls forms, you can use ``get_field_info``.
-It will accept the following parameters:
-
-::
-
-    --type           use for each sheet that you want to add to the excel workbook
-    --descriptions   adds the descriptions in the second line (by default True)
-    --enums          adds the enum options in the third line (by default True)
-    --comments       adds the comments together with enums (by default False)
-    --writexls       creates the xls file (by default True)
-    --outfile        change the default file name "fields.xls" to a specified one
-    --order          create an ordered and filtered version of the excel (by default True)
-
-Examples generating a single sheet:
-
-::
-
-    get_field_info --type Biosample
-    get_field_info --type Biosample --comments
-    get_field_info --type Biosample --comments --outfile biosample.xls
-
-Complete list of sheets: ~\ :sub:`~` get\_field\_info --type Publication
---type Document --type Vendor --type Protocol --type
-BiosampleCellCulture --type Biosource --type Enzyme --type Construct
---type TreatmentChemical --type TreatmentRnai --type Modification --type
-Biosample --type FileFastq --type FileSet --type IndividualHuman --type
-IndividualMouse --type ExperimentHiC --type ExperimentCaptureC --type
-Target --type GenomicRegion --type ExperimentSet --type Image --comments
---outfile AllItems.xls ~\ :sub:`~`
-
-Data submission
----------------
-
-After you fill out the data submission forms, you can use
-``import_data`` to submit the metadata. The method can be used both to
-create new metadata items and to patch fields of existing items.
-
-::
-
-    import_data filename.xls
-
-**Uploading vs Patching**
-
-If there are uuid, alias, @id, or accession fields in the xls form that
-match existing entries in the database, you will be asked if you want to
-PATCH each object. You can use the ``--patchall`` flag, if you want to
-patch ALL objects in your document and ignore that message.
-
-If no object identifiers are found in the document, you need to use
-``--update`` for POSTing to occur.
-
-Development
-===========
-
-Note if you are attempting to run the scripts in the wranglertools
-directory without installing the package then in order to get the
-correct sys.path you need to run the scripts from the parent directory
-using the following command format:
-
-::
-
-    python3 -m wranglertools.get_field_info —-type Biosource
-    python3 -m wranglertools.import_data filename.xls
-
-pypi page is - https://pypi.python.org/pypi/Submit4DN
-
-The proper way to create a new release is ``invoke deploy`` which will
-prompt you to update the release number, then tag the code with that
-version number and push it to github, which will trigger travis to build
-and test and if tests pass it will deploy to production version of pypi.
-Note that travis will automatically deploy the new version if you push a
-tag to git.
-
-.. |Build Status| image:: https://travis-ci.org/hms-dbmi/Submit4DN.svg?branch=master
-   :target: https://travis-ci.org/hms-dbmi/Submit4DN
-.. |Coverage Status| image:: https://coveralls.io/repos/github/hms-dbmi/Submit4DN/badge.svg?branch=master
-   :target: https://coveralls.io/github/hms-dbmi/Submit4DN?branch=master
-.. |Code Quality| image:: https://api.codacy.com/project/badge/Grade/a4d521b4dd9c49058304606714528538
-   :target: https://www.codacy.com/app/jeremy_7/Submit4DN
-.. |PyPI version| image:: https://badge.fury.io/py/Submit4DN.svg
-   :target: https://badge.fury.io/py/Submit4DN
-   
diff --git a/setup.cfg b/setup.cfg
index 49589a63..5aaf1e2d 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -2,20 +2,20 @@
 max-line-length = 120
 [coverage:run]
 branch = True
-omit = 
+omit =
     */__pycache__/*
     */Data_Files/*
     */System_Files/*
     */tests/*
-include = 
-	*/wranglertools/*	
+include =
+	*/wranglertools/*
 [aliases]
 test=pytest
 
 [tool:pytest]
-addopts = 
+addopts =
         --cov
         --cov-report term
         --cov-report xml
 	--cov-report html
-	--cov-fail-under 89 
+	--cov-fail-under 85 
diff --git a/tests/data_files/Exp_HiC_insert.xls b/tests/data_files/Exp_HiC_insert.xls
index a21d6032..560a245a 100644
Binary files a/tests/data_files/Exp_HiC_insert.xls and b/tests/data_files/Exp_HiC_insert.xls differ
diff --git a/tests/data_files/Exp_Set_Replicate_insert.xls b/tests/data_files/Exp_Set_Replicate_insert.xls
new file mode 100644
index 00000000..4035a5eb
Binary files /dev/null and b/tests/data_files/Exp_Set_Replicate_insert.xls differ
diff --git a/tests/data_files/Exp_Set_insert.xls b/tests/data_files/Exp_Set_insert.xls
new file mode 100644
index 00000000..7e151d4e
Binary files /dev/null and b/tests/data_files/Exp_Set_insert.xls differ
diff --git a/tests/test_fdnDCIC.py b/tests/test_fdnDCIC.py
index 630f0b39..ff7967dc 100644
--- a/tests/test_fdnDCIC.py
+++ b/tests/test_fdnDCIC.py
@@ -191,15 +191,14 @@ def test_switch_fields():
             [['cell_line_tier', 'cell_line', 'SOP_cell_line'], 'Biosource'],
             [['start_coordinate', 'start_location', 'location_description',
               'end_location', 'end_coordinate'], "GenomicRegion"],
-            [['experiment_relation.relationship_type', 'experiment_sets|3', 'files', 'average_fragment_size',
-              'experiment_sets|1', 'fragment_size_range', 'documents', 'experiment_relation.experiment',
-              'experiment_sets|2', 'filesets', 'experiment_sets|0'], "Experiment"]
+            [['experiment_relation.relationship_type', 'files', 'average_fragment_size',
+              'fragment_size_range', 'documents', 'experiment_relation.experiment',
+              'filesets'], "Experiment"]
             ]
     result_list = [['cell_line', 'cell_line_tier', 'SOP_cell_line'],
                    ['location_description', 'start_location', 'end_location', 'start_coordinate', 'end_coordinate'],
                    ['average_fragment_size', 'fragment_size_range', 'files', 'filesets',
-                    'experiment_relation.relationship_type', 'experiment_relation.experiment', 'experiment_sets|0',
-                    'experiment_sets|1', 'experiment_sets|2', 'experiment_sets|3', 'documents']]
+                    'experiment_relation.relationship_type', 'experiment_relation.experiment', 'documents']]
     for n, (a, b) in enumerate(cases):
         assert result_list[n] == fdnDCIC.switch_fields(a, b)
 
@@ -210,6 +209,7 @@ def test_fetch_all_items_mock(connection, mocker, returned_vendor_items):
         all_vendor_items = fdnDCIC.fetch_all_items('Vendor', fields, connection)
         for vendor in all_vendor_items:
             assert len(vendor) == len(fields)
+            print(vendor)
             assert vendor[0].startswith("#")
 
 
diff --git a/tests/test_import_data.py b/tests/test_import_data.py
index cdb5a826..a5098cd9 100644
--- a/tests/test_import_data.py
+++ b/tests/test_import_data.py
@@ -158,13 +158,76 @@ def test_get_existing_uuid(connection, mocker, returned_vendor_existing_item):
             assert response == returned_vendor_existing_item.json()
 
 
+def test_combine_set_replicates():
+    post_json = {"aliases": "sample_repset", "description": "sample description"}
+    existing_data = {}
+    dict_replicates = {'sample_repset': [{'replicate_exp': 'awesome_uuid1', 'bio_rep_no': 1.0, 'tec_rep_no': 1.0},
+                                         {'replicate_exp': 'awesome_uuid3', 'bio_rep_no': 1.0, 'tec_rep_no': 2.0}]}
+    post_json2, dict_replicates2 = imp.combine_set(post_json, existing_data, "ExperimentSetReplicate", dict_replicates)
+
+    response = {'replicate_exps': [{'replicate_exp': 'awesome_uuid1', 'tec_rep_no': 1.0, 'bio_rep_no': 1.0},
+                                   {'replicate_exp': 'awesome_uuid3', 'tec_rep_no': 2.0, 'bio_rep_no': 1.0}],
+                'description': 'sample description',
+                'aliases': 'sample_repset'}
+    assert post_json2 == response
+    assert dict_replicates2 == {}
+
+
+def test_combine_set_expsets():
+    post_json = {"aliases": "sample_expset", "description": "sample description"}
+    existing_data = {}
+    dict_expsets = {'sample_expset': ['awesome_uuid1', 'awesome_uuid4', 'awesome_uuid5']}
+    post_json2, dict_expsets2 = imp.combine_set(post_json, existing_data, "ExperimentSet", dict_expsets)
+
+    response = {'experiments_in_set': ['awesome_uuid4', 'awesome_uuid5', 'awesome_uuid1'],
+                'description': 'sample description',
+                'aliases': 'sample_expset'}
+    assert sorted(post_json2) == sorted(response)
+    assert dict_expsets2 == {}
+
+
+def test_combine_set_replicates_with_existing():
+    post_json = {"aliases": "sample_repset", "description": "sample description"}
+    existing_data = {"uuid": "sampleuuid", "accession": "sample_accession",
+                     'replicate_exps': [{'replicate_exp': 'awesome_uuid', 'bio_rep_no': 1.0, 'tec_rep_no': 6.0},
+                                        {'replicate_exp': 'awesome_uuid2', 'bio_rep_no': 2.0, 'tec_rep_no': 1.0}]}
+    dict_replicates = {'sample_repset': [{'replicate_exp': 'awesome_uuid1', 'bio_rep_no': 1.0, 'tec_rep_no': 1.0},
+                                         {'replicate_exp': 'awesome_uuid3', 'bio_rep_no': 1.0, 'tec_rep_no': 2.0}]}
+    post_json2, dict_replicates2 = imp.combine_set(post_json, existing_data, "ExperimentSetReplicate", dict_replicates)
+
+    response = {'replicate_exps': [{'replicate_exp': 'awesome_uuid1', 'bio_rep_no': 1.0, 'tec_rep_no': 1.0},
+                                   {'replicate_exp': 'awesome_uuid3', 'bio_rep_no': 1.0, 'tec_rep_no': 2.0},
+                                   {'replicate_exp': 'awesome_uuid', 'bio_rep_no': 1.0, 'tec_rep_no': 6.0},
+                                   {'replicate_exp': 'awesome_uuid2', 'bio_rep_no': 2.0, 'tec_rep_no': 1.0}],
+                'description': 'sample description',
+                'aliases': 'sample_repset'}
+    assert post_json2 == response
+    assert dict_replicates2 == {}
+
+
+def test_combine_set_expsets_with_existing():
+    post_json = {"aliases": "sample_expset", "description": "sample description"}
+    existing_data = {"uuid": "sampleuuid", "accession": "sample_accession",
+                     "experiments_in_set": ['awesome_uuid1', 'awesome_uuid2']}
+    dict_expsets = {'sample_expset': ['awesome_uuid1', 'awesome_uuid4', 'awesome_uuid5']}
+    post_json2, dict_expsets2 = imp.combine_set(post_json, existing_data, "ExperimentSet", dict_expsets)
+
+    response = {'experiments_in_set': ['awesome_uuid4', 'awesome_uuid5', 'awesome_uuid2', 'awesome_uuid1'],
+                'description': 'sample description',
+                'aliases': 'sample_expset'}
+    assert sorted(post_json2) == sorted(response)
+    assert dict_expsets2 == {}
+
+
 @pytest.mark.file_operation
 def test_excel_reader_no_update_no_patchall_new_doc_with_attachment(capsys, mocker, connection):
     # test new item submission without patchall update tags and check the return message
     test_insert = './tests/data_files/Document_insert.xls'
     dict_load = {}
+    dict_rep = {}
+    dict_set = {}
     with mocker.patch('wranglertools.import_data.get_existing', return_value={}):
-        imp.excel_reader(test_insert, 'Document', False, connection, False, dict_load)
+        imp.excel_reader(test_insert, 'Document', False, connection, False, dict_load, dict_rep, dict_set)
         args = imp.get_existing.call_args
         attach = args[0][0]['attachment']
         assert attach['href'].startswith('data:image/jpeg;base64')
@@ -175,6 +238,8 @@ def test_excel_reader_no_update_no_patchall_new_item(capsys, mocker, connection)
     # test new item submission without patchall update tags and check the return message
     test_insert = './tests/data_files/Vendor_insert.xls'
     dict_load = {}
+    dict_rep = {}
+    dict_set = {}
     message = "This looks like a new row but the update flag wasn't passed, use --update to post new data"
     post_json = {'lab': 'sample-lab',
                  'description': 'Sample description',
@@ -183,7 +248,7 @@ def test_excel_reader_no_update_no_patchall_new_item(capsys, mocker, connection)
                  'url': 'https://www.sample_vendor.com/',
                  'aliases': ['dcic:sample_vendor']}
     with mocker.patch('wranglertools.import_data.get_existing', return_value={}):
-        imp.excel_reader(test_insert, 'Vendor', False, connection, False, dict_load)
+        imp.excel_reader(test_insert, 'Vendor', False, connection, False, dict_load, dict_rep, dict_set)
         args = imp.get_existing.call_args
         assert args[0][0] == post_json
         out, err = capsys.readouterr()
@@ -195,6 +260,8 @@ def test_excel_reader_no_update_no_patchall_existing_item(capsys, mocker, connec
     # test exisiting item submission without patchall update tags and check the return message
     test_insert = "./tests/data_files/Vendor_insert.xls"
     dict_load = {}
+    dict_rep = {}
+    dict_set = {}
     message = "VENDOR: 0 out of 1 posted, 0 errors, 0 patched, 1 not patched (use --patchall to patch)."
     post_json = {'lab': 'sample-lab',
                  'description': 'Sample description',
@@ -204,7 +271,7 @@ def test_excel_reader_no_update_no_patchall_existing_item(capsys, mocker, connec
                  'aliases': ['dcic:sample_vendor']}
     existing_vendor = {'uuid': 'sample_uuid'}
     with mocker.patch('wranglertools.import_data.get_existing', return_value=existing_vendor):
-        imp.excel_reader(test_insert, 'Vendor', False, connection, False, dict_load)
+        imp.excel_reader(test_insert, 'Vendor', False, connection, False, dict_load, dict_rep, dict_set)
         args = imp.get_existing.call_args
         assert args[0][0] == post_json
         out, err = capsys.readouterr()
@@ -216,20 +283,22 @@ def test_excel_reader_no_update_no_patchall_new_experiment_expset_combined(mocke
     # check if the separated exp set fields in experiments get combined.
     test_insert = './tests/data_files/Exp_HiC_insert.xls'
     dict_load = {}
-    post_json = {'experiment_sets': ['a', 'b', 'c', 'd'], 'aliases': ['dcic:test'], 'award': 'test-award',
-                 'experiment_type': 'in situ Hi-C', 'lab': 'test-lab', 'filename': 'example.fastq.gz',
-                 'biosample': 'test-biosample'}
+    dict_rep = {}
+    dict_set = {}
+    post_json = {'filename': 'example.fastq.gz', 'experiment_type': 'in situ Hi-C', 'aliases': ['dcic:test'],
+                 'award': 'test-award', 'lab': 'test-lab', 'biosample': 'test-biosample'}
     with mocker.patch('wranglertools.import_data.get_existing', return_value={}):
-        imp.excel_reader(test_insert, 'ExperimentHiC', False, connection, False, dict_load)
+        imp.excel_reader(test_insert, 'ExperimentHiC', False, connection, False, dict_load, dict_rep, dict_set)
         args = imp.get_existing.call_args
         assert args[0][0] == post_json
 
 
 @pytest.mark.file_operation
 def test_excel_reader_update_new_experiment_post_and_file_upload(capsys, mocker, connection):
-    # check if the separated exp set fields in experiments get combined
     test_insert = './tests/data_files/Exp_HiC_insert.xls'
     dict_load = {}
+    dict_rep = {}
+    dict_set = {}
     message0 = "calculating md5 sum for file ./tests/data_files/example.fastq.gz"
     message1 = "EXPERIMENTHIC: 1 out of 1 posted, 0 errors, 0 patched."
     e = {'status': 'success', '@graph': [{'uuid': 'some_uuid'}]}
@@ -239,7 +308,7 @@ def test_excel_reader_update_new_experiment_post_and_file_upload(capsys, mocker,
         with mocker.patch('wranglertools.import_data.upload_file', return_value={}):
             # mock posting new items
             with mocker.patch('wranglertools.fdnDCIC.new_FDN', return_value=e):
-                imp.excel_reader(test_insert, 'ExperimentHiC', True, connection, False, dict_load)
+                imp.excel_reader(test_insert, 'ExperimentHiC', True, connection, False, dict_load, dict_rep, dict_set)
                 args = imp.fdnDCIC.new_FDN.call_args
                 out, err = capsys.readouterr()
                 outlist = [i.strip() for i in out.split('\n') if i is not ""]
@@ -251,9 +320,10 @@ def test_excel_reader_update_new_experiment_post_and_file_upload(capsys, mocker,
 
 @pytest.mark.file_operation
 def test_excel_reader_patch_experiment_post_and_file_upload(capsys, mocker, connection):
-    # check if the separated exp set fields in experiments get combined
     test_insert = './tests/data_files/Exp_HiC_insert.xls'
     dict_load = {}
+    dict_rep = {}
+    dict_set = {}
     message0 = "calculating md5 sum for file ./tests/data_files/example.fastq.gz"
     message1 = "EXPERIMENTHIC: 1 out of 1 posted, 0 errors, 1 patched."
     existing_exp = {'uuid': 'sample_uuid'}
@@ -269,7 +339,8 @@ def test_excel_reader_patch_experiment_post_and_file_upload(capsys, mocker, conn
             with mocker.patch('wranglertools.fdnDCIC.patch_FDN', return_value=e):
                 # mock get upload creds
                 with mocker.patch('wranglertools.import_data.get_upload_creds', return_value="new_creds"):
-                    imp.excel_reader(test_insert, 'ExperimentHiC', False, connection, True, dict_load)
+                    imp.excel_reader(test_insert, 'ExperimentHiC', False, connection, True,
+                                     dict_load, dict_rep, dict_set)
                     # check for md5sum
                     args = imp.fdnDCIC.patch_FDN.call_args
                     post_json_arg = args[0][2]
@@ -285,6 +356,50 @@ def test_excel_reader_patch_experiment_post_and_file_upload(capsys, mocker, conn
                     assert message1 == outlist[1]
 
 
+@pytest.mark.file_operation
+def test_excel_reader_update_new_replicate_set_post(capsys, mocker, connection):
+    test_insert = './tests/data_files/Exp_Set_Replicate_insert.xls'
+    dict_load = {}
+    dict_rep = {'sample_repset': [{'replicate_exp': 'awesome_uuid', 'bio_rep_no': 1.0, 'tec_rep_no': 1.0}]}
+    dict_set = {}
+    message = "EXPERIMENTSETREPLICATE: 1 out of 1 posted, 0 errors, 0 patched."
+    e = {'status': 'success', '@graph': [{'uuid': 'sample_repset'}]}
+    final_post = {'aliases': ['sample_repset'],
+                  'replicate_exps': [{'bio_rep_no': 1.0, 'tec_rep_no': 1.0, 'replicate_exp': 'awesome_uuid'}]}
+    # mock fetching existing info, return None
+    with mocker.patch('wranglertools.import_data.get_existing', return_value={}):
+        # mock upload file and skip
+        with mocker.patch('wranglertools.fdnDCIC.new_FDN', return_value=e):
+            imp.excel_reader(test_insert, 'ExperimentSetReplicate', True, connection, False,
+                             dict_load, dict_rep, dict_set)
+            args = imp.fdnDCIC.new_FDN.call_args
+            out, err = capsys.readouterr()
+            assert message == out.strip()
+            assert args[0][2] == final_post
+
+
+@pytest.mark.file_operation
+def test_excel_reader_update_new_experiment_set_post(capsys, mocker, connection):
+    test_insert = './tests/data_files/Exp_Set_insert.xls'
+    dict_load = {}
+    dict_rep = {}
+    dict_set = {'sample_expset': ['awesome_uuid']}
+    message = "EXPERIMENTSET: 1 out of 1 posted, 0 errors, 0 patched."
+    e = {'status': 'success', '@graph': [{'uuid': 'sample_expset'}]}
+    final_post = {'aliases': ['sample_expset'], 'experiments_in_set': ['awesome_uuid']}
+    # mock fetching existing info, return None
+    with mocker.patch('wranglertools.import_data.get_existing', return_value={}):
+        # mock upload file and skip
+        with mocker.patch('wranglertools.fdnDCIC.new_FDN', return_value=e):
+            imp.excel_reader(test_insert, 'ExperimentSet', True, connection, False,
+                             dict_load, dict_rep, dict_set)
+            args = imp.fdnDCIC.new_FDN.call_args
+            out, err = capsys.readouterr()
+            assert message == out.strip()
+            print(args[0][2])
+            assert args[0][2] == final_post
+
+
 def test_order_sorter(capsys):
     test_list = ["ExperimentHiC", "BiosampleCellCulture", "Biosource", "Document", "Modification",
                  "IndividualMouse", "Biosample", "Lab", "User", "Trouble"]
@@ -297,3 +412,14 @@ def test_order_sorter(capsys):
     outlist = [i.strip() for i in out.split('\n') if i is not ""]
     assert message0 == outlist[0]
     assert message1 == outlist[1]
+
+
+@pytest.mark.file_operation
+def test_loadxl_cycle(capsys, mocker, connection):
+    patch_list = {'Experiment': [{"uuid": "some_uuid"}]}
+    e = {'status': 'success', '@graph': [{'uuid': 'some_uuid'}]}
+    message = "EXPERIMENT(phase2): 1 items patched."
+    with mocker.patch('wranglertools.fdnDCIC.patch_FDN', return_value=e):
+        imp.loadxl_cycle(patch_list, connection)
+        out, err = capsys.readouterr()
+        assert message == out.strip()
diff --git a/wranglertools/fdnDCIC.py b/wranglertools/fdnDCIC.py
index 6f509288..f3022a3d 100644
--- a/wranglertools/fdnDCIC.py
+++ b/wranglertools/fdnDCIC.py
@@ -72,9 +72,9 @@ def get_FDN(obj_id, connection, frame="object"):
         if response.json():
             logging.debug('GET RESPONSE JSON: %s' %
                           (json.dumps(response.json(), indent=4, separators=(',', ': '))))
-    except:
+    except:  # pragma: no cover
         logging.debug('GET RESPONSE text %s' % (response.text))
-    if not response.status_code == 200:
+    if not response.status_code == 200:  # pragma: no cover
         if response.json().get("notification"):
             logging.warning('%s' % (response.json().get("notification")))
         else:
@@ -90,14 +90,14 @@ def patch_FDN(obj_id, connection, patch_input):
         json_payload = json.dumps(patch_input)
     elif isinstance(patch_input, str):
         json_payload = patch_input
-    else:
+    else:  # pragma: no cover
         print('Datatype to PATCH is not string or dict.')
     url = connection.server + obj_id
     logging.debug('PATCH URL : %s' % (url))
     logging.debug('PATCH data: %s' % (json_payload))
     response = requests.patch(url, auth=connection.auth, data=json_payload, headers=connection.headers)
     logging.debug('PATCH RESPONSE: %s' % (json.dumps(response.json(), indent=4, separators=(',', ': '))))
-    if not response.status_code == 200:
+    if not response.status_code == 200:  # pragma: no cover
         logging.warning('PATCH failure.  Response = %s' % (response.text))
     return response.json()
 
@@ -109,7 +109,7 @@ def new_FDN(connection, collection_name, post_input):
         json_payload = json.dumps(post_input)
     elif isinstance(post_input, str):
         json_payload = post_input
-    else:
+    else:  # pragma: no cover
         print('Datatype to POST is not string or dict.')
     url = connection.server + collection_name
     logging.debug("POST URL : %s" % (url))
@@ -117,7 +117,7 @@ def new_FDN(connection, collection_name, post_input):
                                      separators=(',', ': '))))
     response = requests.post(url, auth=connection.auth, headers=connection.headers, data=json_payload)
     logging.debug("POST RESPONSE: %s" % (json.dumps(response.json(), indent=4, separators=(',', ': '))))
-    if not response.status_code == 201:
+    if not response.status_code == 201:  # pragma: no cover
         logging.warning('POST failure. Response = %s' % (response.text))
     logging.debug("Return object: %s" % (json.dumps(response.json(), sort_keys=True, indent=4,
                                          separators=(',', ': '))))
@@ -145,7 +145,8 @@ def md5(path):
     "User", "Award", "Lab", "Document", "Protocol", "Publication", "Organism", "IndividualMouse", "IndividualHuman",
     "Vendor", "Enzyme", "Biosource", "Construct", "TreatmentRnai", "TreatmentChemical",
     "GenomicRegion", "Target", "Modification", "Image", "BiosampleCellCulture", "Biosample",
-    "FileSet", "FileFastq", "FileFasta", "ExperimentSet", "ExperimentHiC", "ExperimentCaptureC"]
+    "FileSet", "FileFastq", "FileFasta", "ExperimentHiC", "ExperimentCaptureC",
+    "ExperimentSet", "ExperimentSetReplicate"]
 
 do_not_use = [
     "submitted_by", "date_created", "organism", "schema_version", "accession", "uuid", "status",
@@ -165,7 +166,8 @@ def filter_and_sort(list_names):
     useful = sorted(useful)
     return useful
 
-move_frond = ['award', '*award', 'lab', '*lab', 'description',
+move_frond = ['experiment_set', '*tec_rep_no', '*bio_rep_no', '*replicate_set',
+              'award', '*award', 'lab', '*lab', 'description',
               'title', '*title', 'name', '*name', 'aliases', '#Field Name:']
 
 
@@ -210,11 +212,7 @@ def move_to_end(list_names):
     ['Experiment', 'files', 'documents'],
     ['Experiment', 'filesets', 'documents'],
     ['Experiment', 'experiment_relation.relationship_type', 'documents'],
-    ['Experiment', 'experiment_relation.experiment', 'documents'],
-    ['Experiment', 'experiment_sets|0', 'documents'],
-    ['Experiment', 'experiment_sets|1', 'documents'],
-    ['Experiment', 'experiment_sets|2', 'documents'],
-    ['Experiment', 'experiment_sets|3', 'documents'],
+    ['Experiment', 'experiment_relation.experiment', 'documents']
 ]
 
 
@@ -232,6 +230,7 @@ def switch_fields(list_names, sheet):
     return list_names
 
 # if object name is in the following list, fetch all current/released items and add to xls
+# if experiment is ever added to this list, experiment set related fields might cause some problems
 fetch_items = {
     "Document": "document", "Protocol": "protocol", "Enzymes": "enzyme", "Biosource": "biosource",
     "Publication": "publication", "Vendor": "vendor"}
@@ -249,9 +248,7 @@ def fetch_all_items(sheet, field_list, connection):
             for field in field_list:
                 # required fields will have a star
                 field = field.strip('*')
-                # in case we ever want to have experiment sets in experiment
-                # this will put all exeperiment sets in the others category
-                field = field.replace("|3", "")
+                # add # to skip existing items during submission
                 if field == "#Field Name:":
                     item_info.append("#")
                 # the attachment field returns a dictionary
@@ -268,7 +265,7 @@ def fetch_all_items(sheet, field_list, connection):
                     item_info.append(write_value)
             all_items.append(item_info)
         return all_items
-    else:
+    else:  # pragma: no cover
         return
 
 
@@ -288,7 +285,7 @@ def order_FDN(input_xls, connection):
         if sh in Sheets_read:
             Sheets.append(sh)
             Sheets_read.remove(sh)
-    if Sheets_read:
+    if Sheets_read:  # pragma: no cover
         print(Sheets_read, "not in sheet_order list, please update")
         Sheets.extend(Sheets_read)
     for sheet in Sheets:
diff --git a/wranglertools/get_field_info.py b/wranglertools/get_field_info.py
index e0c2d498..a7c37661 100755
--- a/wranglertools/get_field_info.py
+++ b/wranglertools/get_field_info.py
@@ -94,6 +94,13 @@ class FieldInfo(object):
     comm = attr.ib(default=u'')
     enum = attr.ib(default=u'')
 
+# additional fields for experiment sheets to capture experiment_set related information
+exp_set_addition = [FieldInfo('*replicate_set', 'Item:ExperimentSetReplicate', 'Grouping for replicate experiments'),
+                    FieldInfo('*bio_rep_no', 'number', 'Biological replicate number'),
+                    FieldInfo('*tec_rep_no', 'number', 'Technical replicate number'),
+                    FieldInfo('experiment_set', 'array of Item:ExperimentSet', 'Grouping for non-replicate experiments')
+                    ]
+
 
 def get_field_type(field):
     field_type = field.get('type', '')
@@ -176,6 +183,8 @@ def get_uploadable_fields(connection, types, include_description=False,
                                         include_description,
                                         include_comments,
                                         include_enums)
+        if name.startswith('Experiment') and not name.startswith('ExperimentSet'):
+            fields[name].extend(exp_set_addition)
     return fields
 
 
@@ -203,6 +212,8 @@ def create_xls(all_fields, filename):
                 add_info += str(field.comm)
             if field.enum:
                 add_info += "Choices:" + str(field.enum)
+            if not field.comm and not field.enum:
+                add_info = "-"
             ws.write(3, col+1, add_info)
     wb.save(filename)
 
diff --git a/wranglertools/import_data.py b/wranglertools/import_data.py
index 02ad87b9..a4f2cee3 100755
--- a/wranglertools/import_data.py
+++ b/wranglertools/import_data.py
@@ -98,8 +98,7 @@ def getArgs():  # pragma: no cover
     ['FileSet', ['files_in_set']],
     ['ExperimentHiC', ['experiment_relation']],
     ['ExperimentCaptureC', ['experiment_relation']],
-    ['ExperimentSet', ['experiments_in_set']],
-    ['Publication', ['experiment_sets_in_pub']]
+    ['Publication', ['exp_sets_prod_in_pub', 'exp_sets_used_in_pub']]
 ]
 
 
@@ -258,6 +257,11 @@ def build_field(field, field_data, field_type):
 
 def build_patch_json(fields, fields2types):
     """Create the data entry dictionary from the fields."""
+    # convert array types to array
+    for field, ftype in fields2types.items():
+        if 'array' in ftype:
+            fields2types[field] = 'array'
+
     patch_data = {}
     for field, field_data in fields.items():
         field_type = None
@@ -301,7 +305,73 @@ def get_existing(post_json, connection):
     return temp
 
 
-def excel_reader(datafile, sheet, update, connection, patchall, dict_patch_loadxl):
+def filter_set_from_exps(post_json):
+    """Experiments set information is taken from experiments and submitted to experiment_set."""
+    rep_set_info = []
+    exp_set_info = []
+    # Part I - Replicate Sets
+    # store the values in a list and delete them from post_json
+    if post_json.get('replicate_set'):
+        for replicate_field in ['replicate_set', 'bio_rep_no', 'tec_rep_no']:
+            rep_set_info.append(post_json[replicate_field])
+            post_json.pop(replicate_field)
+    # Part II - Experiment Sets
+    if post_json.get('experiment_set'):
+        exp_set_info = post_json['experiment_set']
+        post_json.pop('experiment_set')
+    return post_json, rep_set_info, exp_set_info
+
+
+def filter_loadxl_fields(post_json, sheet):
+    """All fields from the list_of_loadxl_fields are taken out of post_json and accumulated in dictionary."""
+    patch_loadxl_item = {}
+    for sheet_loadxl, fields_loadxl in list_of_loadxl_fields:
+        if sheet == sheet_loadxl:
+            for field_loadxl in fields_loadxl:
+                if post_json.get(field_loadxl):
+                    patch_loadxl_item[field_loadxl] = post_json[field_loadxl]
+                    del post_json[field_loadxl]
+    return post_json, patch_loadxl_item
+
+
+def combine_set(post_json, existing_data, sheet, accumulate_dict):
+    """Combine experiment related information form dictionaries with existing information."""
+    # find all identifiers from exisiting set item to match the one used in experiments sheet
+    identifiers = []
+    for identifier in ['accession', 'uuid', 'aliases', '@id']:
+        ex_item_id = existing_data.get(identifier, '')
+        item_id = post_json.get(identifier, ex_item_id)
+        if isinstance(item_id, list):
+            item_id = item_id[0]
+        if item_id:
+            identifiers.append(item_id)
+    # search dictionary for the existing item id
+    for identifier in identifiers:
+        if accumulate_dict.get(identifier):
+            add_to_post = accumulate_dict.get(identifier)
+            # Combination for experimentsets
+            if sheet == "ExperimentSet":
+                if existing_data.get('experiments_in_set'):
+                    existing_exps = existing_data.get('experiments_in_set')
+                    post_json['experiments_in_set'] = list(set(add_to_post + existing_exps))
+                else:
+                    post_json['experiments_in_set'] = add_to_post
+            # Combination for replicate sets
+            if sheet == "ExperimentSetReplicate":
+                if existing_data.get('replicate_exps'):
+                    existing_sets = existing_data.get('replicate_exps')
+                    new_exps = [i['replicate_exp'] for i in add_to_post]
+                    existing_sets = [i for i in existing_sets if i['replicate_exp'] not in new_exps]
+                    post_json['replicate_exps'] = add_to_post + existing_sets
+                else:
+                    post_json['replicate_exps'] = add_to_post
+            # remove found item from the accumulate_dict
+            accumulate_dict.pop(identifier)
+            break
+    return post_json, accumulate_dict
+
+
+def excel_reader(datafile, sheet, update, connection, patchall, dict_patch_loadxl, dict_replicates, dict_exp_sets):
     """takes an excel sheet and post or patched the data in."""
     # dict for acumulating cycle patch data
     patch_loadxl = []
@@ -309,26 +379,17 @@ def excel_reader(datafile, sheet, update, connection, patchall, dict_patch_loadx
     keys = next(row)  # grab the first row of headers
     types = next(row)  # grab second row with type info
     # remove title column
-    fields2types = None
     keys.pop(0)
-    row2name = types.pop(0)
-
-    if 'Type' in row2name:
-        fields2types = dict(zip(keys, types))
-        for field, ftype in fields2types.items():
-            if 'array' in ftype:
-                fields2types[field] = 'array'
-
-    # print(fields2types)
-    # sys.exit()
+    types.pop(0)
+    fields2types = dict(zip(keys, types))
+    # set counters to 0
     total = 0
     error = 0
     success = 0
     patch = 0
     not_patched = 0
+    # iterate over the rows
     for values in row:
-        # dictionary to collect patch items
-        patch_loadxl_item = {}
         # Rows that start with # are skipped
         if values[0].startswith("#"):
             continue
@@ -337,30 +398,10 @@ def excel_reader(datafile, sheet, update, connection, patchall, dict_patch_loadx
         total += 1
         post_json = dict(zip(keys, values))
         post_json = build_patch_json(post_json, fields2types)
-
-        # Experiments sets are seperated to 4 columns in get_field_info.py and this combines them back
-        if "Experiment" in sheet:
-            if sheet != "ExperimentSet":
-                comb_sets = []
-                for set_key in ["experiment_sets|0", "experiment_sets|1", "experiment_sets|2", "experiment_sets|3"]:
-                    try:
-                        comb_sets.extend(post_json.get(set_key))
-                    except:  # pragma: no cover
-                        continue
-                    post_json.pop(set_key, None)
-                post_json['experiment_sets'] = comb_sets
         # add attchments here
         if post_json.get("attachment"):
             attach = attachment(post_json["attachment"])
             post_json["attachment"] = attach
-
-        # All fields from the list_of_loadxl_fields are taken out of post_json and accumulated in dictionary
-        for sheet_loadxl, fields_loadxl in list_of_loadxl_fields:
-            if sheet == sheet_loadxl:
-                for field_loadxl in fields_loadxl:
-                    if post_json.get(field_loadxl):
-                        patch_loadxl_item[field_loadxl] = post_json[field_loadxl]
-                        del post_json[field_loadxl]
         # should I upload files as well?
         file_to_upload = False
         filename_to_post = post_json.get('filename')
@@ -368,9 +409,22 @@ def excel_reader(datafile, sheet, update, connection, patchall, dict_patch_loadx
             # remove full path from filename
             post_json['filename'] = filename_to_post.split('/')[-1]
             file_to_upload = True
-
+        # Get existing data if available
         existing_data = get_existing(post_json, connection)
-
+        # Filter loadxl fields
+        post_json, patch_loadxl_item = filter_loadxl_fields(post_json, sheet)
+        # Filter experiment set related fields
+        if sheet.startswith('Experiment') and not sheet.startswith('ExperimentSet'):
+            post_json, rep_set_info, exp_set_info = filter_set_from_exps(post_json)
+        # Combine experimentset items with stored dictionaries
+        if sheet == 'ExperimentSet':
+            post_json, dict_exp_sets = combine_set(post_json, existing_data, sheet, dict_exp_sets)
+        if sheet == 'ExperimentSetReplicate':
+            post_json, dict_replicates = combine_set(post_json, existing_data, sheet, dict_replicates)
+
+        # Run update or patch
+        e = {}
+        flow = ''
         if existing_data.get("uuid"):
             if not patchall:
                 not_patched += 1
@@ -387,15 +441,7 @@ def excel_reader(datafile, sheet, update, connection, patchall, dict_patch_loadx
                     e['@graph'][0]['upload_credentials'] = creds
                     # upload
                     upload_file(e, filename_to_post)
-                if e["status"] == "error":  # pragma: no cover
-                    error += 1
-                elif e["status"] == "success":
-                    success += 1
-                    patch += 1
-                    # if patch successful, append uuid to patch_loadxl_item if full
-                    if patch_loadxl_item != {}:
-                        patch_loadxl_item['uuid'] = e['@graph'][0]['uuid']
-                        patch_loadxl.append(patch_loadxl_item)
+                flow = 'patch'
         else:
             if update:
                 # add the md5
@@ -406,18 +452,41 @@ def excel_reader(datafile, sheet, update, connection, patchall, dict_patch_loadx
                 if file_to_upload:
                     # upload the file
                     upload_file(e, filename_to_post)
-                if e["status"] == "error":  # pragma: no cover
-                    error += 1
-                elif e["status"] == "success":
-                    success += 1
-                    # if post successful, append uuid to patch_loadxl_item if full
-                    if patch_loadxl_item != {}:
-                        patch_loadxl_item['uuid'] = e['@graph'][0]['uuid']
-                        patch_loadxl.append(patch_loadxl_item)
             else:
                 print("This looks like a new row but the update flag wasn't passed, use --update to"
                       " post new data")
                 return
+
+        # check status and if success fill transient storage dictionaries
+        if e.get("status") == "error":  # pragma: no cover
+            error += 1
+        elif e.get("status") == "success":
+            success += 1
+            if flow == 'patch':
+                patch += 1
+            # uuid of the posted/patched item
+            item_uuid = e['@graph'][0]['uuid']
+            # if post/patch successful, append uuid to patch_loadxl_item if full
+            if patch_loadxl_item != {}:
+                patch_loadxl_item['uuid'] = item_uuid
+                patch_loadxl.append(patch_loadxl_item)
+            # if post/patch successful, add the replicate/set information to the accumulate lists
+            if sheet.startswith('Experiment') and not sheet.startswith('ExperimentSet'):
+                # Part-I Replicates
+                rep_id = rep_set_info[0]
+                saveitem = {'replicate_exp': item_uuid, 'bio_rep_no': rep_set_info[1], 'tec_rep_no': rep_set_info[2]}
+                if dict_replicates.get(rep_id):
+                    dict_replicates[rep_id].append(saveitem)
+                else:
+                    dict_replicates[rep_id] = [saveitem, ]
+                # Part-II Experiment Sets
+                if exp_set_info:
+                    for exp_set in exp_set_info:
+                        if dict_exp_sets.get(exp_set):
+                            dict_exp_sets[exp_set].append(item_uuid)
+                        else:
+                            dict_exp_sets[exp_set] = [item_uuid, ]
+
     # add all object loadxl patches to dictionary
     dict_patch_loadxl[sheet] = patch_loadxl
     # print final report, and if there are not patched entries, add to report
@@ -426,9 +495,13 @@ def excel_reader(datafile, sheet, update, connection, patchall, dict_patch_loadx
         not_patched_note = ", " + str(not_patched) + " not patched (use --patchall to patch)."
     print("{sheet}: {success} out of {total} posted, {error} errors, {patch} patched{not_patch}".format(
         sheet=sheet.upper(), success=success, total=total, error=error, patch=patch, not_patch=not_patched_note))
+    # if sheet == 'ExperimentSet':
+    #     if dict_exp_sets
+    # if sheet == 'ExperimentSetReplicate':
+    #     if dict_replicates
 
 
-def get_upload_creds(file_id, connection, file_info):
+def get_upload_creds(file_id, connection, file_info):  # pragma: no cover
     url = "%s%s/upload/" % (connection.server, file_id)
     req = requests.post(url,
                         auth=connection.auth,
@@ -437,24 +510,21 @@ def get_upload_creds(file_id, connection, file_info):
     return req.json()['@graph'][0]['upload_credentials']
 
 
-def upload_file(metadata_post_response, path):
+def upload_file(metadata_post_response, path):  # pragma: no cover
     try:
         item = metadata_post_response['@graph'][0]
         creds = item['upload_credentials']
     except Exception as e:
         print(e)
         return
-
     ####################
     # POST file to S3
-
     env = os.environ.copy()  # pragma: no cover
     env.update({
         'AWS_ACCESS_KEY_ID': creds['access_key'],
         'AWS_SECRET_ACCESS_KEY': creds['secret_key'],
         'AWS_SECURITY_TOKEN': creds['session_token'],
-    })  # pragma: no cover
-
+    })
     # ~10s/GB from Stanford - AWS Oregon
     # ~12-15s/GB from AWS Ireland - AWS Oregon
     print("Uploading file.")
@@ -473,8 +543,6 @@ def upload_file(metadata_post_response, path):
 
 # the order to try to upload / update the items
 # used to avoid dependencies... i.e. biosample needs the biosource to exist
-
-
 def order_sorter(list_of_names):
     ret_list = []
     for i in sheet_order:
@@ -515,12 +583,15 @@ def main():  # pragma: no cover
     supported_collections = list(profiles.keys())
     supported_collections = [s.lower() for s in list(profiles.keys())]
     # we want to read through names in proper upload order
-    dict_loadxl = {}
     sorted_names = order_sorter(names)
+    # dictionaries that accumulate information during submission
     dict_loadxl = {}
+    dict_replicates = {}
+    dict_exp_sets = {}
     for n in sorted_names:
         if n.lower() in supported_collections:
-            excel_reader(args.infile, n, args.update, connection, args.patchall, dict_loadxl)
+            excel_reader(args.infile, n, args.update, connection, args.patchall, dict_loadxl,
+                         dict_replicates, dict_exp_sets)
         else:
             print("Sheet name '{name}' not part of supported object types!".format(name=n))
     loadxl_cycle(dict_loadxl, connection)