diff --git a/app/assets/javascripts/single_page/dynamic_table.js.erb b/app/assets/javascripts/single_page/dynamic_table.js.erb
index 7bf238efcb..c344d5e762 100644
--- a/app/assets/javascripts/single_page/dynamic_table.js.erb
+++ b/app/assets/javascripts/single_page/dynamic_table.js.erb
@@ -21,7 +21,7 @@ const defaultCols = [{
 
 const objectInputTemp = '<input type="hidden" name="_NAME_[]" id="inpt-_NAME_" value="" autocomplete="off" />' +
   '<select name="_NAME_[]" id="select-_NAME_" class="form-control _EXTRACLASS_" title="_TITLE_" data-role="seek-objectsinput" ' +
-  'data-tags-limit="100" multiple="multiple" style="background-color: coral;" data-typeahead-template="_TYPEHEAD_"' +
+  'data-tags-limit="100" _MULTIPLE?_ style="background-color: coral;" data-typeahead-template="_TYPEHEAD_"' +
   'data-typeahead-query-url="_URL_" data-allow-new-items=_ALLOW_FREE_TEXT_>_OPTIONS_</select>';
 
 const typeaheadSamplesUrl = "<%= typeahead_samples_path(linked_sample_type_id: '_LINKED_') %>";
@@ -59,22 +59,21 @@ const handleSelect = (e) => {
         }
 
         c["render"] = function(data_, type, full, meta) {
-          if(c.multi_link){
+          if(c.linked_sample_type){
             data = data_ && Array.isArray(data_) ? data_ : [data_];
             data = data[0]?.id ? data : [];
             return inputObjectsInput(c, data, options, linkedSamplesUrl);
-          }else if(c.is_cv_list && data_ !== "#HIDDEN"){
-            data = data_ && Array.isArray(data_) ? data_ : [data_];
-            data = data.map((e) => {
-              if (e?.id){
-                return e.id
-              } else {
-                return e
-              }
-            });
-
-            return cvListObjectsInput(c, data, options, cvUrl);
-          }else if (data_ === "#HIDDEN") {
+          } else if(c.is_cv_list && data_ !== "#HIDDEN"){
+              data = data_ && Array.isArray(data_) ? data_ : [data_];
+              data = data.map((e) => {
+                if (e?.id){
+                  return e.id
+                } else {
+                  return e
+                }
+              });
+              return cvListObjectsInput(c, data, options, cvUrl);
+          } else if (data_ === "#HIDDEN") {
             return "<em><small>Hidden</small></em>";
           } else {
             return data_;
@@ -565,6 +564,7 @@ function inputObjectsInput(column, data, options, url){
     }, []);
     const hasUnlinkedSamples = unLinkedSamples.length > 0 ? true : false;
 
+    const hasMultipleInputs = column.multi_link ? 'multiple="multiple"' : ''
     const extraClass = hasUnlinkedSamples ? 'select2__error' : '';
     const titleText = hasUnlinkedSamples ? `Sample(s) '${unLinkedSamples.map(uls => uls.title).join(', ')}' not recognised as input. Please correct this issue!` : '';
     setTimeout(ObjectsInput.init);
@@ -576,6 +576,7 @@ function inputObjectsInput(column, data, options, url){
     .replace('_OPTIONS_', existingOptions)
     .replace('_EXTRACLASS_', extraClass)
     .replace('_TITLE_', titleText)
+    .replace('_MULTIPLE?_', hasMultipleInputs)
     .replace('_ALLOW_FREE_TEXT_', false);
   }
 }
@@ -599,6 +600,7 @@ function cvListObjectsInput(column, data, options, url){
     .replace('_OPTIONS_', existingOptions)
     .replace('_EXTRACLASS_', extraClass)
     .replace('_TITLE_', titleText)
+    .replace('_MULTIPLE?_', 'multiple="multiple"')
     .replace('_ALLOW_FREE_TEXT_', allowNewItems);
   }
 }
diff --git a/app/assets/javascripts/single_page/index.js.erb b/app/assets/javascripts/single_page/index.js.erb
index ec97c201fb..8b93dd1657 100644
--- a/app/assets/javascripts/single_page/index.js.erb
+++ b/app/assets/javascripts/single_page/index.js.erb
@@ -242,12 +242,12 @@ async function exportToExcel(tableName, studyId, assayId, sampleTypeId) {
       const val = row[j];
 
       // Check whether sample has one or more hidden Inputs or if sample is completely hidden
-      if (attr.toLowerCase().includes('input')) {
-        if (Array.isArray(val)){
-          hasHiddenInputs = val.some(input => input.title === '#HIDDEN'); // Sample has hidden inputs
-        } else {
-          hasHiddenInputs = val === '#HIDDEN'; // Sample is completely hidden
-        }
+      if (Array.isArray(val)){
+        hasHiddenInputs = hasHiddenInputs || val.some(input => input.title === '#HIDDEN'); // Sample has hidden Registered Samples in list
+      } else if(typeof val === 'object' && val !== null && 'title' in val){
+        hasHiddenInputs = hasHiddenInputs || (val.title === '#HIDDEN'); // Sample has hidden Registered Sample
+      } else {
+        hasHiddenInputs = hasHiddenInputs || (val === '#HIDDEN'); // Sample is completely hidden
       }
 
       // The source inputs are wrapped in an object and must be unwrapped first
diff --git a/app/assets/javascripts/templates.js b/app/assets/javascripts/templates.js
index 11bea4dea6..2584f23ed6 100644
--- a/app/assets/javascripts/templates.js
+++ b/app/assets/javascripts/templates.js
@@ -11,7 +11,7 @@ Templates.init = function (elem) {
   const columnDefs = [
     { orderable: false, targets: [0, 7, 11] },
     {
-      targets: [3, 4, 9, 10],
+      targets: [3, 4, 5, 10, 11, 13],
       visible: false,
       searchable: false
     },
@@ -33,6 +33,7 @@ Templates.init = function (elem) {
     { title: "Description", width: "40%" },
     { title: "attribute_type_id" },
     { title: "cv_id" },
+    { title: "allow_cv_free_text" },
     { title: "Unit", width: "5%" },
     { title: "Data type", width: "10%" },
     {
@@ -56,7 +57,8 @@ Templates.init = function (elem) {
           ? ""
           : '<a class="btn btn-danger btn-sm" href="javascript:void(0)" onClick="remove(this)">Remove</a>';
       }
-    }
+    },
+    { title: "linked sample type id", width: "10%" }
   ];
 
   Templates.table = elem.DataTable({
@@ -115,13 +117,15 @@ Templates.mapData = (data) =>
     item.description,
     item.attribute_type_id,
     item.cv_id,
+    item.allow_cv_free_text,
     item.unit_id,
     item.data_type,
     item.is_title,
     item.pid,
     item.pos,
     item.isa_tag_id,
-    item.isa_tag_title
+    item.isa_tag_title,
+    item.linked_sample_type_id
   ]);
 
 function loadFilterSelectors(data) {
@@ -183,14 +187,14 @@ function get_filtered_isa_tags(level) {
 function updateIsaTagSelect(template_level, attribute_row) {
   const isa_tags = get_filtered_isa_tags(template_level);
 
-  // Remove all options first, except blank one
-  $j(attribute_row).find('select[data-attr="isa_tag_title"] option:not([value=""])').each(function() {
+  // Remove all options first from the select items that were not disabled, except blank one
+  $j(attribute_row).find('select[data-attr="isa_tag_title"]:not(:disabled) option:not([value=""])').each(function() {
     $j(this).remove();
   });
 
   // Append filtered option to a new attribute row
   $j.each(isa_tags, function (i, tag) {
-    $j(attribute_row).find('select[data-attr="isa_tag_title"]').append($j('<option>', {
+    $j(attribute_row).find('select[data-attr="isa_tag_title"]:not(:disabled)').append($j('<option>', {
       value: tag.value,
       text: tag.text
     }));
@@ -231,32 +235,36 @@ const applyTemplate = () => {
     });
     index++;
 
+    const isInputRow = row[7] === 'Registered Sample List' && row[1].includes('Input') && row[11] === null
     newRow = $j(newRow.replace(/replace-me/g, index));
-
     $j(newRow).find('[data-attr="required"]').prop("checked", row[0]);
     $j(newRow).find('[data-attr="title"]').val(row[1]);
     $j(newRow).find('[data-attr="description"]').val(row[2]);
     $j(newRow).find('[data-attr="type"]').val(row[3]);
     $j(newRow).find('[data-attr="cv_id"]').val(row[4]);
-    $j(newRow).find('[data-attr="unit"]').val(row[5]);
-    $j(newRow).find(".sample-type-is-title").prop("checked", row[7]);
-    $j(newRow).find('[data-attr="pid"]').val(row[8]);
-    $j(newRow).find('[data-attr="isa_tag_id"]').val(row[10]);
-    $j(newRow).find('[data-attr="isa_tag_title"]').val(row[10]);
+    $j(newRow).find('[data-attr="allow_cv_free_text"]').prop("checked", row[5]);
+    $j(newRow).find('[data-attr="unit"]').val(row[6]);
+    $j(newRow).find(".sample-type-is-title").prop("checked", row[8]);
+    $j(newRow).find('[data-attr="pid"]').val(row[9]);
+    $j(newRow).find('[data-attr="isa_tag_id"]').val(row[11]);
+    $j(newRow).find('[data-attr="isa_tag_title"]').val(row[11]);
     $j(newRow).find('[data-attr="isa_tag_title"]').attr('disabled', true);
 
     // Show the CV block if cv_id is not empty
     if (row[4]) $j(newRow).find(".controlled-vocab-block").show();
 
-    // Show the sample-type-block block if type is SEEK sample
-    const is_seek_sample = $j(newRow)
-      .find(".sample-type-attribute-type")
-      .find(":selected")
-      .data("is-seek-sample");
-    if (is_seek_sample) {
-      // Select the first item by default and hide the row
-      $j(newRow).find(".linked-sample-type-selection optgroup option:first").attr("selected", "selected");
+    // If input-row: use input-sample-type-id
+    // else: set the linked_sample_type_id
+    if (isInputRow) {
+      const previousSampleTypeId = $j('#isa_assay_input_sample_type_id').val();
+      if(previousSampleTypeId){
+        $j(newRow).find('.linked-sample-type-selection').val(previousSampleTypeId)
+      } else {
+        $j(newRow).find(".linked-sample-type-selection optgroup option:first").attr("selected", "selected");
+      }
       $j(newRow).hide();
+    } else {
+      $j(newRow).find('.linked-sample-type-selection').val(row[13])
     }
 
     $j(`${attribute_table} ${addAttributeRow}`).before(newRow);
diff --git a/app/controllers/single_pages_controller.rb b/app/controllers/single_pages_controller.rb
index 6bc8b6b9c8..e25a7db2c6 100644
--- a/app/controllers/single_pages_controller.rb
+++ b/app/controllers/single_pages_controller.rb
@@ -162,6 +162,10 @@ def upload_samples
       sa_attr.title if sa_attr.sample_attribute_type.base_type == Seek::Samples::BaseType::SEEK_SAMPLE_MULTI
     end
 
+    @registered_sample_fields = @sample_type.sample_attributes.map do |sa_attr|
+      sa_attr.title if sa_attr.sample_attribute_type.base_type == Seek::Samples::BaseType::SEEK_SAMPLE
+    end
+
     @cv_list_fields = @sample_type.sample_attributes.map do |sa_attr|
       sa_attr.title if sa_attr.sample_attribute_type.base_type == Seek::Samples::BaseType::CV_LIST
     end
@@ -266,6 +270,12 @@ def generate_excel_samples(samples_data, sample_fields, sample_type_attributes)
             subsample
           end
           obj.merge!(sample_fields[i] => parsed_excel_input_samples)
+        elsif @registered_sample_fields.include?(sample_fields[i])
+          parsed_excel_registered_sample = JSON.parse(excel_sample[i].gsub(/"=>/x, '":'))
+          unless Sample.find(parsed_excel_registered_sample['id'])&.authorized_for_view?
+            raise "Unauthorized Sample was detected in spreadsheet: #{parsed_excel_registered_sample.inspect}"
+          end
+          obj.merge!(sample_fields[i] => parsed_excel_registered_sample)
         elsif @cv_list_fields.include?(sample_fields[i])
           parsed_cv_terms = JSON.parse(excel_sample[i])
           # CV validation for CV_LIST attributes
diff --git a/app/controllers/templates_controller.rb b/app/controllers/templates_controller.rb
index b75b1d2743..7ac3d984d2 100644
--- a/app/controllers/templates_controller.rb
+++ b/app/controllers/templates_controller.rb
@@ -157,7 +157,8 @@ def template_params
                                        template_attributes_attributes: %i[id title pos required description
                                                                           sample_attribute_type_id isa_tag_id is_title
                                                                           sample_controlled_vocab_id pid
-                                                                          unit_id _destroy] })
+                                                                          unit_id _destroy allow_cv_free_text
+                                                                          linked_sample_type_id] })
   end
 
   def find_template
diff --git a/app/helpers/dynamic_table_helper.rb b/app/helpers/dynamic_table_helper.rb
index 8369da6315..6bdacab953 100644
--- a/app/helpers/dynamic_table_helper.rb
+++ b/app/helpers/dynamic_table_helper.rb
@@ -30,9 +30,12 @@ def link_sequence(sample_type)
   end
 
   def dt_rows(sample_type)
+    registered_sample_attributes = sample_type.sample_attributes.select { |sa| sa.sample_attribute_type.base_type == Seek::Samples::BaseType::SEEK_SAMPLE }
+    registered_sample_multi_attributes = sample_type.sample_attributes.select { |sa| sa.sample_attribute_type.base_type == Seek::Samples::BaseType::SEEK_SAMPLE_MULTI }
+
     sample_type.samples.map do |s|
       if s.can_view?
-        sanitized_json_metadata = hide_unauthorized_inputs(JSON(s.json_metadata))
+        sanitized_json_metadata = hide_unauthorized_inputs(JSON(s.json_metadata), registered_sample_attributes, registered_sample_multi_attributes)
         ['', s.id, s.uuid] +
           sanitized_json_metadata.values
       else
@@ -42,11 +45,20 @@ def dt_rows(sample_type)
     end
   end
 
-  def hide_unauthorized_inputs(json_metadata)
-    input_key = json_metadata.keys.detect { |jmdk| jmdk.downcase.include? 'input' }
+  def hide_unauthorized_inputs(json_metadata, registered_sample_attributes, registered_sample_multi_attributes)
+    registered_sample_multi_attributes.map(&:title).each do |rsma|
+      json_metadata = transform_registered_sample_multi(json_metadata, rsma)
+    end
+    registered_sample_attributes.map(&:title).each do |rma|
+      json_metadata = transform_registered_sample_single(json_metadata, rma)
+    end
+
+    json_metadata
+  end
 
+  def transform_registered_sample_multi(json_metadata, input_key)
     unless input_key.nil?
-      json_metadata[input_key] = json_metadata[input_key].map do |input|
+        json_metadata[input_key] = json_metadata[input_key].map do |input|
         input_exists = Sample.where(id: input['id']).any?
         if !input_exists
           input
@@ -57,7 +69,21 @@ def hide_unauthorized_inputs(json_metadata)
         end
       end
     end
+    json_metadata
+  end
 
+  def transform_registered_sample_single(json_metadata, input_key)
+    unless input_key.nil?
+      input = json_metadata[input_key]
+      input_exists = Sample.where(id: input['id']).any?
+      if !input_exists
+        json_metadata[input_key] = input
+      elsif Sample.find(input['id']).can_view?
+        json_metadata[input_key] = input
+      else
+        json_metadata[input_key] = { 'id' => input['id'], 'type' => input['type'], 'title' => '#HIDDEN' }
+      end
+    end
     json_metadata
   end
 
@@ -66,10 +92,12 @@ def dt_cols(sample_type)
       attribute = { title: a.title, name: sample_type.id.to_s, required: a.required, description: a.description,
                     is_title: a.is_title }
       attribute.merge!({ cv_id: a.sample_controlled_vocab_id }) unless a.sample_controlled_vocab_id.blank?
+      is_seek_sample = a.sample_attribute_type.base_type == Seek::Samples::BaseType::SEEK_SAMPLE
       is_seek_multi_sample = a.sample_attribute_type.base_type == Seek::Samples::BaseType::SEEK_SAMPLE_MULTI
       is_cv_list = a.sample_attribute_type.base_type == Seek::Samples::BaseType::CV_LIST
       cv_allows_free_text =  a.allow_cv_free_text
       attribute.merge!({ multi_link: true, linked_sample_type: a.linked_sample_type.id }) if is_seek_multi_sample
+      attribute.merge!({ multi_link: false, linked_sample_type: a.linked_sample_type.id }) if is_seek_sample
       attribute.merge!({is_cv_list: , cv_allows_free_text:}) if is_cv_list
       attribute
     end
diff --git a/app/helpers/templates_helper.rb b/app/helpers/templates_helper.rb
index 0e2b451828..80f97a8734 100644
--- a/app/helpers/templates_helper.rb
+++ b/app/helpers/templates_helper.rb
@@ -63,6 +63,10 @@ def template_attribute_details_table(attributes)
   def template_attribute_type_link(template_attribute)
     type = template_attribute.sample_attribute_type.title
 
+    if template_attribute.sample_attribute_type.seek_sample? || template_attribute.sample_attribute_type.seek_sample_multi?
+      type += ' - ' + link_to(template_attribute.linked_sample_type&.title, template_attribute.linked_sample_type)
+    end
+
     if template_attribute.sample_attribute_type.controlled_vocab?
       type += ' - ' + link_to(template_attribute.sample_controlled_vocab.title,
                               template_attribute.sample_controlled_vocab)
@@ -75,6 +79,7 @@ def map_template_attributes(attribute)
       attribute_type_id: attribute.sample_attribute_type_id,
       data_type: SampleAttributeType.find(attribute.sample_attribute_type_id)&.title,
       cv_id: attribute.sample_controlled_vocab_id,
+      allow_cv_free_text: attribute.allow_cv_free_text,
       title: attribute.title,
       is_title: attribute.is_title,
       short_name: attribute.short_name,
@@ -84,7 +89,8 @@ def map_template_attributes(attribute)
       unit_id: attribute.unit_id,
       pos: attribute.pos,
       isa_tag_id: attribute.isa_tag_id,
-      isa_tag_title: attribute.isa_tag&.title
+      isa_tag_title: attribute.isa_tag&.title,
+      linked_sample_type_id: attribute.linked_sample_type_id
     }
   end
 end
diff --git a/app/models/template.rb b/app/models/template.rb
index 39dcc0ee6d..ede505d782 100644
--- a/app/models/template.rb
+++ b/app/models/template.rb
@@ -33,11 +33,17 @@ def resolve_inconsistencies
   end
 
   def validate_template_attributes
-    errors.add(:base, '[Template attribute]: Some attributes are missing ISA tags') unless none_empty_isa_tag
+    unless attributes_with_empty_isa_tag.none?
+      attributes_with_empty_isa_tag.map do |attribute|
+        errors.add("[#{:template_attributes}]:", "Attribute '#{attribute.title}' is missing an ISA tag")
+      end
+    end
+
     if test_tag_occurences.any?
       test_tag_occurences.map do |tag|
-        errors.add(:base,
-                   "[Template attribute]: The <em>'#{tag}'</em> ISA tag is not allowed to be used more then once".html_safe)
+        attributes_with_duplicate_tags = template_attributes.select { |tat| tat.isa_tag&.title == tag }.map(&:title)
+        errors.add("[#{:template_attributes}]:",
+                   "The '#{tag}' ISA Tag was used in these attributes => #{attributes_with_duplicate_tags.inspect}. This ISA tag is not allowed to be used more then once!")
       end
     end
 
@@ -56,8 +62,8 @@ def resolve_controlled_vocabs_inconsistencies
     end
   end
 
-  def none_empty_isa_tag
-    template_attributes.select { |ta| !ta.title.include?('Input') && ta.isa_tag_id.nil? }.none?
+  def attributes_with_empty_isa_tag
+    template_attributes.select { |ta| !ta.title.include?('Input') && ta.isa_tag_id.nil? }
   end
 
   def test_tag_occurences
@@ -74,7 +80,7 @@ def test_input_occurence
 
   def test_attribute_title_uniqueness
     template_attribute_titles = template_attributes.map(&:title).uniq
-    duplicate_attributes = template_attribute_titles.map do |tat|
+    template_attribute_titles.map do |tat|
       if template_attributes.select { |ta| ta.title.downcase == tat.downcase }.map(&:title).count > 1
         errors.add(:template_attributes, "Attribute names must be unique, there are duplicates of #{tat}")
         return tat
diff --git a/app/models/template_attribute.rb b/app/models/template_attribute.rb
index 8e8d4b1ee2..65574d7855 100644
--- a/app/models/template_attribute.rb
+++ b/app/models/template_attribute.rb
@@ -4,6 +4,8 @@ class TemplateAttribute < ApplicationRecord
   belongs_to :template, inverse_of: :template_attributes
   belongs_to :unit
   belongs_to :isa_tag
+  belongs_to :linked_sample_type, class_name: 'SampleType'
+
   validates :title, presence: true
 
   before_save :default_pos
diff --git a/app/views/isa_studies/_sample_types_form.html.erb b/app/views/isa_studies/_sample_types_form.html.erb
index 8889467eb3..b1d7bf1ebd 100644
--- a/app/views/isa_studies/_sample_types_form.html.erb
+++ b/app/views/isa_studies/_sample_types_form.html.erb
@@ -5,6 +5,9 @@
 <% main_field_name = id_suffix[1..-1] %>
 <% isa_element ||= "study" %>
 
+<span id='modal-dialogues'>
+    <%= sample_controlled_vocab_model_dialog('cv-modal') %>
+</span>
 <%=  f.fields_for main_field_name, sample_type do |field| %>
 
 	<% unless action == :edit %>
diff --git a/app/views/isa_studies/new.html.erb b/app/views/isa_studies/new.html.erb
index feace3fc75..38f08dc616 100644
--- a/app/views/isa_studies/new.html.erb
+++ b/app/views/isa_studies/new.html.erb
@@ -1,9 +1,6 @@
 <% if Investigation.authorized_for('view').none? %>
   <%= button_link_to("New #{t('investigation')}", 'arrow_right', new_investigation_path) -%>
 <% else %>
-  <span id='modal-dialogues'>
-    	<%= sample_controlled_vocab_model_dialog('cv-modal') %>
-	</span>
   <h1>New <%=t('isa_study')%></h1>
 
   <%= render :partial => "templates/template_modal" -%>
diff --git a/app/views/sample_types/_sample_attribute_form.html.erb b/app/views/sample_types/_sample_attribute_form.html.erb
index 8aa5493470..69004977cb 100644
--- a/app/views/sample_types/_sample_attribute_form.html.erb
+++ b/app/views/sample_types/_sample_attribute_form.html.erb
@@ -22,7 +22,7 @@
 <% allow_name_change = constraints.allow_name_change?(sample_attribute) %>
 <% seek_sample_multi = sample_attribute&.seek_sample_multi? %>
 <% link_to_self = sample_attribute && sample_attribute.deferred_link_to_self %>
-<% hide_seek_sample_multi = seek_sample_multi && displaying_single_page? %>
+<% hide_seek_sample_multi = seek_sample_multi && displaying_single_page? && sample_attribute&.isa_tag.blank? && sample_attribute&.title.downcase.include?('input') %>
 <% isa_tags_options = IsaTag.all.map { |it| [it.title, it.id] } %>
 <% display_isa_tag ||= false %>
 <% isa_tag_id = sample_attribute&.isa_tag_id %>
@@ -73,7 +73,7 @@
       <div>
         <label>
           <%= hidden_field_tag "#{field_name_prefix}[allow_cv_free_text]", '0'  %>
-          <%= check_box_tag "#{field_name_prefix}[allow_cv_free_text]", '1', allow_cv_free_text  %>
+          <%= check_box_tag "#{field_name_prefix}[allow_cv_free_text]", '1', allow_cv_free_text, data: { attr: 'allow_cv_free_text' } %>
           <%= t('samples.allow_free_text_checkbox_label') %> <%= allow_free_text_help_icon %>
         </label>
       </div>
diff --git a/app/views/single_pages/_duplicate_samples_panel.html.erb b/app/views/single_pages/_duplicate_samples_panel.html.erb
index a5d6d213c9..b05064fdd6 100644
--- a/app/views/single_pages/_duplicate_samples_panel.html.erb
+++ b/app/views/single_pages/_duplicate_samples_panel.html.erb
@@ -20,15 +20,17 @@
               <% if @multiple_input_fields.include?(key)%>
                 <td>
                   <% val.each do |sub_sample| %>
-                    <span class="badge", title='ID: <%= sub_sample['id'] %>'><%= sub_sample['title'] %></span>
+                    <span class="badge", title='ID: <%= sub_sample['id'] %>' data-attr_type="seek-sample-multi"><%= sub_sample['title'] %></span>
                   <% end %>
                 </td>
               <% elsif @cv_list_fields.include?(key) %>
                 <td>
                   <% val.each do |cv_term| %>
-                    <span class="label label-default", title='<%= cv_term %>'><%= cv_term %></span>
+                    <span class="label label-default", title='<%= cv_term %>' data-attr_type="cv-list"><%= cv_term %></span>
                   <% end %>
                 </td>
+              <% elsif @registered_sample_fields.include?(key) %>
+                <td><span class="badge", title='<%= val['id'] %>' data-attr_type="seek-sample"><%= val['title'] %></span></td>
               <% else %>
                 <td id='<%= "#{dupl_sample['duplicate']['id']}[#{key}]" %>' ><%= val %></td>
               <% end %>
@@ -49,6 +51,8 @@
                         <span class="label label-default", title='<%= cv_term %>'><%= cv_term %></span>
                       <% end %>
                     </td>
+                  <% elsif @registered_sample_fields.include?(key) %>
+                    <td><span class="badge", title='<%= val['id'] %>'><%= val['title'] %></span></td>
                   <% else %>
                     <td><%= val%></td>
                   <% end %>
diff --git a/app/views/single_pages/_new_samples_panel.html.erb b/app/views/single_pages/_new_samples_panel.html.erb
index 6f57cb0d87..1b163ec3da 100644
--- a/app/views/single_pages/_new_samples_panel.html.erb
+++ b/app/views/single_pages/_new_samples_panel.html.erb
@@ -21,15 +21,19 @@
                 <% if @multiple_input_fields.include?(key)%>
                   <td id='<%= "new-sample-#{new_sample_id}[#{key}]" %>' >
                     <% val.each do |sub_sample| %>
-                      <span class="badge", title='ID: <%= sub_sample['id'] %>'><%= sub_sample['title'] %></span>
+                      <span class="badge", title='ID: <%= sub_sample['id'] %>' data-attr_type="seek-sample-multi"><%= sub_sample['title'] %></span>
                     <% end %>
                   </td>
                 <% elsif @cv_list_fields.include?(key) %>
                   <td id='<%= "new-sample-#{new_sample_id}[#{key}]" %>' >
                     <% val.each do |cv_term| %>
-                      <span class="label label-default", title='<%= cv_term %>'><%= cv_term %></span>
+                      <span class="label label-default", title='<%= cv_term %>' data-attr_type="cv-list"><%= cv_term %></span>
                     <% end %>
                   </td>
+                <% elsif @registered_sample_fields.include?(key) %>
+                  <td id='<%= "new-sample-#{new_sample_id}[#{key}]" %>' >
+                    <span class="badge", title='<%= val['id'] %>' data-attr_type="seek-sample"><%= val['title'] %></span>
+                  </td>
                 <% else %>
                   <td id='<%= "new-sample-#{new_sample_id}[#{key}]" %>' ><%= val %></td>
                 <% end %>
diff --git a/app/views/single_pages/_update_samples_panel.html.erb b/app/views/single_pages/_update_samples_panel.html.erb
index 856169798c..4349edd71b 100644
--- a/app/views/single_pages/_update_samples_panel.html.erb
+++ b/app/views/single_pages/_update_samples_panel.html.erb
@@ -20,15 +20,19 @@
                 <% if @multiple_input_fields.include?(key)%>
                   <td class='<%= (val != db_sample[key]) ? "warning" : "default" %>' id='<%= "update-sample-#{update_sample['id']}[#{key}]"%>' >
                     <% val.each do |sub_sample| %>
-                      <span class="badge", title='ID: <%= sub_sample['id'] %>'><%= sub_sample['title'] %></span>
+                      <span class="badge" title='ID: <%= sub_sample['id'] %>' data-attr_type="seek-sample-multi"><%= sub_sample['title'] %></span>
                     <% end %>
                   </td>
                 <% elsif @cv_list_fields.include?(key) %>
                   <td class='<%= (val != db_sample[key]) ? "warning" : "default" %>' id='<%= "update-sample-#{update_sample['id']}[#{key}]"%>' >
                     <% val.each do |cv_term| %>
-                      <span class="label label-default", title='<%= cv_term %>'><%= cv_term %></span>
+                      <span class="label label-default" title='<%= cv_term %>' data-attr_type="cv-list"><%= cv_term %></span>
                     <% end %>
                   </td>
+                <% elsif @registered_sample_fields.include?(key) %>
+                  <td class='<%= (val != db_sample[key]) ? "warning" : "default" %>' id='<%= "update-sample-#{update_sample['id']}[#{key}]"%>'>
+                    <span class="badge" title='<%= val['id'] %>' data-attr_type="seek-sample"><%= val['title'] %></span>
+                  </td>
                 <% else %>
                   <td class='<%= (val != db_sample[key]) ? "warning" : "default" %>' id='<%= "update-sample-#{update_sample['id']}[#{key}]"%>' ><%= val %></td>
                 <% end %>
@@ -41,15 +45,17 @@
                 <% if @multiple_input_fields.include?(key)%>
                   <td>
                     <% val.each do |sub_sample| %>
-                      <span class="badge", title='ID: <%= sub_sample['id'] %>'><%= sub_sample['title'] %></span>
+                      <span class="badge" title='ID: <%= sub_sample['id'] %>'><%= sub_sample['title'] %></span>
                     <% end %>
                   </td>
                 <% elsif @cv_list_fields.include?(key) %>
                   <td>
                     <% val.each do |cv_term| %>
-                      <span class="label label-default", title='<%= cv_term %>'><%= cv_term %></span>
+                      <span class="label label-default" title='<%= cv_term %>'><%= cv_term %></span>
                     <% end %>
                   </td>
+                <% elsif @registered_sample_fields.include?(key) %>
+                  <td><span class="badge" title='<%= val['id'] %>'><%= val['title'] %></span></td>
                 <% else %>
                   <td><%= val %></td>
                 <% end %>
diff --git a/app/views/single_pages/sample_upload_content.html.erb b/app/views/single_pages/sample_upload_content.html.erb
index 5ab66142f4..9102c2d905 100644
--- a/app/views/single_pages/sample_upload_content.html.erb
+++ b/app/views/single_pages/sample_upload_content.html.erb
@@ -122,16 +122,20 @@
     cells = $j(row).find('td:not(:has(".danger"))').toArray();
     samplesObj = {};
     cells.map(function(cell){
-      val = cell.textContent;
-      key = cell.id.match(/\[.*\]/)[0].replace('[', "").replace("]", '');
-      const multiInputfields = $j(cell).find('span[class*="badge"]').toArray();
-      const cvListFields = $j(cell).find('span[class*="label"]').toArray();
+      const val = cell.textContent;
+      const key = cell.id.match(/\[.*\]/)[0].replace('[', "").replace("]", '');
+      const multiInputfields = $j(cell).find('span[data-attr_type="seek-sample-multi"]').toArray();
+      const cvListFields = $j(cell).find('span[data-attr_type="cv-list"]').toArray();
+      const seekSample = $j(cell).find('span[data-attr_type="seek-sample"]');
+
       if (multiInputfields.length > 0 ){
         const inputIds = multiInputfields.map(is => is.title.split(" ").pop()).join(',');
         samplesObj[key] = inputIds;
       } else if (cvListFields.length > 0){
         cvTerms = cvListFields.map(cvt => cvt.title)
         samplesObj[key] = cvTerms;
+      } else if (seekSample.length > 0) {
+        samplesObj[key] = seekSample[0].title
       } else {
         samplesObj[key] = val;
       }
diff --git a/app/views/templates/_template_attribute_form.html.erb b/app/views/templates/_template_attribute_form.html.erb
index e5a7d3b6ec..7523991b3f 100644
--- a/app/views/templates/_template_attribute_form.html.erb
+++ b/app/views/templates/_template_attribute_form.html.erb
@@ -10,6 +10,7 @@
 <% attribute_type_id = template_attribute ? template_attribute.sample_attribute_type_id : nil %>
 <% sample_controlled_vocab_id = template_attribute ? template_attribute.sample_controlled_vocab_id : nil %>
 <% unit_id = template_attribute ? template_attribute.unit_id : nil %>
+<% linked_sample_type_id = template_attribute&.linked_sample_type_id %>
 <% field_name_prefix = "template[template_attributes_attributes][#{index}]" %>
 <% seek_sample_multi = template_attribute.try(:seek_sample_multi?) %>
 <% is_title = template_attribute ? template_attribute.is_title : false %>
@@ -17,6 +18,7 @@
 <% isa_tag_id = template_attribute&.isa_tag_id %>
 <% isa_tag_title = template_attribute&.isa_tag&.title %>
 <% is_parent_attribute ||= false %>
+<% allow_cv_free_text = template_attribute&.allow_cv_free_text || false %>
 
 <tr class="sample-attribute <%= 'success' if template_attribute.nil? -%>" data-index="<%= index-%>">
   <th scope="row" class="attribute-position">
@@ -45,17 +47,25 @@
   <td>
     <%= select_tag "#{field_name_prefix}[sample_attribute_type_id]",
                    options_for_select(SampleAttributeType.all.sort_by(&:title).sort_by { |t| t.default? ? 0 : 1 }.map do |t|
-                     [t.title, t.id,{'data-is-cv': t.controlled_vocab?,'data-is-seek-sample': t.seek_sample? || t.seek_sample_multi? }]
+                     [t.title, t.id,{'data-use-cv': t.controlled_vocab?,'data-is-seek-sample': t.seek_sample? || t.seek_sample_multi? }]
                    end, attribute_type_id),
                    class: 'form-control sample-type-attribute-type', data: {attr: "type"} %>
 
-    <div class='controlled-vocab-block' style="<%= 'display:none;' unless template_attribute.try(:controlled_vocab?) %>">
+    <div class='controlled-vocab-block' style="<%= 'display:none;' unless template_attribute.try(:controlled_vocab?) || template_attribute.try(:seek_cv_list?) %>">
       <br/>
       <%= select_tag "#{field_name_prefix}[sample_controlled_vocab_id]",
                      options_for_select(SampleControlledVocab.all.map { |scv| [scv.title, scv.id, {'data-editable': scv.can_edit?}] },
                       sample_controlled_vocab_id),include_blank: true,
                       class: 'form-control controlled-vocab-selection', data: {attr: "cv_id"} %>
 
+      <div>
+        <label>
+          <%= hidden_field_tag "#{field_name_prefix}[allow_cv_free_text]", '0'  %>
+          <%= check_box_tag "#{field_name_prefix}[allow_cv_free_text]", '1', allow_cv_free_text  %>
+          <%= t('samples.allow_free_text_checkbox_label') %> <%= allow_free_text_help_icon %>
+        </label>
+      </div>
+
       <%= button_link_to('Edit', 'edit', '#', class:'cv-edit-button', disabled: true, target: :_blank) %>
       <%= create_sample_controlled_vocab_modal_button  %>
 
@@ -73,7 +83,7 @@
         end
       %>
       <%= select_tag "#{field_name_prefix}[linked_sample_type_id]",
-                     grouped_options_for_select(options, nil),
+                     grouped_options_for_select(options, linked_sample_type_id),
                      include_blank: true,
                      class: 'form-control linked-sample-type-selection' %>
     </div>
diff --git a/app/views/templates/edit.html.erb b/app/views/templates/edit.html.erb
index 3fe83a434e..70f37c2266 100644
--- a/app/views/templates/edit.html.erb
+++ b/app/views/templates/edit.html.erb
@@ -13,7 +13,7 @@
       .addClass('hidden'); // Hide the row
 
     // Update the ISA tag select
-    const attribute_row = "#new-attribute-row"
+    const attribute_row = ".sample-attribute";
     updateIsaTagSelect("<%= @template.level %>", attribute_row);
   });
 </script>
diff --git a/app/views/templates/new.html.erb b/app/views/templates/new.html.erb
index a0b617a870..aaa65faa53 100644
--- a/app/views/templates/new.html.erb
+++ b/app/views/templates/new.html.erb
@@ -5,8 +5,7 @@
 <p>
   Templates can be defined manually through the form below or based on repository templates.
 </p>
-
-<div class="asset_form"> 
+<div class="asset_form">
   <%= render partial: 'templates/form', locals: { tab: tab } %>
 </div>
 
@@ -22,7 +21,7 @@
       .addClass('hidden'); // Hide the row
 
     // Update the ISA tag select
-    const attribute_row = "#new-attribute-row"
+    const attribute_row = ".sample-attribute";
     updateIsaTagSelect("<%= @template.level %>", attribute_row);
   });
 </script>
diff --git a/db/migrate/20231218133053_add_linked_sample_type_to_templates.rb b/db/migrate/20231218133053_add_linked_sample_type_to_templates.rb
new file mode 100644
index 0000000000..e6d6da6ff5
--- /dev/null
+++ b/db/migrate/20231218133053_add_linked_sample_type_to_templates.rb
@@ -0,0 +1,5 @@
+class AddLinkedSampleTypeToTemplates < ActiveRecord::Migration[6.1]
+  def change
+    add_column :template_attributes, :linked_sample_type_id, :integer
+  end
+end
diff --git a/db/schema.rb b/db/schema.rb
index fb7fd16c3c..22e12632eb 100644
--- a/db/schema.rb
+++ b/db/schema.rb
@@ -10,7 +10,7 @@
 #
 # It's strongly recommended that you check this file into your version control system.
 
-ActiveRecord::Schema.define(version: 2023_12_18_113249) do
+ActiveRecord::Schema.define(version: 2023_12_18_133053) do
 
   create_table "activity_logs", id: :integer, force: :cascade do |t|
     t.string "action"
@@ -2098,6 +2098,7 @@
     t.integer "isa_tag_id"
     t.string "pid"
     t.boolean "allow_cv_free_text", default: false
+    t.integer "linked_sample_type_id"
     t.index ["template_id", "title"], name: "index_template_id_asset_id_title"
   end
 
diff --git a/db/seeds/008_miappe_custom_metadata.seeds.rb b/db/seeds/008_miappe_extended_metadata.seeds.rb
similarity index 64%
rename from db/seeds/008_miappe_custom_metadata.seeds.rb
rename to db/seeds/008_miappe_extended_metadata.seeds.rb
index c314b5dd50..c44742422d 100644
--- a/db/seeds/008_miappe_custom_metadata.seeds.rb
+++ b/db/seeds/008_miappe_extended_metadata.seeds.rb
@@ -1,40 +1,40 @@
 
 unless ExtendedMetadataType.where(title:'MIAPPE metadata v1.1', supported_type:'Investigation').any?
-  cmt = ExtendedMetadataType.new(title: 'MIAPPE metadata v1.1', supported_type:'Investigation')
-  cmt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'id', required:true, sample_attribute_type: SampleAttributeType.where(title:'String').first)
-  cmt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'submission_date', sample_attribute_type: SampleAttributeType.where(title:'Date').first)
-  cmt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'license', sample_attribute_type: SampleAttributeType.where(title:'String').first)
-  cmt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'miappe_version', required:true, sample_attribute_type: SampleAttributeType.where(title:'Integer').first)
-  cmt.save!
+  emt = ExtendedMetadataType.new(title: 'MIAPPE metadata v1.1', supported_type:'Investigation')
+  emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'id', required:true, sample_attribute_type: SampleAttributeType.where(title:'String').first)
+  emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'submission_date', sample_attribute_type: SampleAttributeType.where(title:'Date').first)
+  emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'license', sample_attribute_type: SampleAttributeType.where(title:'String').first)
+  emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'miappe_version', required:true, sample_attribute_type: SampleAttributeType.where(title:'Integer').first)
+  emt.save!
   puts 'Seeded Investigation extended metadata for MIAPPE v1.1'
 end
 
 unless ExtendedMetadataType.where(title:'MIAPPE metadata v1.1', supported_type:'Study').any?
-  cmt = ExtendedMetadataType.new(title: 'MIAPPE metadata v1.1', supported_type:'Study')
-  cmt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'id', required:true, sample_attribute_type: SampleAttributeType.where(title:'String').first)
-  cmt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'study_start_date', required:true, sample_attribute_type: SampleAttributeType.where(title:'Date').first)
-  cmt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'study_end_date', sample_attribute_type: SampleAttributeType.where(title:'Date').first)
-  cmt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'contact_institution', required:true, sample_attribute_type: SampleAttributeType.where(title:'String').first)
-  cmt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'geographic_location_country', required:true, sample_attribute_type: SampleAttributeType.where(title:'String').first)
-  cmt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'experimental_site_name', required:true, sample_attribute_type: SampleAttributeType.where(title:'String').first)
-  cmt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'latitude', sample_attribute_type: SampleAttributeType.where(title:'String').first)
-  cmt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'longitude', sample_attribute_type: SampleAttributeType.where(title:'String').first)
-  cmt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'altitude', sample_attribute_type: SampleAttributeType.where(title:'String').first)
-  cmt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'description_of_the_experimental_design', required:true, sample_attribute_type: SampleAttributeType.where(title:'String').first)
-  cmt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'type_of_experimental_design', sample_attribute_type: SampleAttributeType.where(title:'String').first)
-  cmt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'observation_unit_level_hierarchy', sample_attribute_type: SampleAttributeType.where(title:'String').first)
-  cmt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'observation_unit_description', required:true, sample_attribute_type: SampleAttributeType.where(title:'String').first)
-  cmt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'description_of_growth_facility', required:true, sample_attribute_type: SampleAttributeType.where(title:'String').first)
-  cmt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'type_of_growth_facility', sample_attribute_type: SampleAttributeType.where(title:'String').first)
-  cmt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'cultural_practices', sample_attribute_type: SampleAttributeType.where(title:'String').first)
+  emt = ExtendedMetadataType.new(title: 'MIAPPE metadata v1.1', supported_type:'Study')
+  emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'id', required:true, sample_attribute_type: SampleAttributeType.where(title:'String').first)
+  emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'study_start_date', required:true, sample_attribute_type: SampleAttributeType.where(title:'Date').first)
+  emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'study_end_date', sample_attribute_type: SampleAttributeType.where(title:'Date').first)
+  emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'contact_institution', required:true, sample_attribute_type: SampleAttributeType.where(title:'String').first)
+  emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'geographic_location_country', required:true, sample_attribute_type: SampleAttributeType.where(title:'String').first)
+  emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'experimental_site_name', required:true, sample_attribute_type: SampleAttributeType.where(title:'String').first)
+  emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'latitude', sample_attribute_type: SampleAttributeType.where(title:'String').first)
+  emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'longitude', sample_attribute_type: SampleAttributeType.where(title:'String').first)
+  emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'altitude', sample_attribute_type: SampleAttributeType.where(title:'String').first)
+  emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'description_of_the_experimental_design', required:true, sample_attribute_type: SampleAttributeType.where(title:'String').first)
+  emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'type_of_experimental_design', sample_attribute_type: SampleAttributeType.where(title:'String').first)
+  emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'observation_unit_level_hierarchy', sample_attribute_type: SampleAttributeType.where(title:'String').first)
+  emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'observation_unit_description', required:true, sample_attribute_type: SampleAttributeType.where(title:'String').first)
+  emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'description_of_growth_facility', required:true, sample_attribute_type: SampleAttributeType.where(title:'String').first)
+  emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'type_of_growth_facility', sample_attribute_type: SampleAttributeType.where(title:'String').first)
+  emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'cultural_practices', sample_attribute_type: SampleAttributeType.where(title:'String').first)
 
-  cmt.save!
+  emt.save!
   puts 'Seeded Study extended metadata for MIAPPE v1.1'
 end
 
 unless ExtendedMetadataType.where(title:'MIAPPE metadata v1.1', supported_type:'Assay').any?
-  cmt = ExtendedMetadataType.new(title: 'MIAPPE metadata v1.1', supported_type: 'Assay')
-  cmt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'level', sample_attribute_type: SampleAttributeType.where(title:'String').first)
-  cmt.save!
+  emt = ExtendedMetadataType.new(title: 'MIAPPE metadata v1.1', supported_type: 'Assay')
+  emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'level', sample_attribute_type: SampleAttributeType.where(title:'String').first)
+  emt.save!
   puts 'Seeded Assay extended metadata for MIAPPE v1.1'
 end
\ No newline at end of file