Skip to content
Snippets Groups Projects
Commit 2398aa24 authored by Gervaise Henry's avatar Gervaise Henry :cowboy:
Browse files

Merge branch 'repository' into 'develop' 

Repository

See merge request !8
parents 2d60ed65 54c6ddf9
2 merge requests!9Develop,!8Repository
Expand all Hide whitespace changes
Inline Side-by-side
Showing
with 21668 additions and 283 deletions
config.toml
+ 6
− 6
View file @ 2398aa24
......@@ -49,12 +49,12 @@ paginate = 10
weight = 3
identifier = "publications"
url = "/publications/"
# [[menu.main]]
# name = "Biorepository"
# pre = "<i class='fas fa-stethoscope fa-fw'></i>"
# weight = 4
# identifier = "repository"
# url = "/repository/"
[[menu.main]]
name = "Biorepository"
pre = "<i class='fas fa-stethoscope fa-fw'></i>"
weight = 4
identifier = "repository"
url = "/repository/"
[[menu.main]]
name = "Single-Cell Data"
pre = "<i class='fas fa-chart-bar fa-fw'></i>"
......
data/repository/filters.json 0 → 100644
+ 66
− 0
View file @ 2398aa24
[
{"id": "disease", "parent": "#", "text": "Disease Phenotype", "a_attr": { "class": "no_checkbox" }, "disabled": true},
{"id": "disease.d", "parent":"disease", "text": "Donor (normal)"},
{"id": "disease.b", "parent":"disease", "text": "BPH"},
{"id": "disease.c", "parent":"disease", "text": "Prostate Cancer"},
{"id": "demographics", "parent": "#", "text": "Demographics", "a_attr": { "class": "no_checkbox" }, "disabled": true},
{"id": "ethnicity", "parent":"demographics", "text": "Ethnicity", "a_attr": { "class": "no_checkbox" }, "disabled": true},
{"id": "ethn.aa", "parent":"ethnicity", "text": "African American"},
{"id": "ethn.as", "parent":"ethnicity", "text": "Asian"},
{"id": "ethn.ca", "parent":"ethnicity", "text": "Caucasian"},
{"id": "ethn.hi", "parent":"ethnicity", "text": "Hispanic"},
{"id": "ethn.uk", "parent":"ethnicity", "text": "Unknown Ethnicity"},
{"id": "age", "parent":"demographics", "text": "Age", "a_attr": { "class": "no_checkbox" }, "disabled": true},
{"id": "age.40", "parent":"age", "text": "<40yo"},
{"id": "age.50", "parent":"age", "text": "41-50yo"},
{"id": "age.60", "parent":"age", "text": "51-60yo"},
{"id": "age.70", "parent":"age", "text": "61-70yo"},
{"id": "age.80", "parent":"age", "text": "71-80yo"},
{"id": "age.90", "parent":"age", "text": "81-90yo"},
{"id": "age.100", "parent":"age", "text": "91+yo"},
{"id": "age.uk", "parent":"age", "text": "Unknown Age"},
{"id": "clinical", "parent":"#", "text": "Clinical Features", "a_attr": { "class": "no_checkbox" }, "disabled": true},
{"id": "bmi", "parent":"clinical", "text": "BMI", "a_attr": { "class": "no_checkbox" }, "disabled": true},
{"id": "bmi.uw", "parent":"bmi", "text": "Underweight"},
{"id": "bmi.nw", "parent":"bmi", "text": "Normal"},
{"id": "bmi.ow", "parent":"bmi", "text": "Overweight"},
{"id": "bmi.ob", "parent":"bmi", "text": "Obese"},
{"id": "bmi.vo", "parent":"bmi", "text": "Very Obese"},
{"id": "bmi.so", "parent":"bmi", "text": "Severely Obese"},
{"id": "bmi.uk", "parent":"bmi", "text": "Unknown BMI"},
{"id": "t2d", "parent":"clinical", "text": "Type 2 Diabetes", "a_attr": { "class": "no_checkbox" }, "disabled": true},
{"id": "t2d.y", "parent":"t2d", "text": "Yes"},
{"id": "t2d.n", "parent":"t2d", "text": "No"},
{"id": "t2d.uk", "parent":"t2d", "text": "Unknown"},
{"id": "bph", "parent":"clinical", "text": "BPH Features", "a_attr": { "class": "no_checkbox" }, "disabled": true},
{"id": "bphsurgery", "parent":"bph", "text": "BPH Surgery", "a_attr": { "class": "no_checkbox" }, "disabled": true},
{"id": "bphsurg.simp", "parent":"bphsurgery", "text": "Simple Prostatectomy"},
{"id": "bphsurg.turp", "parent":"bphsurgery", "text": "TURP"},
{"id": "bphsurg.uk", "parent":"bphsurgery", "text": "Unknown Surgery"},
{"id": "5ari", "parent":"bph", "text": "5ARI", "a_attr": { "class": "no_checkbox" }, "disabled": true},
{"id": "5ari.y", "parent":"5ari", "text": "Yes 5ARI"},
{"id": "5ari.n", "parent":"5ari", "text": "No 5ARI"},
{"id": "5ari.uk", "parent":"5ari", "text": "Unknown 5ARI"},
{"id": "5aril", "parent":"bph", "text": "5ARI Length (months)", "a_attr": { "class": "no_checkbox" }, "disabled": true},
{"id": "5aril.10", "parent":"5aril", "text": "<10mnths 5ARI"},
{"id": "5aril.20", "parent":"5aril", "text": "10-20mnths 5ARI"},
{"id": "5aril.30", "parent":"5aril", "text": "20+mnths 5ARI"},
{"id": "5aril.uk", "parent":"5aril", "text": "Unknown 5ARI"},
{"id": "5aril.na", "parent":"5aril", "text": "NA 5ARI"},
{"id": "prostatevol", "parent":"clinical", "text": "Prostate Volume", "a_attr": { "class": "no_checkbox" }, "disabled": true},
{"id": "prvol.low", "parent":"prostatevol", "text": "Low Volumne"},
{"id": "prvol.med", "parent":"prostatevol", "text": "Medium Volume"},
{"id": "prvol.hi", "parent":"prostatevol", "text": "High Volume"},
{"id": "prvol.vhi", "parent":"prostatevol", "text": "Very High Volume"},
{"id": "prvol.uk", "parent":"prostatevol", "text": "Unknown Volume"},
{"id": "repo", "parent":"#", "text": "Repository", "a_attr": { "class": "no_checkbox" }, "disabled": true},
{"id": "repo.pr", "parent":"repo", "text": "Prostate", "a_attr": { "class": "no_checkbox" }, "disabled": true},
{"id": "repo.pr.cry", "parent":"repo.pr", "text": "Pr Cryopreserved Cells"},
{"id": "repo.pr.ff", "parent":"repo.pr", "text": "Pr Flash Frozen Tissue"},
{"id": "repo.pr.ffpe", "parent":"repo.pr", "text": "Pr FFPE"},
{"id": "repo.pr.oct", "parent":"repo.pr", "text": "Pr OCT"},
{"id": "repo.bl", "parent":"repo", "text": "Bladder"},
{"id": "repo.sv", "parent":"repo", "text": "Seminal Vesicle"},
{"id": "repo.vd", "parent":"repo", "text": "Vas Deferencec"},
{"id": "repo.ut", "parent":"repo", "text": "Ureter"}
]
\ No newline at end of file
data/repository/repository.json 0 → 100644
+ 10152
− 0
View file @ 2398aa24
This diff is collapsed.
data/scRNAseq_huPr_D/updated_cleaned_json.json 0 → 100644
+ 10154
− 0
View file @ 2398aa24
This diff is collapsed.
layouts/custom/contact.html
+ 3
− 5
View file @ 2398aa24
......@@ -7,16 +7,14 @@
<div class="content">
<p style="text-align: center">
Questions about our research or need a tip on one of our protocols?
Interested in collaborations? Email us, mention any person, project, or
activity of interest,and we will get back to you soon!
Questions about our research or need a tip on one of our protocols? Interested in collaborations? Email us,
mention any person, project, or activity of interest,and we will get back to you soon!
</p>
<hr>
<div style="text-align: center">
<iframe
src="https://www.google.com/maps/embed?pb=!1m18!1m12!1m3!1d3353.0540362781526!2d-96.84412528424524!3d32.81733318923467!2m3!1f0!2f0!3f0!3m2!1i1024!2i768!4f13.1!3m3!1m2!1s0x864e9c04b088e599%3A0x2e63ea34f8b2150b!2sUT%20Southwestern%20Medical%20Center!5e0!3m2!1sen!2sus!4v1576207208811!5m2!1sen!2sus"
width="600" height="450" frameborder="0" style="border:0"
allowfullscreen=""></iframe>
width="600" height="450" frameborder="0" style="border:0" allowfullscreen=""></iframe>
</div>
<hr>
<div style="text-align: center">
......
layouts/custom/hu.donor.deep.html
+ 9
− 9
View file @ 2398aa24
......@@ -160,19 +160,19 @@
$(function () {
var genes = {{ index .Site.Data.sc_data.hu_donor_pr_deep.genes }};
var selectedGene = $("#gene").autocomplete({
source: genes.genes,
maxResults: 10,
maxShowItems: 10,
minLength: 1,
source: genes.genes,
maxResults: 10,
maxShowItems: 10,
minLength: 1,
});
});
$("#analysis").click(function (event) {
});
$("#analysis").click(function (event) {
event.preventDefault();
var genes = {{ index .Site.Data.sc_data.hu_donor_pr_deep.genes }};
_gene = $("#gene").val().toUpperCase();
if ($.inArray(_gene, genes.genes) < 0) {
alert("Gene " + _gene + " not exist in the data.")
return
alert("Gene " + _gene + " not exist in the data.")
return
}
document.getElementById("label.gene").innerHTML = _gene
document.getElementById("label.populations").innerHTML = "Separated by " + $("#populations").val().toUpperCase()
......@@ -186,6 +186,6 @@
var img = document.getElementById("img.ViolinBox");
img.src = "https://s3.us-east-2.amazonaws.com/images.gse117403.deep/images/ViolinBox/" + $("#populations").val() + "/genes/" + _gene + "_1.png"
return (_gene)
});
});
</script>
</head>
\ No newline at end of file
layouts/custom/hu.donor.shallow.html
+ 159
− 159
View file @ 2398aa24
{{ partial "header.html" . }}
<div class="header">
<h1>{{ .Title }}</h1>
<h2>{{ .Description }}</h2>
<h1>{{ .Title }}</h1>
<h2>{{ .Description }}</h2>
</div>
<div class="content">
{{ .Content }}
{{ .Content }}
</div>
<style>
.content {
margin: 0;
max-width: none;
}
.select {
float: top;
z-index: 1;
top: 0px;
background: #191818;
overflow-x: hidden;
padding: 8px 10px;
}
.columnS {
float: left;
text-align: center;
width: 50%;
}
.columnF {
float: left;
text-align: center;
width: 33.33%;
}
.row:after {
content: "";
display: table;
clear: both;
}
.content {
margin: 0;
max-width: none;
}
img {
max-width: 100%;
height: auto;
}
.select {
float: top;
z-index: 1;
top: 0px;
background: #191818;
overflow-x: hidden;
padding: 8px 10px;
}
@media (max-width: 1000px) {
.columnS {
text-align: right;
width: 100%;
float: left;
text-align: center;
width: 50%;
}
.columnF {
width: 100%;
float: left;
text-align: center;
width: 33.33%;
}
.row:after {
content: "";
display: table;
clear: both;
}
br {
display: none;
img {
max-width: 100%;
height: auto;
}
@media (max-width: 1000px) {
.columnS {
text-align: right;
width: 100%;
}
.columnF {
width: 100%;
}
br {
display: none;
}
}
}
</style>
<body>
<div class="select">
<div class="columnS ui-widget">
<label for="gene" style="font-family:sans-serif; font-size:18px;"><b>Gene:</b></label>
<br>
<input id="gene" size="19">
</div>
<div class="columnS">
<label for="populations" style="font-size:18px;">
<b>Select a group of cell populations:</b>
</label>
<br>
<select name="populations" id="populations">
<option selected="selected" value="Population"> Cell Populations</option>
<option>Lineage</option>
<option value="Zone">Prostatic Zone</option>
<option>Patient</option>
</select>
</div>
<br>
<div style="text-align:center">
<button type="submit" id="analysis" class="btn btn-primary">Run Analysis</button>
</div>
<hr>
<div>
<span style="font-size:16px; font-weight:bold;">Experimental details:</span>
<br>
<span style="font-size:16px;">
Single Cell RNA-Sequencing was conducted on 32,194 cells from peripheral zone and transition zone from the
prostate of three 18-38 year old organ donors using the 10x Genomics platform. The cells were clustered and
identified by correlation of their transcriptomes to known cell types. Gene expression can be compared by
population identity, cell lineage, patient, or dissected prostatic zone. This is the original sequencing depth
published.
</span>
</div>
</div>
<div align="center">
<h1 id="label.gene">NO GENE SELECTED</h1>
<h2 id="label.populations"></h2>
<div class="columnF">
<h4 id="label.ClusterVis">
</h3>
<div class="img">
<img id="img.ClusterVis" src="" />
<div class="select">
<div class="columnS ui-widget">
<label for="gene" style="font-family:sans-serif; font-size:18px;"><b>Gene:</b></label>
<br>
<input id="gene" size="19">
</div>
<br>
</div>
<div class="columnF">
<h4 id="label.Feature">
</h3>
<div class="img">
<img id="img.Feature" src="" />
<div class="columnS">
<label for="populations" style="font-size:18px;">
<b>Select a group of cell populations:</b>
</label>
<br>
<select name="populations" id="populations">
<option selected="selected" value="Population"> Cell Populations</option>
<option>Lineage</option>
<option value="Zone">Prostatic Zone</option>
<option>Patient</option>
</select>
</div>
<br>
<div style="text-align:center">
<button type="submit" id="analysis" class="btn btn-primary">Run Analysis</button>
</div>
<hr>
<div>
<span style="font-size:16px; font-weight:bold;">Experimental details:</span>
<br>
<span style="font-size:16px;">
Single Cell RNA-Sequencing was conducted on 32,194 cells from peripheral zone and transition zone from
the prostate of three 18-38 year old organ donors using the 10x Genomics platform. The cells were
clustered and identified by correlation of their transcriptomes to known cell types. Gene expression can
be compared by population identity, cell lineage, patient, or dissected prostatic zone. This is the
original sequencing depth published.
</span>
</div>
</div>
<div class="columnF">
<h4 id="label.ViolinBox">
</h3>
<div class="img">
<img id="img.ViolinBox" src="" />
<div align="center">
<h1 id="label.gene">NO GENE SELECTED</h1>
<h2 id="label.populations"></h2>
<div class="columnF">
<h4 id="label.ClusterVis">
</h3>
<div class="img">
<img id="img.ClusterVis" src="" />
</div>
<br>
</div>
<div class="columnF">
<h4 id="label.Feature">
</h3>
<div class="img">
<img id="img.Feature" src="" />
</div>
<br>
</div>
<div class="columnF">
<h4 id="label.ViolinBox">
</h3>
<div class="img">
<img id="img.ViolinBox" src="" />
</div>
<br>
</div>
<br>
</div>
</div>
<hr>
<div align="left">
<div><span style="font-size:18px; font-weight:bold;">Publication found at:</span></div>
<div><span style="font-size:16px;"> <a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=30566875"
target="_blank">Cell Reports</a></span></div>
<div><span style="font-size:18px; font-weight:bold;">Raw data found at:</span></div>
<div><span style="font-size:16px;"> <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117403"
target="_blank">GEO:
GSE117403</a></span></div>
<div><span style="font-size:16px;"><a href="https://doi.org/10.25548/W-R8CM" target="_blank">GUDMAP:
W-R8CM</a></span></div>
</div>
<hr>
<div align="left">
<div><span style="font-size:18px; font-weight:bold;">Publication found at:</span></div>
<div><span style="font-size:16px;"> <a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=30566875"
target="_blank">Cell Reports</a></span></div>
<div><span style="font-size:18px; font-weight:bold;">Raw data found at:</span></div>
<div><span style="font-size:16px;"> <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117403"
target="_blank">GEO:
GSE117403</a></span></div>
<div><span style="font-size:16px;"><a href="https://doi.org/10.25548/W-R8CM" target="_blank">GUDMAP:
W-R8CM</a></span></div>
</div>
</body>
{{ partial "footer.html" . }}
<head>
<link rel="stylesheet" href="https://ajax.googleapis.com/ajax/libs/jqueryui/1.12.1/themes/smoothness/jquery-ui.css">
<script src="https://ajax.googleapis.com/ajax/libs/jquery/3.4.1/jquery.min.js"></script>
<script src="https://ajax.googleapis.com/ajax/libs/jqueryui/1.12.1/jquery-ui.min.js"></script>
<style>
.ui-autocomplete {
max-height: 200px;
overflow-y: auto;
overflow-x: hidden;
}
</style>
<script>
$(function () {
$("#populations").selectmenu({ width: 230 });
});
$(function () {
var genes = {{ index .Site.Data.sc_data.hu_donor_pr_shallow.genes }};
var selectedGene = $("#gene").autocomplete({
source: genes.genes,
maxResults: 10,
maxShowItems: 10,
minLength: 1,
});
});
$("#analysis").click(function (event) {
event.preventDefault();
var genes = {{ index .Site.Data.sc_data.hu_donor_pr_shallow.genes }};
_gene = $("#gene").val().toUpperCase();
if ($.inArray(_gene, genes.genes) < 0) {
alert("Gene " + _gene + " not exist in the data.")
return
}
document.getElementById("label.gene").innerHTML = _gene
document.getElementById("label.populations").innerHTML = "Separated by " + $("#populations").val().toUpperCase()
document.getElementById("label.ClusterVis").innerHTML = "Cluster Visualization"
var img = document.getElementById("img.ClusterVis");
img.src = "https://s3.us-east-2.amazonaws.com/data.images.gse117403/images/" + $("#populations").val() + "/tsne.png"
document.getElementById("label.Feature").innerHTML = "Feature Plot"
var img = document.getElementById("img.Feature");
img.src = "https://s3.us-east-2.amazonaws.com/data.images.gse117403/images/tsne/" + "genes/" + _gene + "_1.png"
document.getElementById("label.ViolinBox").innerHTML = "Violin Box Plot"
var img = document.getElementById("img.ViolinBox");
img.src = "https://s3.us-east-2.amazonaws.com/data.images.gse117403/images/ViolinBox/" + $("#populations").val() + "/genes/" + _gene + "_1.png"
return (_gene)
});
</script>
<link rel="stylesheet" href="https://ajax.googleapis.com/ajax/libs/jqueryui/1.12.1/themes/smoothness/jquery-ui.css">
<script src="https://ajax.googleapis.com/ajax/libs/jquery/3.4.1/jquery.min.js"></script>
<script src="https://ajax.googleapis.com/ajax/libs/jqueryui/1.12.1/jquery-ui.min.js"></script>
<style>
.ui-autocomplete {
max-height: 200px;
overflow-y: auto;
overflow-x: hidden;
}
</style>
<script>
$(function () {
$("#populations").selectmenu({ width: 230 });
});
$(function () {
var genes = {{ index .Site.Data.sc_data.hu_donor_pr_shallow.genes }};
var selectedGene = $("#gene").autocomplete({
source: genes.genes,
maxResults: 10,
maxShowItems: 10,
minLength: 1,
});
});
$("#analysis").click(function (event) {
event.preventDefault();
var genes = {{ index .Site.Data.sc_data.hu_donor_pr_shallow.genes }};
_gene = $("#gene").val().toUpperCase();
if ($.inArray(_gene, genes.genes) < 0) {
alert("Gene " + _gene + " not exist in the data.")
return
}
document.getElementById("label.gene").innerHTML = _gene
document.getElementById("label.populations").innerHTML = "Separated by " + $("#populations").val().toUpperCase()
document.getElementById("label.ClusterVis").innerHTML = "Cluster Visualization"
var img = document.getElementById("img.ClusterVis");
img.src = "https://s3.us-east-2.amazonaws.com/data.images.gse117403/images/" + $("#populations").val() + "/tsne.png"
document.getElementById("label.Feature").innerHTML = "Feature Plot"
var img = document.getElementById("img.Feature");
img.src = "https://s3.us-east-2.amazonaws.com/data.images.gse117403/images/tsne/" + "genes/" + _gene + "_1.png"
document.getElementById("label.ViolinBox").innerHTML = "Violin Box Plot"
var img = document.getElementById("img.ViolinBox");
img.src = "https://s3.us-east-2.amazonaws.com/data.images.gse117403/images/ViolinBox/" + $("#populations").val() + "/genes/" + _gene + "_1.png"
return (_gene)
});
</script>
</head>
\ No newline at end of file
layouts/custom/people.html
+ 4
− 0
View file @ 2398aa24
......@@ -10,18 +10,22 @@
.column {
float: left;
}
.left {
width: 25%;
}
.right {
width: 75%;
}
.row:after {
content: "";
display: table;
clear: both;
}
}
img.pic {
width: 175px;
padding: 7px;
......
layouts/custom/publications.html
+ 27
− 26
View file @ 2398aa24
......@@ -5,12 +5,15 @@
.column {
float: left;
}
.left {
width: 25%;
}
.right {
width: 75%;
}
.row:after {
content: "";
display: table;
......@@ -26,35 +29,33 @@
<br>
<div>
{{ range first 10 (.Pages.ByParam "odate" ).Reverse }}
<div class="row">
<div class="column left">
<img src="images/{{.Params.ppic}}" alt="" width="100px;"
style="border:5px double black; border-radius:20%;">
</div>
<div class="column right">
<h3>{{.Params.pname}}</h3>
</div>
<div class="row">
<div class="column left">
<img src="images/{{.Params.ppic}}" alt="" width="100px;"
style="border:5px double black; border-radius:20%;">
</div>
<div class="column right">
<h3>{{.Params.pname}}</h3>
</div>
{{ if not (eq .Params.ppubmed "") }}
<h4><i><a
href="https://www.ncbi.nlm.nih.gov/pubmed?term={{.Params.ppubmed}}"
target="_blank">
{{else}}
<h4><i><a href="{{.Params.plink}}">
{{end}}
{{.Params.pauthor}}, {{.Params.pjournal}},{{.Params.pdate}}</a></i></h4>
{{ range first 1 .Params.prepo }}
{{ if not (eq .title "") }}
</div>
{{ if not (eq .Params.ppubmed "") }}
<h4><i><a href="https://www.ncbi.nlm.nih.gov/pubmed?term={{.Params.ppubmed}}" target="_blank">
{{else}}
<h4><i><a href="{{.Params.plink}}">
{{end}}
{{.Params.pauthor}}, {{.Params.pjournal}},{{.Params.pdate}}</a></i></h4>
{{ range first 1 .Params.prepo }}
{{ if not (eq .title "") }}
<u>Data Repository:</u><br>
{{end}}
{{end}}
{{ range .Params.prepo }}
{{ if not (eq .title "") }}
{{end}}
{{end}}
{{ range .Params.prepo }}
{{ if not (eq .title "") }}
<a href="{{.loc}}" target="_blank">{{.title}}</a><br>
{{end}}
{{end}}
<hr><br>
{{end}}
{{end}}
{{end}}
<hr><br>
{{end}}
</div>
</div>
......
layouts/custom/repository.html 0 → 100644
+ 900
− 0
View file @ 2398aa24
This diff is collapsed.
layouts/custom/research.html
+ 42
− 74
View file @ 2398aa24
......@@ -11,28 +11,33 @@
display: table;
clear: both;
}
div.fig {
padding: 1px;
border: 1px solid black;
margin: auto;
background-color: LightGrey;
}
div.fig img {
width: 500px;
max-width: 100%;
height: auto;
padding: 1px;
}
div.lab {
text-align: justify;
padding-left: 10px;
padding-right: 10px;
}
@media (min-width: 1000px) {
div.fig {
float: left;
margin: 1px 10px 1px 1px;
}
br {
display: none;
}
......@@ -42,41 +47,30 @@
<div class="section">
<H1 align="center">Overview</H1>
<p style="text-align:justify; font-size:18px">
The main goals of the Strand lab are to create accurate cellular
atlases of the human and mouse lower
urinary tract, characterize the molecular and cellular alterations
in human lower urinary tract disease, and
The main goals of the Strand lab are to create accurate cellular atlases of the human and mouse lower
urinary tract, characterize the molecular and cellular alterations in human lower urinary tract disease, and
build appropriate models of the human disease in novel mouse models.
</p>
</div>
<div class="section">
<H1 align="center">Benign Prostatic Hyperplasia</H1>
<div class="fig" style="max-width:250px">
<img src="/research.images/prostate.jpg" alt="prostate" class="img"
/>
<img src="/research.images/prostate.jpg" alt="prostate" class="img" />
<div class="lab">
<p>Cross-section of a prostate gland, showing the transition
zone (TZ) and the peripheral zone (PZ)</p>
<p>Cross-section of a prostate gland, showing the transition zone (TZ) and the peripheral zone (PZ)</p>
</div>
<p class="br"></p>
</div>
<p style="text-align:justify; font-size:18px">
A goal of the Strand laboratory is to understand the cellular and
molecular biology of lower urinary tract
symptoms (LUTS) due to benign prostatic hyperplasia (BPH) or bladder
dysfunction. BPH/LUTS is present in the
vast majority of men over 70 years old resulting in medical
treatment or surgical intervention.
A goal of the Strand laboratory is to understand the cellular and molecular biology of lower urinary tract
symptoms (LUTS) due to benign prostatic hyperplasia (BPH) or bladder dysfunction. BPH/LUTS is present in the
vast majority of men over 70 years old resulting in medical treatment or surgical intervention.
</p>
<p style="text-align:justify; font-size:18px">
We focus on translational questions related to progression of
BPH/LUTS in order to develop new targets for
therapeutic intervention. In particular, we are interested in
characterizing the cellular composition of
particular phenotypes that are resistant to current therapies. We
use a combination of single cell RNA
sequencing, flow cytometry and immunohistochemistry on normal and
diseased human specimens to build a
We focus on translational questions related to progression of BPH/LUTS in order to develop new targets for
therapeutic intervention. In particular, we are interested in characterizing the cellular composition of
particular phenotypes that are resistant to current therapies. We use a combination of single cell RNA
sequencing, flow cytometry and immunohistochemistry on normal and diseased human specimens to build a
cellular atlas of prostate and bladder disease.
</p>
</div>
......@@ -84,82 +78,56 @@
<div class="section">
<H1 align="center">Pathological Heterogeneity in BPH</H1>
<div class="fig" style="max-width:500px">
<img src="/research.images/pheno.jpg" alt="phenotypes" class="img"
/>
<img src="/research.images/pheno.jpg" alt="phenotypes" class="img" />
<div class="lab">
<p>Phenotypic diversity in BPH. Left: glandular enlargement.
Middle: Stromal enlargement. Right: Mixed
<p>Phenotypic diversity in BPH. Left: glandular enlargement. Middle: Stromal enlargement. Right: Mixed
type.</p>
</div>
</div>
<p style="text-align:justify; font-size:18px">
We believe that the basis for heterogeneous clinical responses in
BPH is pathologic diversity. There are a
number of phenotypes evident across and even within patients. In one
area, a patient can display a stromal
We believe that the basis for heterogeneous clinical responses in BPH is pathologic diversity. There are a
number of phenotypes evident across and even within patients. In one area, a patient can display a stromal
tumor while the other area display an epithelial nodule.
</p>
<p style="text-align:justify; font-size:18px">
Our goal is to provide a rational basis for therapeutically treating
these individual phenotypes by
dissecting them macroscopically and then comparing their
cell-specific molecular profiles to reduce the
noise of cellular heterogeneity and inflammation. Our first goal is
to identify a cell or cells of origin
for the varying phenotypes by phenotyping the tissues with single
cell RNA sequencing. This includes a
comprehensive evaluation of the immune and inflammatory infiltrate
as well as fluctuations in epithelial and
Our goal is to provide a rational basis for therapeutically treating these individual phenotypes by
dissecting them macroscopically and then comparing their cell-specific molecular profiles to reduce the
noise of cellular heterogeneity and inflammation. Our first goal is to identify a cell or cells of origin
for the varying phenotypes by phenotyping the tissues with single cell RNA sequencing. This includes a
comprehensive evaluation of the immune and inflammatory infiltrate as well as fluctuations in epithelial and
stromal subpopulations.
</p>
<p style="text-align:justify; font-size:18px">
We are subsequently isolating the cell types of interest and
performing molecular profiling. Based on these
targets, we will use our mouse and cell culture models to
experimentally test our hypotheses.
We are subsequently isolating the cell types of interest and performing molecular profiling. Based on these
targets, we will use our mouse and cell culture models to experimentally test our hypotheses.
</p>
</div>
<div class="section">
<H1 align="center">Clinical Heterogeneity in BPH</H1>
<p style="text-align:justify; font-size:18px">
It is clear from clinical trials of medications for BPH that
personalized therapies will be needed due to
the highly variable responses. Typically, patients complaining of
lower urinary tract symptoms are placed on
an alpha-adrenergic receptor blocker as a first line therapy due to
its fast-acting relief of symptoms.
These drugs relieve smooth muscle tone and are most effective in
patients with early stage disease
displaying a high smooth muscle to epithelial tissue composition.
However, as the prostate enlarges,
epithelial nodules predominate the tissue decreasing the likelihood
of alpha-blocker efficacy.
It is clear from clinical trials of medications for BPH that personalized therapies will be needed due to
the highly variable responses. Typically, patients complaining of lower urinary tract symptoms are placed on
an alpha-adrenergic receptor blocker as a first line therapy due to its fast-acting relief of symptoms.
These drugs relieve smooth muscle tone and are most effective in patients with early stage disease
displaying a high smooth muscle to epithelial tissue composition. However, as the prostate enlarges,
epithelial nodules predominate the tissue decreasing the likelihood of alpha-blocker efficacy.
</p>
<p style="text-align:justify; font-size:18px">
The second-line therapy for BPH is a 5 alpha reductase inhibitor
(5ARI), which induces epithelial apoptosis
by decreasing the levels of intra-prostatic dihyrotestosterone
(DHT). This therapy is effective at reducing
The second-line therapy for BPH is a 5 alpha reductase inhibitor (5ARI), which induces epithelial apoptosis
by decreasing the levels of intra-prostatic dihyrotestosterone (DHT). This therapy is effective at reducing
prostate size by 25 percent in most patients.
</p>
<p style="text-align:justify; font-size:18px">
Importantly, either therapy only reduces symptomatic progression by
34 percent, suggesting
androgen-independent mechanisms of prostate growth and symptoms need
to be targeted. Responses to current
drugs are further reduced in patients with obesity, diabetes, and
dyslipidemia.
Importantly, either therapy only reduces symptomatic progression by 34 percent, suggesting
androgen-independent mechanisms of prostate growth and symptoms need to be targeted. Responses to current
drugs are further reduced in patients with obesity, diabetes, and dyslipidemia.
</p>
<p style="text-align:justify; font-size:18px">
These data suggest that there are further measures that are
necessary for every patient, and completely
novel measures necessary for individual patients. Our goal is to
characterize the cellular composition of
particular phenotypes, and more deeply understand the molecular
changes driving these phenotypes. We use a
combination of single cell RNA sequencing, flow cytometry, and
immunohistochemistry on specimens from young
These data suggest that there are further measures that are necessary for every patient, and completely
novel measures necessary for individual patients. Our goal is to characterize the cellular composition of
particular phenotypes, and more deeply understand the molecular changes driving these phenotypes. We use a
combination of single cell RNA sequencing, flow cytometry, and immunohistochemistry on specimens from young
organ donors and older men with prostatic enlargement.
</p>
</div>
......
layouts/custom/sc.data.html
+ 4
− 4
View file @ 2398aa24
{{ partial "header.html" . }}
<div class="header">
<h1>{{ .Title }}</h1>
<h2>{{ .Description }}</h2>
<h1>{{ .Title }}</h1>
<h2>{{ .Description }}</h2>
</div>
<div class="content">
{{ range .Pages.ByWeight }}
{{ range .Pages.ByWeight }}
<li><a href="{{.Permalink}}">{{.Params.name}}</a></li>
{{ end }}
{{ end }}
</div>
{{ partial "footer.html" . }}
\ No newline at end of file
static/css/.sidenavRepository.css.swn 0 → 100644
+ 0
− 0
View file @ 2398aa24
File added
static/css/.sidenavRepository.css.swo 0 → 100644
+ 0
− 0
View file @ 2398aa24
File added
static/css/.sidenavRepository.css.swp 0 → 100644
+ 0
− 0
View file @ 2398aa24
File added
static/css/sidenavRepository.css 0 → 100644
+ 59
− 0
View file @ 2398aa24
/* the sidebar menu */
.sidenav {
width: 30% ;
position: fixed/* stay in place on scroll */
/* z-index:1; /* stay on top*/
top : 0; /* stay on top*/
left: 0; /* on left side of screen */
background: #eee;
padding-top: 2px;
padding-right:2px;
}
/* Sidenav filters */
.sidenav a, .dropdown-btn {
padding: 6px 6px 6px 6px;
text-decoration: none;
color: #818181;
display: block;
border: none;
background: none;
width:100%;
text-align: left;
cursor: pointer;
outline: none;
}
.numbers {
text-align: right;
padding: 0px 0px 0px 0px;
float: right;
}
#filter {
padding-left: 15px;
font-size: 85%;
clear: left;
}
/* On mouse-over */
.sidenav a:hover, .dropdown-btn:hover {
color: #cacfd2 ;
}
/* Add an active class to the active dropdown button */
.active {
background-color: #909497 ;
color: white;
}
/*change style of sidebar on smaller screens */
@media screen and (max-height:450px){
.sidenav {padding-top: 15px;}
.sidenav a {font-size: 18px;}
}
static/js/repoFilterLogic.js 0 → 100644
+ 0
− 0
View file @ 2398aa24
static/js/repositoryJS.js 0 → 100644
+ 83
− 0
View file @ 2398aa24
//$(document).ready(function(){
//* Loop through all dropdown buttons to toggle between hiding and showing its dropdown content - This allows the user to have multiple dropdowns without any conflict */
var dropdown = document.getElementsByClassName("dropdown-btn");
var i;
for (i = 0; i < dropdown.length; i++) {
dropdown[i].addEventListener("click", function() {
this.classList.toggle("active");
var dropdownContent = this.nextElementSibling;
if (dropdownContent.style.display === "block") {
dropdownContent.style.display = "none";
} else {
dropdownContent.style.display = "block";
}
});
}
/* Get files matching filters
//declare global vars
var results = []; //array of records that match the filters
var data = {{ index .Site.Data.scRNAseq_huPr_D.updated_cleaned_json }};
var numbers = $("#filter").find(".numbers"); //array of all the places we want to update with the # of records that match the filters
var filters = [];//array of current filters
//filtering function
$("input").click(function(){
// get specific vars
var name = $(this).attr("name");
var value = $(this).attr("value");
var id = name + value;
id= id.replace(/\s+/g, '');
var filterVar = {"name": name, "value":value, "id":id};
// if checkbox is checked: add filter values to filter
if ($(this).prop("checked") == true){
filters.push(filterVar);
/* var i;
for (i =0; i < data.length; i++){
if( data[i][name] == value){
results.push(data[i]);
$("#"+id).text[numbers.length];
}
}*/
/* }
//if checkbox is not checked: remove filter values from filter
else if ($(this).prop("checked") == false){
var i;
for (i=0; i<filter.length; i++){
if (filter[i][id]== id){
filter.splice(i, 1);
i--;
}
}
}
//check data to pull all records that match the current filters
var i;
var j;
for (i = 0; i<filters.length; i++){
var count = 0;
$('#displayFiles').text(numbers.length);
for (j=0; j <data.length; j++){
// var id2 = results[j][name]. + results[j][name];
// id2 = id2.replace(/\s+/g, '');
// $('#displayFiles').text(id2);
if (id2 == numbers[i][id]){
count++;
$('#displayFiles').text(count);
}
}
}
});
});
*/
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment