-
Notifications
You must be signed in to change notification settings - Fork 0
Expand file tree
/
Copy pathdata_webs.htm
More file actions
203 lines (159 loc) · 13.1 KB
/
data_webs.htm
File metadata and controls
203 lines (159 loc) · 13.1 KB
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
<!DOCTYPE HTML>
<html lang="en-US">
<head>
<META http-equiv="Content-Type" content="text/html; charset=UTF-8">
<META name="viewport" content="width=device-width, initial-scale=1">
<title>Slavov Lab | Protein, RNA and metabolite data from single-cell and bulk samples</title>
<meta name="description" content="Download and explore data interactively: single cell proteomes, mass spectrometry protein data, RNA and metabolite data" />
<META NAME="keywords" CONTENT="Datasets, data portals, single-cell mass spec proteomics, Gene expression, mass spec, metabolism, glycolysis, cell, growth">
<link rel="stylesheet" type="text/css" href="bin/nslavov_index.css">
<link rel="stylesheet" type="text/css" href="bin/nslavov_tr_table.css" >
<link rel="shortcut icon" href="index_files/icons/Slavov-Laboratory.ico">
<link rel="canonical" href="https://slavovlab.net/data_webs.htm">
<script type="text/javascript">
if (screen.width < 600) {
window.location = "https://slavovlab.net/data_webs_m.htm";
}
</script>
<script async src="https://www.googletagmanager.com/gtag/js?id=UA-4005755-5"></script>
<script language="javascript" type="text/javascript" SRC="google_track.js"></script>
</head>
<body>
<!-- ============ Logo ============== class="Header_Text" -->
<table class="Global" cellpadding="0" cellspacing="0" border="0">
<tr><td height="15" ></td></tr>
<tr>
<td align="center" height="140" style="width: 140px" >
<a href="https://slavovlab.net" title="Slavov lab | Quantitative Systems Biology" rel="home">
<img src="index_files/SlavovLab.JPG" alt="Slavov lab | Quantitative Biology" height="80" border=0></a>
</td>
<td height="140" >
<div class="header_title" "><!-- style="font-family: 'Josefin Slab', serif; letter-spacing: 0.7px; line-height:35px; font-size:30px; -->
<a href="https://slavovlab.net" title="Slavov Lab | Quantitative Systems Biology" rel="home">Slavov Laboratory | Quantitative Biology</a>
</div>
<div class="header_subtitle1" >
Seeking principles
</div>
<div class="header_subtitle3">
in the regulation of protein synthesis, functions and degradation
</div>
</td>
</tr>
<tr><td height="10" colspan="2" align="center">
<div class="ssmed_tablestyle_rb"> <div class="ssmed_tablestyle_lb"> <div class="ssmed_tablestyle_rt"> <div class="ssmed_tablestyle_lt"> <div class="area_table">
<!-- <div style="font-size:25px; line-height:65px;" >Publications</div> -->
<div Class="TopLinks" >
<a href="index.html" >Home</a> |
<a href="publications.htm">Publications</a> |
<a href="research.htm" >Research</a> |
<a href="people.htm">People</a> |
<a href="data_webs.htm" id="active">Data</a> |
<a href="Talks.htm" >Talks</a> |
<a href="https://blog.slavovlab.net/" target="_blank" >Blog</a>
</div>
</div> </div> </div> </div> </div>
</td>
<tr><td height="55" colspan="2" ></td></tr>
<tr>
<!-- ============ Content Column ============== -->
<td colspan="2" align="center" ><div class="Content2">
<h1 class="HeadingStyle" style="letter-spacing: 2px; font-size: 28px;" >Datasets & Resources from the Slavov Lab</h1>
We are committed to openly share our methodology and datasets, including metadata and computational pipelines
needed for reproducing our research workflows. We also organized the formulation of community
<a href="https://single-cell.net/guidelines" title="Community guidelines and standardized metrics for enhancing
rigor, data quality and alignment between laboratories.">guidelines</a> for performing, analyzing and reporting single-cell
proteomics by mass spectrometry. Below are links to relevant resources from the Slavov Laboratory,
the <a href="https://center.single-cell.net">Single-cell Proteomics Center</a> and collaborators.
<ul type="circle" style="line-height: 180%; letter-spacing: 1.5px; Font-Size: 16px;">
<li><a href="#dataset-portals" title="single-cell proteomics datasets and methods" >Explore Interactively and Download Data</a></li>
<li><a href="#Resources" title="Research Resources for Single-cell proteomics and cell physiology">Research Resources</a></li>
<li><a href="#Protocols" >Protocols</a></li>
<li><a href="#research-news" >Research News</a></li>
</ul>
<br>
<br>
<!-- ============ Page Heading ============== -->
<h1 class="HeadingStyle" id="dataset-portals">Methods & Data websites</h1>
<ul type="circle" style="line-height: 180%">
<li><a href="https://scp.slavovlab.net/BayesPG" target="_blank" title="Protein regulation inference by Bayesian modeling of single-cell RNA and protein abundance" >2024 | BayesPG: Protein regulation inference</a>
<li><a href="https://decode.slavovlab.net" target="_blank" title="Alternate RNA decoding results in stable and abundant proteins in mammals" >2024 | Decode: Beyond the genetic code: Alternate translation</a>
<li><a href="https://scp.slavovlab.net/QuantQC" target="_blank" title="an R package for evaluation, benchmarking and processing of single-cell proteomics data, especially data from experiments using nPOP" >2023 | QuantQC: Processing & QC pipeline for single-cell proteomics</a>
<li><a href="https://scp.slavovlab.net/pSCoPE" target="_blank" title="Prioritized single-cell proteomics by pSCoPE" >2022 | pSCoPE: Prioritized single-cell proteomics</a>
<li><a href="https://plexDIA.slavovlab.net" target="_blank" title="Increasing the throughput of sensitive proteomics by plexDIA" >2021 | plexDIA: Increasing the throughput of sensitive proteomics</a>
<li><a href="https://scp.slavovlab.net/nPOP" title="nano-ProteOmic sample Preparation (nPOP)" target="_blank" >2021 | Droplet sample preparation for single-cell proteomics</a>
<li><a href="https://scope2.slavovlab.net/mass-spec/protocol" title="Protocol for multiplexed single-cell proteomics by Mass Spectrometry" target="_blank" >2021 | Multiplexed single-cell proteomics using SCoPE2</a>
<li><a href="https://scope2.slavovlab.net/mass-spec/Isobaric-carrier-optimization" title="Optimizing accuracy and depth of protein quantification in experiments using isobaric carriers" target="_blank" >2020 | Optimizing experiments using isobaric carriers</a>
<li><a href="https://scope2.slavovlab.net" title="Next-generation Single-Cell ProtEomics by Mass Spectrometry" target="_blank" >2019 | SCoPE2: Quantifying proteins in single cells with multiplexed mass-spec</a>
<li><a href="https://do-ms.slavovlab.net" title="Data-driven optimization of LC-MS/MS" target="_blank" >2019 | DO-MS: Data-Driven Optimization of Mass Spectrometry Methods</a>
<li><a href="https://dart-id.slavovlab.net" title="Data-driven Alignment of Retention Times for IDentification of peptides" target="_blank" >2018 | Increasing single-cell proteome coverage by DART-ID</a>
<li><a href="https://sample-prep.slavovlab.net/mass-spec/mPOP" title="Minimal ProteOmic sample Preparation (mPOP)" target="_blank" >2018 | Automated sample preparation for high-throughput single-cell proteomics</a>
<li><a href="2016_SCoPE-MS/index.html" title="First-generation Single-Cell ProtEomics by Mass Spectrometry" target="_blank" >2016 | Single-Cell ProtEomics by Mass Spectrometry (SCoPE-MS)</a>
<li><a href="2016_PTR/index.html" target="_blank" >2016 | Post-transcriptional regulation across human tissues</a>
<li><a href="https://slavovlab.net/2015_Ribosome_Data/index.html" title="Direct evidence for ribosome specialization" target="_blank" >2015 | Protein Composition of Ribosomes across Growth Conditions</a>
<li><a href="https://pubmed.ncbi.nlm.nih.gov/30282776/" target="_blank">2014 | Quantifying homologous proteins and proteoforms</a>
<li><a href="2014_Exponential_Cell_Growth/index.html" target="_blank" >2014 | Metabolic Remodeling during Exponential Cell Growth</a>
<li><a href="https://slavovlab.net/2012_Aerobic_glycolysis/index.html" target="_blank" >2013 | Growth Deregulation and Aerobic Glycolysis</a>
<li><a href="http://genomics-pubs.princeton.edu/YMC_in_Ethanol_Batch/index.html" target="_blank" >2011 | Metabolic Cycling without Cell Division Cycling</a>
<li><a href="https://slavovlab.net/2010_Growth_Rate_Response/index.html" title="Transcriptional and metabolic responses to growth rate" target="_blank" >2010 | Transcriptional and metabolic growth rate response</a>
<!--
<li><a href="http://genomics.princeton.edu/~nslavov/fish.htm" target="_blank" >FISH </a>
<li><a href="https://web.northeastern.edu/slavovlab/meta/ATP.html" target="_blank" >Linking metabolites and transcripts </a>
http://www.genomics.princeton.edu/~nslavov/ymc/metabolites.html
<li><a href="http://genomics.princeton.edu/~nslavov/apoptosis/" target="_blank" >Apoptosis</a> -->
</ul>
<i> For best viewing of the data webs, use Chrome or Firefox.</i>
<br><br>
<h1 class="HeadingStyle" id="Resources">Resources</h1>
<ul type="circle" style="line-height: 180%">
<li> <a href="https://scp.slavovlab.net" title="Single-Cell Proteomics Methods, Data and Protocols" target="_blank" >Single-Cell Proteomics Methods, Data and Protocols</a>
<li> <a href="https://github.com/SlavovLab" title="Code from Slavov Laboratory" target="_blank" >GitHub repositories for code</a>
<li> <a href="https://center.single-cell.net/" title="Single-Cell Proteomics Center" target="_blank" >Single Cell Proteomics Center</a>
<li> <a href="https://center.single-cell.net/single-cell-proteomics/dissemination" title="Disseminating single-cell proteomics technology and facilitating its broader adoption" target="_blank" >Technology dissemination</a>
<li> <a href="https://www.protocols.io/workspaces/slavovlab/publications" target="_blank" >Lab Protocols @ protocols.io</a> <br>
</ul>
<h1 class="HeadingStyle" id="Protocols">Protocols</h1>
<ul type="circle" style="line-height: 180%">
<li> <a href="https://scp.slavovlab.net/protocols" title="Protocols for multiplexed Single-Cell Proteomics by mass spec" target="_blank" >Multiplexed Single-Cell Proteomics</a> <br>
<li> <a href="https://scope2.slavovlab.net/mass-spec/protocol" title="SCoPE2 protocol for multiplexed Single-Cell Proteomics" target="_blank" >Single-Cell Proteomics by SCoPE2</a> <br>
<li> <a href="https://scp.slavovlab.net/sample-preparation" target="_blank" >Sample preparation for single-cell proteomics</a> <br>
<li> <a href="Slavov-Lab-Publications/Protocols/glucose_limit.pdf" target="_blank" >Glucose-Limited Medium</a> <br>
<li> <a href="Slavov-Lab-Publications/Protocols/ethanol_limit_ethanol_cs.pdf" target="_blank" >Ethanol-Limited Medium</a> <br>
<li> <a href="Slavov-Lab-Publications/Protocols/phosphate_limit_ethanol_cs.pdf" target="_blank" >Phosphate-Limited Medium with Ethanol as a Sole Source of Carbon and Energy</a> <br>
<li> <a href="Slavov-Lab-Publications/Protocols/nitrogen_limit_ethanol_cs.pdf" target="_blank" >Nitrogen-Limited Medium with Ethanol as a Sole Source of Carbon and Energy</a> <br>
<li> <a href="http://genomics-pubs.princeton.edu/grr/Experimental_Design.html" target="_blank" >Media Characterization</a> <br>
<li> <a href="Slavov-Lab-Publications/Protocols/stress_resistance.pdf" target="_blank" >Measuring heat and oxidative stress resistance of yeast cells</a> <br>
<li> <a href="Slavov-Lab-Publications/Protocols/Methanol_Chloroform_Protein_Purification.pdf" target="_blank" >Methanol-Chloroform Purification of Proteins</a> <br>
<li> <a href="mESC_cultures.htm" target="_blank" >Culturing Mouse Embryonic Stem Cells</a> <br>
</ul>
<br><br>
<h1 class="HeadingStyle" id="research-news">News and Recently Published Research</h1>
<a href="https://center.single-cell.net/single-cell-proteomics/news" title="News from the Single Cell Proteomics Center" target="_blank" >News from the Single Cell Proteomics Center</a><br>
<a href="https://twitter.com/SlavovLab" target="_blank" >Slavov Lab @ X</a><br>
<a href="https://www.linkedin.com/company/slavovlab/" target="_blank" >Slavov Lab @ Linkedin</a><br>
<!-- <a href="https://www.facebook.com/Single.Cell.Proteomics/" target="_blank" >Single Cell Proteomics</a> -->
<br>
<br>
<!--
<i> For best viewing of some data webs you may need plugins that can be found at: </i>
<ol type="i">
<li> PDF plugins:
<a href="https://addons.mozilla.org/en-US/firefox/addon/636" target="_blank">Firefox</a>,
<a href="http://code.google.com/p/firefox-mac-pdf/" target="_blank">PDFKit for Firefox</a>,
<a href=" http://www.opera.com/support/kb/view/723/" target="_blank">Opera</a>
<li> Java Embedding Plugin: <a href="http://www.versiontracker.com/dyn/moreinfo/macosx/23790&vid=515869">Mac OS </a>
<br>
-->
</div>
</td>
<tr><td height="100" colspan="2" align="center">
</tr>
<!-- ============ Footer ============== -->
<tr><td colspan="2" class="Footer">
<div class="FooterWrap">
<div class="Copyright">Copyright © <a href="https://coe.northeastern.edu/people/slavov-nikolai/" target="_blank" title="Professor Slavov Faculty Profile" >Nikolai Slavov</a> | <a href="https://www.researchgate.net/profile/Nikolai_Slavov" target="_blank" title="Professor Slavov" >Николай Славов</a></div>
</div>
</td></tr></table>
</body>
</html>