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<option value="abstract">Abstract</option>
<option value="abstract-text">Abstract (text)</option>
</select>
</div>
<div class="include-supplemental-container">
<input type="checkbox" aria-label="Include MeSH and other data" name="include-supplemental" id="email-include-supplemental" class="email-include-supplemental">
<label for="email-include-supplemental" class="email-include-supplemental-label">MeSH and other data</label>
</div>
<div class="form-field recaptcha ">
<div class="g-recaptcha" id="id-recaptcha" data-sitekey="6LfsWHMdAAAAAClKbtOpjQ2pMjgsGxvv7NdZW9uI"></div>
</div>
<div id="captcha-error-message" class="usa-input-error-message captcha-validation-message" role="alert"></div>
<div class="action-panel-actions">
<button class="action-panel-submit"
type="submit"
data-loading-label="Sending..."
data-ga-category="save_share"
data-ga-action="email"
data-ga-label="send">
Send email
</button>
<button class="action-panel-cancel"
aria-label="Close 'Email citations' panel"
ref="linksrc=close_email_panel"
aria-controls="email-action-panel"
aria-expanded="false"
data-ga-category="save_share"
data-ga-action="email"
data-ga-label="cancel">
Cancel
</button>
</div>
<input type="hidden" name="email-search-details" value="" />
<input type="hidden" name="email-search-details-hash" value="0e42663a6c3bd85498fcb88798998fed7bfdc45d457db35281e41afe13cc0524" />
</form>
</div>
</div>
<div id="collections-action-panel"
class="collections-action-panel action-panel in-progress-dots-panel"
aria-hidden="true"
data-collections-open-panel-enabled="false"
data-collections-open-panel-url-hash="#open-collections-panel">
<div class="inner-wrap">
<h3 class="action-panel-heading">
Add to Collections
</h3>
<form id="collections-action-panel-form"
class="collections-action-panel-form action-panel-content action-form action-panel-smaller-selectors"
data-existing-collections-url="/list-existing-collections/"
data-add-to-existing-collection-url="/add-to-existing-collection/"
data-create-and-add-to-new-collection-url="/create-and-add-to-new-collection/"
data-get-article-ids-by-search-url="/get-article-ids-by-search/"
data-myncbi-max-collection-name-length="100"
data-add-to-collection-max-amount="1000"
data-collections-root-url="https://www.ncbi.nlm.nih.gov/myncbi/collections/">
<input type="hidden" name="csrfmiddlewaretoken" value="wy4H1UU6isureA9MUgzMMWI9ZqXXA6YaNlOMEKnsS3hV81fCxzcOg4eNxuF9tHwu">
<div class="choice-group" role="radiogroup">
<ul class="radio-group-items">
<li>
<input type="radio"
id="collections-action-panel-new"
class="collections-new"
name="collections"
value="new"
data-ga-category="save_share"
data-ga-action="collections"
data-ga-label="collections_radio_new">
<label for="collections-action-panel-new">Create a new collection</label>
</li>
<li>
<input type="radio"
id="collections-action-panel-existing"
class="collections-existing"
name="collections"
value="existing"
checked="true"
data-ga-category="save_share"
data-ga-action="collections"
data-ga-label="collections_radio_existing">
<label for="collections-action-panel-existing">Add to an existing collection</label>
</li>
</ul>
</div>
<div class="controls-wrapper">
<div class="action-panel-control-wrap new-collections-controls">
<label for="collections-action-panel-add-to-new" class="action-panel-label required-field-asterisk">
Name your collection:
</label>
<input
type="text"
name="add-to-new-collection"
id="collections-action-panel-add-to-new"
class="collections-action-add-to-new"
pattern="[^&quot;&amp;=&lt;&gt;\/]*" title="The following characters are not allowed in the Name field: &quot;&amp;=&lt;&gt;/"
maxlength="100"
data-ga-category="save_share"
data-ga-action="create_collection"
data-ga-label="non_favorties_collection">
<div class="collections-new-name-too-long usa-input-error-message selection-validation-message">
Name must be less than 100 characters
</div>
</div>
<div class="action-panel-control-wrap existing-collections-controls">
<label for="collections-action-panel-add-to-existing" class="action-panel-label">
Choose a collection:
</label>
<select id="collections-action-panel-add-to-existing"
class="action-panel-selector collections-action-add-to-existing"
data-ga-category="save_share"
data-ga-action="select_collection"
data-ga-label="($('#collections-action-add-to-existing').val() === 'Favorites') ? 'Favorites' : 'non_favorites_collection'">
</select>
<div class="collections-retry-load-on-error usa-input-error-message selection-validation-message">
Unable to load your collection due to an error<br>
<a href="#">Please try again</a>
</div>
</div>
</div>
<div class="action-panel-actions">
<button class="action-panel-submit"
type="submit"
data-loading-label="Adding..."
data-pinger-ignore
data-ga-category="save_share"
data-ga-action="collections"
data-ga-label="add">
Add
</button>
<button class="action-panel-cancel"
aria-label="Close 'Add to Collections' panel"
ref="linksrc=close_collections_panel"
aria-controls="collections-action-panel"
aria-expanded="false"
data-ga-category="save_share"
data-ga-action="collections"
data-ga-label="cancel">
Cancel
</button>
</div>
</form>
</div>
</div>
<div id="bibliography-action-panel"
class="bibliography-action-panel action-panel in-progress-dots-panel"
aria-hidden="true"
data-bibliography-open-panel-enabled="false"
data-bibliography-open-panel-url-hash="#open-bibliography-panel">
<div class="inner-wrap">
<h3 class="action-panel-heading">
Add to My Bibliography
</h3>
<form id="bibliography-action-panel-form"
class="bibliography-action-panel-form action-panel-content action-form action-panel-smaller-selectors"
data-add-to-bibliography-max-amount="100"
data-add-to-bibliography-batch-size="10"
data-bibliography-delegates-url="/list-bibliography-delegates/"
data-add-to-bibliography-url="/add-to-bibliography/"
data-get-article-ids-by-search-url="/get-article-ids-by-search/"
data-mybib-root-url="https://www.ncbi.nlm.nih.gov/myncbi/collections/mybibliography/">
<input type="hidden" name="csrfmiddlewaretoken" value="wy4H1UU6isureA9MUgzMMWI9ZqXXA6YaNlOMEKnsS3hV81fCxzcOg4eNxuF9tHwu">
<div class="action-panel-control-wrap bibliographies-controls">
<div class="choice-group">
<ul class="bibliographies-action-add radio-group-items">
<li>
<input name="bibliography" id="my-bibliography" class="my-bibliography" type="radio" checked/>
<label for="my-bibliography">My Bibliography</label>
</li>
</ul>
</div>
</div>
<div class="bibliographies-retry-load-on-error usa-input-error-message selection-validation-message">
Unable to load your delegates due to an error<br>
<a href="#">Please try again</a>
</div>
<div class="action-panel-actions">
<button class="action-panel-submit"
type="submit"
data-loading-label="Adding..."
data-pinger-ignore>
Add
</button>
<button class="action-panel-cancel"
aria-label="Close 'Add to bibliography' panel"
ref="linksrc=close_bibliography_panel"
aria-controls="bibliography-action-panel"
aria-expanded="false"
data-ga-category="save_share"
data-ga-action="mybib"
data-ga-label="cancel">
Cancel
</button>
</div>
</form>
</div>
</div>
<div id="saved-search-action-panel" class="saved-search-action-panel action-panel " aria-hidden="true"
data-saved-search-open-panel-enabled="false"
data-saved-search-open-panel-url-hash="#open-saved-search-panel">
<div class="inner-wrap">
<h2 class="action-panel-heading">
Your saved search
</h2>
<form id="saved-search-action-panel-form"
class="saved-search-action-panel-form action-panel-content action-form"
data-create-saved-search-url="/create-saved-search/"
data-try-search-terms-url="/try-search-term/"
data-saved-search-root-url="https://www.ncbi.nlm.nih.gov/myncbi/searches/">
<input type="hidden" name="csrfmiddlewaretoken" value="wy4H1UU6isureA9MUgzMMWI9ZqXXA6YaNlOMEKnsS3hV81fCxzcOg4eNxuF9tHwu">
<div class="action-panel-control-wrap">
<label for="saved-search-name" class="action-panel-label saved-search-name-label required-field-asterisk">
Name of saved search:
</label>
<input maxlength="200"
type="text"
name="saved-search-name"
id="saved-search-name"
class="saved-search-name"
value=""
required
pattern="[^&quot;&amp;=&lt;&gt;\/]*" title="The following characters are not allowed in the Name field: &quot;&amp;=&lt;&gt;/">
</div>
<div class="action-panel-control-wrap">
<label for="saved-search-term" class="action-panel-label required-field-asterisk">
Search terms:
</label>
<textarea name="saved-search-term" id="saved-search-term" class="saved-search-term" required></textarea>
</div>
<div class="test-search-term-wrap">
<a href="#" class="try-search-term">Test search terms</a>
</div>
<div class="choice-group action-panel-extra-margin-top">
<span class="action-panel-label" id="fieldset-label">
Would you like email updates of new search results?
</span>
<fieldset id="saved-search-alert" aria-describedby="fieldset-label">
<legend class="usa-sr-only">Saved Search Alert Radio Buttons</legend>
<ul class="radio-group-items">
<li>
<input type="radio" id="saved-search-alert-yes" class="saved-search-alert-yes" name="saved-search-alert" value="yes" checked>
<label for="saved-search-alert-yes" class="action-panel-label">Yes</label>
</li>
<li>
<input aria-label="No radio input" type="radio" id="saved-search-alert-no" class="saved-search-alert-no" name="saved-search-alert" value="no">
<label for="saved-search-alert-no" class="action-panel-label">No</label>
</li>
</ul>
</fieldset>
</div>
<div class="alert-schedule-wrap">
<div class="action-panel-control-wrap">
<label class="action-panel-label">
Email:
</label>
<span aria-label="Email address" id="saved-search-email" class="action-panel-label"><span class="action-panel-label-bold"></span> (<a class="myncbi-account-settings" href="https://www.ncbi.nlm.nih.gov/account/settings/">change</a>)</span>
</div>
<div class="action-panel-control-wrap action-panel-extra-margin-top">
<label for="saved-search-frequency" class="action-panel-label">
Frequency:
</label>
<select id="saved-search-frequency" class="no-border-panel-selector saved-search-frequency">
<option value="monthly">Monthly</option>
<option value="weekly">Weekly</option>
<option value="daily">Daily</option>
</select>
</div>
<div class="action-panel-control-wrap saved-search-monthly-additional">
<label for="saved-search-monthly-on-day" class="action-panel-label">
Which day?
</label>
<select id="saved-search-monthly-on-day" class="no-border-panel-selector">
<option value="Sunday">The first Sunday</option>
<option value="Monday">The first Monday</option>
<option value="Tuesday">The first Tuesday</option>
<option value="Wednesday">The first Wednesday</option>
<option value="Thursday">The first Thursday</option>
<option value="Friday">The first Friday</option>
<option value="Saturday">The first Saturday</option>
<option value="day">The first day</option>
<option value="weekday">The first weekday</option>
</select>
</div>
<div class="action-panel-control-wrap saved-search-weekly-additional">
<label for="saved-search-weekly-on-day" class="action-panel-label">
Which day?
</label>
<select id="saved-search-weekly-on-day" class="no-border-panel-selector saved-search-weekly-on-day">
<option value="Sunday">Sunday</option>
<option value="Monday">Monday</option>
<option value="Tuesday">Tuesday</option>
<option value="Wednesday">Wednesday</option>
<option value="Thursday">Thursday</option>
<option value="Friday">Friday</option>
<option value="Saturday">Saturday</option>
</select>
</div>
<div class="action-panel-control-wrap">
<label for="saved-search-report" class="action-panel-label">
Report format:
</label>
<select id="saved-search-report" class="no-border-panel-selector saved-search-report">
<option value="DocSum">Summary</option>
<option value="DocSumText">Summary (text)</option>
<option value="Abstract">Abstract</option>
<option value="AbstractText">Abstract (text)</option>
<option value="MEDLINE">PubMed</option>
</select>
</div>
<div class="action-panel-control-wrap">
<label for="saved-search-amount" class="action-panel-label">
Send at most:
</label>
<select id="saved-search-amount" class="no-border-panel-selector saved-search-amount">
<option value="1">1 item</option>
<option value="5" selected>5 items</option>
<option value="10">10 items</option>
<option value="20">20 items</option>
<option value="50">50 items</option>
<option value="100">100 items</option>
<option value="200">200 items</option>
</select>
</div>
<div>
<input type="checkbox" id="saved-search-send-if-no-result" class="saved-search-send-if-no-result" name="saved-search-send-if-no-result">
<label for="saved-search-send-if-no-result" class="action-panel-label smaller-checkbox">
Send even when there aren't any new results
</label>
</div>
<div class="action-panel-control-wrap option-text-in-email-wrap">
<label for="saved-search-email-text" class="action-panel-label">
Optional text in email:
</label>
<textarea name="saved-search-email-text"
id="saved-search-email-text"
class="saved-search-email-text"></textarea>
</div>
</div>
<div class="action-panel-actions">
<button class="action-panel-submit"
type="submit"
data-loading-label="Saving..."
data-ga-category="save_share"
data-ga-action="alert"
data-ga-label="save">
Save
</button>
<button class="action-panel-cancel"
aria-label="Close 'Your saved search' panel"
ref="linksrc=close_saved_search_panel"
aria-controls="saved-search-action-panel"
aria-expanded="false"
data-ga-category="save_share"
data-ga-action="alert"
data-ga-label="cancel">
Cancel
</button>
</div>
</form>
</div>
</div>
<div id="citation-manager-action-panel" class="citation-manager-action-panel action-panel" aria-hidden="true">
<div class="inner-wrap">
<h2 class="action-panel-heading">
Create a file for external citation management software
</h2>
<form id="citation-manager-action-panel-form"
class="action-panel-content action-form"
action="/results-export-ids/"
data-by-search-action="/results-export-search-data/"
data-by-ids-action="/results-export-ids/"
method="post"
data-by-search-method="post"
data-by-ids-method="post">
<input type="hidden" name="csrfmiddlewaretoken" value="wy4H1UU6isureA9MUgzMMWI9ZqXXA6YaNlOMEKnsS3hV81fCxzcOg4eNxuF9tHwu">
<input name="results-format" type="hidden" value="pubmed"/>
<div class="action-panel-actions">
<button class="action-panel-submit"
type="submit"
data-loading-label="Sending..."
data-ga-category="save_share"
data-ga-action="citation_manager"
data-ga-label="save">
Create file
</button>
<button class="action-panel-cancel"
aria-label="Close 'Send citations to citation manager' panel"
ref="linksrc=close_citation_manager_panel"
aria-controls="citation-manager-action-panel"
aria-expanded="false"
data-ga-category="save_share"
data-ga-action="citation_manager"
data-ga-label="cancel">
Cancel
</button>
</div>
</form>
</div>
</div>
<div id="rss-action-panel" class="rss-action-panel action-panel " aria-hidden="true">
<div class="inner-wrap">
<h2 class="action-panel-heading">
Your RSS Feed
</h2>
<form id="rss-action-panel-form"
class="rss-action-panel-form action-panel-content action-form"
data-create-rss-feed-url="/create-rss-feed-url/"
data-search-form-term-value="">
<input type="hidden" name="csrfmiddlewaretoken" value="wy4H1UU6isureA9MUgzMMWI9ZqXXA6YaNlOMEKnsS3hV81fCxzcOg4eNxuF9tHwu">
<div class="action-panel-control-wrap">
<label for="rss-name" class="action-panel-label required-field-asterisk">
Name of RSS Feed:
</label>
<input maxlength="200"
placeholder="Name"
type="text"
name="rss-name"
id="rss-name"
class="rss-name"
value=''
required
pattern="[^&quot;&amp;=&lt;&gt;\/]*" title="The following characters are not allowed in the Name field: &quot;&amp;=&lt;&gt;/">
</div>
<div class="rss-limit-wrap">
<div class="action-panel-control-wrap action-panel-extra-margin-top">
<label for="rss-limit" class="action-panel-label">
Number of items displayed:
</label>
<select id="rss-limit" class="no-border-panel-selector rss-limit">
<option value="5">5</option>
<option value="10">10</option>
<option value="15" selected="selected">15</option>
<option value="20">20</option>
<option value="50">50</option>
<option value="100">100</option>
</select>
</div>
</div>
<div class="action-panel-actions">
<button class="action-panel-submit"
type="submit"
data-loading-label="Creating..."
data-ga-category="save_share"
data-ga-action="alert"
data-ga-label="save">
Create RSS
</button>
<button class="action-panel-cancel"
aria-label="Close 'Your RSS' panel"
ref="linksrc=close_rss_panel"
aria-controls="rss-action-panel"
aria-expanded="false"
data-ga-category="save_share"
data-ga-action="alert"
data-ga-label="cancel">
Cancel
</button>
</div>
<div class="action-panel-control-wrap rss-link-copy-wrap">
<label for="rss-link" class="usa-sr-only">RSS Link</label>
<input placeholder="Your RSS Feed Link" type="text" name="rss-link" id="rss-link" class="rss-link" title="RSS Link">
<button
type="button"
disabled
class="rss-link-copy-button disabled"
data-ga-category="save_share"
data-ga-action="rss"
data-ga-label="copy">
Copy
</button>
</div>
</form>
</div>
</div>
</div>
</div>
<div class="article-page" id="article-page" data-article-pmid="28846708">
<aside class="page-sidebar">
<div class="inner-wrap">
<div class="full-text-links">
<div class="full-view">
<h3 class="title">
Full text links
</h3>
<div class="full-text-links-list">
<a class="link-item
dialog-focus"
href="https://dx.plos.org/10.1371/journal.pone.0179391"
target="_blank"
rel="noopener"
ref="linksrc=fulltextorjournal_fulltext&amp;is_pmc=False&amp;PrId=4656&amp;itool=Abstract-def&amp;log$=linkouticon&amp;uid=28846708&amp;db=pubmed&amp;nlmid=101285081"
title="See full text options at Public Library of Science"
data-ga-category="full_text"
data-ga-action="Public Library of Science"
data-ga-label="28846708"
><img src="https://cdn.ncbi.nlm.nih.gov/corehtml/query/egifs/https:--journals.plos.org-resource-img-external-pone_120x30.png" alt="Public Library of Science full text link"><span class="text">
Public Library of Science
</span></a><a class="link-item
pmc
"
href="https://pmc.ncbi.nlm.nih.gov/articles/pmid/28846708/"
target="_blank"
rel="noopener"
ref="linksrc=fulltextorjournal_fulltext&amp;is_pmc=True&amp;PrId=3494&amp;itool=Abstract-def&amp;log$=linkouticon&amp;uid=28846708&amp;db=pubmed&amp;nlmid=101285081"
title="Free full text at PubMed Central"
data-ga-category="full_text"
data-ga-action="PMC"
data-ga-label="28846708"
><span class="text">
Free PMC article
</span></a>
</div>
</div>
<div class="short-view">
<a href="#" class="full-text-links-button full-text-links-dialog-trigger">
Full text links
</a>
</div>
</div>
<div class="actions-buttons sidebar"><h3 class="title">Actions</h3><div class="inner-wrap"><button class="citation-button citation-dialog-trigger"
aria-label="Open dialog with citation text in different styles"
data-ga-category="save_share"
data-ga-action="cite"
data-ga-label="open"
data-all-citations-url="/28846708/citations/"
data-citation-style="nlm"
data-pubmed-format-link="/28846708/export/"><span class="button-label">Cite</span></button><link type="text/css" href="ncbi-overlay-block/src/overlay-block.css"><div class="collections-button-container" data-article-id="28846708" data-article-db="pubmed"><button class="collections-button collections-dialog-trigger"
aria-label="Save article in MyNCBI collections."
data-ga-category="collections_button"
data-ga-action="click"
data-ga-label="collections_button"
data-collections-open-dialog-enabled="false"
data-collections-open-dialog-url="https://account.ncbi.nlm.nih.gov/?back_url=https%3A%2F%2Fpubmed.ncbi.nlm.nih.gov%2F28846708%2F%23open-collections-dialog"
data-in-collections="false"><span class="button-label">Collections</span></button><div class="overlay" role="dialog"><div id="collections-action-dialog"
class="dialog collections-dialog"
aria-hidden="true"><div class="title">Add to Collections</div><div class="collections-action-panel action-panel"><form id="collections-action-dialog-form"
class="collections-action-panel-form action-panel-content action-form action-panel-smaller-selectors"
data-existing-collections-url="/list-existing-collections/"
data-add-to-existing-collection-url="/add-to-existing-collection/"
data-create-and-add-to-new-collection-url="/create-and-add-to-new-collection/"
data-myncbi-max-collection-name-length="100"
data-collections-root-url="https://www.ncbi.nlm.nih.gov/myncbi/collections/"><input type="hidden" name="csrfmiddlewaretoken" value="wy4H1UU6isureA9MUgzMMWI9ZqXXA6YaNlOMEKnsS3hV81fCxzcOg4eNxuF9tHwu"><div class="choice-group" role="radiogroup"><ul class="radio-group-items"><li><input type="radio"
id="collections-action-dialog-new"
class="collections-new"
name="collections"
value="new"
data-ga-category="collections_button"
data-ga-action="click"
data-ga-label="collections_radio_new"><label for="collections-action-dialog-new">Create a new collection</label></li><li><input type="radio"
id="collections-action-dialog-existing"
class="collections-existing"
name="collections"
value="existing"
checked="true"
data-ga-category="collections_button"
data-ga-action="click"
data-ga-label="collections_radio_existing"><label for="collections-action-dialog-existing">Add to an existing collection</label></li></ul></div><div class="controls-wrapper"><div class="action-panel-control-wrap new-collections-controls"><label for="collections-action-dialog-add-to-new" class="action-panel-label required-field-asterisk">
Name your collection:
</label><input
type="text"
name="add-to-new-collection"
id="collections-action-dialog-add-to-new"
class="collections-action-add-to-new"
pattern="[^&quot;&amp;=&lt;&gt;\/]*" title="The following characters are not allowed in the Name field: &quot;&amp;=&lt;&gt;/"
maxlength="100"
data-ga-category="collections_button"
data-ga-action="create_collection"
data-ga-label="non_favorties_collection"><div class="collections-new-name-too-long usa-input-error-message selection-validation-message">
Name must be less than 100 characters
</div></div><div class="action-panel-control-wrap existing-collections-controls"><label for="collections-action-dialog-add-to-existing" class="action-panel-label">
Choose a collection:
</label><select id="collections-action-dialog-add-to-existing"
class="action-panel-selector collections-action-add-to-existing"
data-ga-category="collections_button"
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RNA sequencing demonstrates large-scale temporal dysregulation of gene expression in stimulated macrophages derived from MHC-defined chicken haplotypes
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RNA sequencing demonstrates large-scale temporal dysregulation of gene expression in stimulated macrophages derived from MHC-defined chicken haplotypes
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><sup class="key">1</sup> College of Veterinary Medicine, Western University of Health Sciences, Pomona, California, United States of America.</li>
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><sup class="key">2</sup> The Applied Genomics Center, Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, California, United States of America.</li>
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><sup class="key">4</sup> Department of Biological Sciences, Northern Illinois University, DeKalb, Illinois, United States of America.</li>
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><sup class="key">5</sup> Department of Biological Sciences, University of Delaware, Newark, Delaware, United States of America.</li>
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Discovering genetic biomarkers associated with disease resistance and enhanced immunity is critical to developing advanced strategies for controlling viral and bacterial infections in different species. Macrophages, important cells of innate immunity, are directly involved in cellular interactions with pathogens, the release of cytokines activating other immune cells and antigen presentation to cells of the adaptive immune response. IFNγ is a potent activator of macrophages and increased production has been associated with disease resistance in several species. This study characterizes the molecular basis for dramatically different nitric oxide production and immune function between the B2 and the B19 haplotype chicken macrophages.A large-scale RNA sequencing approach was employed to sequence the RNA of purified macrophages from each haplotype group (B2 vs. B19) during differentiation and after stimulation. Our results demonstrate that a large number of genes exhibit divergent expression between B2 and B19 haplotype cells both prior and after stimulation. These differences in gene expression appear to be regulated by complex epigenetic mechanisms that need further investigation.
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<p xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:p1="http://pubmed.gov/pub-one"><bold>Competing Interests: </bold>The authors have declared that no competing interests exist.</p>
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<img class="figure-thumb" itemprop="thumbnail"
id="article-image-0"
src="https://cdn.ncbi.nlm.nih.gov/pmc/blobs/91a5/5573159/de4e130e0502/pone.0179391.g001.gif"
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<strong class="figure-label">
<p> Fig 1. Pattern of 13,618 genes expressed… </p>
</strong>
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<div class="figure-caption-medium figure-caption-text" aria-hidden="true">
<strong class="figure-label">
<p> Fig 1. Pattern of 13,618 genes expressed across haplotypes and timepoints. </p>
</strong>
<div class="figure-caption-contents"><p> Visual representation of genes… </p></div>
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<figcaption id="figure-caption-0" class="figure-caption-full figure-caption-text" itemtype="http://schema.org/ImageObject" itemprop="description">
<strong class="figure-label">
Fig 1. Pattern of 13,618 genes expressed across haplotypes and timepoints.
</strong>
<div class="figure-caption-contents">Visual representation of genes within B2 and B19 haplotypes at each of the time points. Figure includes genes expressed in common, genes expressed only in B2, genes expressed only in B19, all genes expressed in B2, all genes expressed in B19, and total non-redundant genes expressed in either B2 or B19 haplotypes.</div>
</figcaption>
</figure>
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data-figure-id="pone.0179391.g002">
<img class="figure-thumb" itemprop="thumbnail"
id="article-image-1"
src="https://cdn.ncbi.nlm.nih.gov/pmc/blobs/91a5/5573159/ffaa7d861e3c/pone.0179391.g002.gif"
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<p> Fig 2. Distinct temporal gene expression patterns… </p>
</strong>
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<strong class="figure-label">
<p> Fig 2. Distinct temporal gene expression patterns in B2 versus B19 monocytes/macrophages. </p>
</strong>
<div class="figure-caption-contents"><p> B-locus haplotypes in… </p></div>
</div>
<figcaption id="figure-caption-1" class="figure-caption-full figure-caption-text" itemtype="http://schema.org/ImageObject" itemprop="description">
<strong class="figure-label">
Fig 2. Distinct temporal gene expression patterns in B2 versus B19 monocytes/macrophages.
</strong>
<div class="figure-caption-contents">B-locus haplotypes in chickens provide a mechanism for genetically perturbing the cluster of immunologically important genes on chromosome 16 and producing phenotypic variation affecting infectious disease susceptibility and resistance. The heat map allows visualization of gene expression between the two genetically distinct haplotypes. Each row represents a gene within the B-locus (listed on the right) and each column corresponds to a particular time point when cells were collected for RNA sequencing. Black pixels indicate zero gene expression for a particular gene at a specific point in time, and dark blue corresponds to very low expression, while brighter blue indicates the next higher levels. Dark purple represents higher expression levels than blue colors, and pink represents the highest levels of gene expression. Monocytes were obtained from each haplotype of chicken and allowed to differentiate into macrophages in vitro for seven, days beginning on day minus 6 (t-6). RNA was sampled on day t-6, day t-3, and again three days later which is denoted as 0 hours (t0), when IFNγ was initially added to the cultures. On t0, RNA was sampled immediately before stimulation with IFNγ. Subsequent time points correspond to the time following interferon stimulation, in hours (1 hour, 2 hours, 4 hours, 8 hours, 16 hours and 24 hours). As visible on the heat map, there are distinct differences in gene expression between the B2 and B19 cells. The most dramatic difference occurs on day t-6. B2 cells exhibit a rapid burst of gene expression, indicated as a single column of pink on the left most edge of the heat map. In contrast, the B19 cells appear to undergo a much slower and prolonged gene expression program that was not as rapidly down regulated as in genes in the B2 cells. Additional gene expression data for a number of proteins involved in cell growth and apoptosis, is shown in the bottom half of the figure to highlight a similar pattern in gene expression and kinetics. The green border indicates the B2 haplotype expression pattern and the red border corresponds to the B19 expression pattern.</div>
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<img class="figure-thumb" itemprop="thumbnail"
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src="https://cdn.ncbi.nlm.nih.gov/pmc/blobs/91a5/5573159/8f49e29f4d85/pone.0179391.g003.gif"
alt="Fig 3" />
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<p> Fig 3. Examples of divergent gene expression… </p>
</strong>
</div>
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<strong class="figure-label">
<p> Fig 3. Examples of divergent gene expression patterns observed in B2 and B19 haplotype macrophages. </p>
</strong>
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<figcaption id="figure-caption-2" class="figure-caption-full figure-caption-text" itemtype="http://schema.org/ImageObject" itemprop="description">
<strong class="figure-label">
Fig 3. Examples of divergent gene expression patterns observed in B2 and B19 haplotype macrophages.
</strong>
<div class="figure-caption-contents">Four distinct patterns were identified as representative of the types of divergent gene expression that re-occur across many genes involved in macrophage differentiation, activation and function in B2 versus B19 macrophages. 1. <b>Day t-6: B2 high vs B19 low</b>. This divergent pattern exhibits strong expression of genes on day -6 in the B2 birds while relatively low levels of expression are observed in the B19 birds at the same time point. Genes of interest include an adenosine receptor (P2RY12) 2. <b><underline>Day t-6: B2 = 1 day vs. B19 = 3 days.</underline></b> This example of divergent patterns is the single peak of day t-6 gene expression in the B2 haplotype cells compared to the prolonged multiple day expression until day t-3 in the B19 haplotype cells. Genes of interest include macrophage differentiation gene GATA, adenosine receptor A2A and macrophage podosome markers VCL and GSN. <b><underline>3. Maximum</underline></b>
<b>IFN</b>γ <b><underline>Stimulation of B2 at 24 h versus 48 h in B19 macrophages.</underline></b> Another interesting divergent gene expression pattern observed between the two haplotypes occurs after stimulation by IFNγ. There is a four-hour difference in peak expression timing for a large number of induced genes. In the B2 haplotype macrophages, the peak expression occurs between 2 and 4 hours, while in the B19 macrophages, the peak expression occurs between 4 and 8 hours. <underline><b>4. Maximum</b></underline>
<b>IFN</b>γ <underline><b>Stimulation: B2 = Coherent vs. B19 = Non-Coherent</b></underline> Another discernable difference in post-stimulatory induction of genes between the B2 macrophages compared to the B19 macrophages is one of coherence. Specifically, there are a number of genes for which the B2 macrophages are able to rapidly turn on and reach relatively high levels of expression within 2 to 4 hours of IFNγ <underline>stimulation</underline>. In contrast, these same genes fail to exhibit a coherent peak of expression, even after 4 to 8 hours, in the B19 cells. Instead, they exhibit a dispersed “smear” of gene expression extending from approximately 1 hour after stimulation to 16 hours post-stimulation.</div>
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<img class="figure-thumb" itemprop="thumbnail"
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alt="Fig 4" />
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<p> Fig 4. RT-PCR validation of transcripts identified… </p>
</strong>
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<div class="figure-caption-medium figure-caption-text" aria-hidden="true">
<strong class="figure-label">
<p> Fig 4. RT-PCR validation of transcripts identified as significantly expressed in RNA sequencing data. </p>
</strong>
<div class="figure-caption-contents"><p> Gene… </p></div>
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<figcaption id="figure-caption-3" class="figure-caption-full figure-caption-text" itemtype="http://schema.org/ImageObject" itemprop="description">
<strong class="figure-label">
Fig 4. RT-PCR validation of transcripts identified as significantly expressed in RNA sequencing data.
</strong>
<div class="figure-caption-contents">Gene expression for ATP6V0C, LITAF, IL18R, TLN-1, TLR2, TLR3, TLR4, TLR5, TLR6, and TLR7 was assessed in B2 and B19 monocytes/macrophages following stimulation with IFNγ. Expression was measured at 0 hours, 2 hours and 4 hours. Expression for transcripts in B2 cells are shown in green and expression for transcripts are shown in red. Standard error is shown for each value. Values were considered statistically significant with p<0.05.</div>
</figcaption>
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<strong class="figure-label">
<p> Fig 5. IFNγ stimulated vs. cytomegalovirus stimulated… </p>
</strong>
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<div class="figure-caption-medium figure-caption-text" aria-hidden="true">
<strong class="figure-label">
<p> Fig 5. IFNγ stimulated vs. cytomegalovirus stimulated macrophage gene expression. </p>
</strong>
<div class="figure-caption-contents"><p> 54 genes, for which gene… </p></div>
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<figcaption id="figure-caption-4" class="figure-caption-full figure-caption-text" itemtype="http://schema.org/ImageObject" itemprop="description">
<strong class="figure-label">
Fig 5. IFNγ stimulated vs. cytomegalovirus stimulated macrophage gene expression.
</strong>
<div class="figure-caption-contents">54 genes, for which gene expression changes were previously described following cytomegalovirus stimulation were used as comparisons for the corresponding genes in the B2 and B19 haplotype birds. A total of 25 published genes exhibited decreases in expression following cytomegalovirus stimulation while 29 genes exhibited increased expression following stimulation. All but one gene (FEZ1) in the B2 cells exhibited increased expression following IFNγ stimulation. In contrast, ten genes displayed decreased expression in the B19 cells. Of the ten exhibiting fold-change < 0 in the B19 cells, seven exhibited decreased expression in the cytomegalovirus stimulated cells. Twenty-eight genes (52%) expressed in the B2 cells matched the direction of the fold change reported in the published data while 33 genes (61%) corresponded between the B19 cells and the published data. Of the ten published genes reported as having greater than at least 5-fold increased expression, 90% of the B2 genes exhibited fold-change in the same direction.</div>
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<p> Fig 6. Identification of divergent gene expression… </p>
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<p> Fig 6. Identification of divergent gene expression patterns between B2 and B19 macrophages. </p>
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Fig 6. Identification of divergent gene expression patterns between B2 and B19 macrophages.
</strong>
<div class="figure-caption-contents">Visualization of divergent gene expression patterns between the B2 and B19 haplotypes. A subset of genes exhibiting divergent gene expression were identified and visualized in heat following hierarchical clustering of the genes (rows), but not the time points (columns). The genes cluster into four major clades (clade1, clade2, clade3, and clade4) with a singleton gene (labelled clade 5). Among these genes, represented in clade1 and clade2, are a number of miRNAs exhibiting strong expression in B2 cells (mir-147, mir-146b, mir-1618, mir-200a, mir-1649, and mir-1648a) compared to the B19 samples. Likewise, miRNAs contained in clade3 and clade4 exhibit greater expression in B19 cells (mir-1627, mir-222b, mir-1633, and mir-19a). Additionally, a number of small nucleolar RNAs (snoRNAs) exhibit similarly dichotomous gene expression patterns (clade4) such that SNORd24, snoZ40, SNORD74, SNORA17, and SNORD12 exhibit substantially higher levels of expression in B19 cells on day -6 compared to B2 cells while B2 cells express such as snoU2_19 (clade2).</div>
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<div class="grants-list"></div><div class="funding-statement">Funded by United States Department of Agriculture 2008-35204-04806 <a target="_blank" href="http://www.reeis.usda.gov/web/crisprojectpages/0214956-impact-of-immune-responses-of-chickens-with-defined-b-haplotypes-on-resistance-to-respiratory-coronavirus-infection.html" rel="noopener nofollow" title="External link: http://www.reeis.usda.gov/web/crisprojectpages/0214956-impact-of-immune-responses-of-chickens-with-defined-b-haplotypes-on-resistance-to-respiratory-coronavirus-infection.html">http://www.reeis.usda.gov/web/crisprojectpages/0214956-impact-of-immune-responses-of-chickens-with-defined-b-haplotypes-on-resistance-to-respiratory-coronavirus-infection.html</a> and Merial Veterinary Scholars Program <a target="_blank" href="http://www.merialscholars.com/Pages/home.aspx" rel="noopener nofollow" title="External link: http://www.merialscholars.com/Pages/home.aspx">http://www.merialscholars.com/Pages/home.aspx</a>.</div>
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