Step-by-Step Protocol for Superparamagnetic Nanoparticle-Based Endosome and Lysosome Isolation from Eukaryotic Cell. View Full Text


Ontology type: schema:Chapter     


Chapter Info

DATE

2019

AUTHORS

Deepak B Thimiri Govinda Raj , Niamat Ali Khan , Srisaran Venkatachalam , Dinh Toi Chu , Sivakumar Arumugam

ABSTRACT

Here, we report our step-by-step protocol for superparamagnetic nanoparticle (SPMNP)-based endosome and lysosome isolation from HeLa. Briefly, we synthesized SPMNP 1.0 with iron oxide (Fe3O4) core using thermal decomposition method. Further, we performed ligand-exchange strategy for surface functionalization of SPMNP 1.0 with dimercaptosuccinic acid (DMSA). Thus, we generated DMSA-SPMNP 2.0 and used DMSA-SPMNP 2.0 to isolate endosomes and lysosome from HeLa cells. Using our SPMNP subcellular fractionation protocol, we are able to isolate high-pure-high-yield lysosomes using DMSA-SPMNP 2.0 for lysosome proteomics and lipidomics in order to better understand subcellular compartments. More... »

References to SciGraph publications

Identifiers

URI

http://scigraph.springernature.com/pub.10.1007/7651_2019_212

DOI

http://dx.doi.org/10.1007/7651_2019_212

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1112157129

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/30771190


Indexing Status Check whether this publication has been indexed by Scopus and Web Of Science using the SN Indexing Status Tool
Incoming Citations Browse incoming citations for this publication using opencitations.net

JSON-LD is the canonical representation for SciGraph data.

TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT

[
  {
    "@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json", 
    "about": [
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0601", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Biochemistry and Cell Biology", 
        "type": "DefinedTerm"
      }, 
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/06", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Biological Sciences", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "Oslo University Hospital", 
          "id": "https://www.grid.ac/institutes/grid.55325.34", 
          "name": [
            "Envirotransgene\u00ae Bio-solutions Global Chennai India and Institute of Cancer Research, Oslo University Hospital, Oslo, Norway. deepak.balaji@bitsaa.org."
          ], 
          "type": "Organization"
        }, 
        "familyName": "Thimiri Govinda Raj", 
        "givenName": "Deepak B", 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "name": [
            "Laboratory of Lipid Metabolism and Cancer, Louvain, Belgium."
          ], 
          "type": "Organization"
        }, 
        "familyName": "Khan", 
        "givenName": "Niamat Ali", 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Anna University, Chennai", 
          "id": "https://www.grid.ac/institutes/grid.252262.3", 
          "name": [
            "Bannari Amman Institute of Technology, Sathyamangalam, TN, India."
          ], 
          "type": "Organization"
        }, 
        "familyName": "Venkatachalam", 
        "givenName": "Srisaran", 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Hanoi Medical University", 
          "id": "https://www.grid.ac/institutes/grid.56046.31", 
          "name": [
            "Faculty of Biology, Hanoi National University of Education, Hanoi, Vietnam.", 
            "Institute for Research and Development, Duy Tan University, Danang, Vietnam.", 
            "School of Odonto Stomatology, Hanoi Medical University, Hanoi, Vietnam."
          ], 
          "type": "Organization"
        }, 
        "familyName": "Chu", 
        "givenName": "Dinh Toi", 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Vellore Institute of Technology University", 
          "id": "https://www.grid.ac/institutes/grid.412813.d", 
          "name": [
            "School of Bio Sciences and Technology (SBST), VIT University, Vellore, TN, India."
          ], 
          "type": "Organization"
        }, 
        "familyName": "Arumugam", 
        "givenName": "Sivakumar", 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "https://doi.org/10.1038/msb.2011.74", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1000680459"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1038/msb.2011.74", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1000680459"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/s40580-016-0082-x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1005313892", 
          "https://doi.org/10.1186/s40580-016-0082-x"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/s40580-016-0082-x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1005313892", 
          "https://doi.org/10.1186/s40580-016-0082-x"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1077194", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1015841885"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1021/ja026501x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1030318270"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1021/ja026501x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1030318270"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1049/mnl.2017.0574", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1092622048"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.jmmm.2017.12.070", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1099721964"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.jmmm.2017.12.070", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1099721964"
        ], 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2019", 
    "datePublishedReg": "2019-01-01", 
    "description": "Here, we report our step-by-step protocol for superparamagnetic nanoparticle (SPMNP)-based endosome and lysosome isolation from HeLa. Briefly, we synthesized SPMNP 1.0 with iron oxide (Fe3O4) core using thermal decomposition method. Further, we performed ligand-exchange strategy for surface functionalization of SPMNP 1.0 with dimercaptosuccinic acid (DMSA). Thus, we generated DMSA-SPMNP 2.0 and used DMSA-SPMNP 2.0 to isolate endosomes and lysosome from HeLa cells. Using our SPMNP subcellular fractionation protocol, we are able to isolate high-pure-high-yield lysosomes using DMSA-SPMNP 2.0 for lysosome proteomics and lipidomics in order to better understand subcellular compartments.", 
    "genre": "chapter", 
    "id": "sg:pub.10.1007/7651_2019_212", 
    "inLanguage": [
      "en"
    ], 
    "isAccessibleForFree": false, 
    "name": "Step-by-Step Protocol for Superparamagnetic Nanoparticle-Based Endosome and Lysosome Isolation from Eukaryotic Cell.", 
    "productId": [
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1007/7651_2019_212"
        ]
      }, 
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1112157129"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "30771190"
        ]
      }
    ], 
    "publisher": {
      "location": "Berlin, Heidelberg", 
      "name": "Springer Berlin Heidelberg", 
      "type": "Organisation"
    }, 
    "sameAs": [
      "https://doi.org/10.1007/7651_2019_212", 
      "https://app.dimensions.ai/details/publication/pub.1112157129"
    ], 
    "sdDataset": "chapters", 
    "sdDatePublished": "2019-04-16T05:13", 
    "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
    "sdPublisher": {
      "name": "Springer Nature - SN SciGraph project", 
      "type": "Organization"
    }, 
    "sdSource": "s3://com-uberresearch-data-dimensions-target-20181106-alternative/cleanup/v134/2549eaecd7973599484d7c17b260dba0a4ecb94b/merge/v9/a6c9fde33151104705d4d7ff012ea9563521a3ce/jats-lookup/v90/0000000337_0000000337/records_37569_00000000.jsonl", 
    "type": "Chapter", 
    "url": "http://link.springer.com/10.1007/7651_2019_212"
  }
]
 

Download the RDF metadata as:Ā  json-ld nt turtle xml License info

HOW TO GET THIS DATA PROGRAMMATICALLY:

JSON-LD is a popular format for linked data which is fully compatible with JSON.

curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1007/7651_2019_212'

N-Triples is a line-based linked data format ideal for batch operations.

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1007/7651_2019_212'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1007/7651_2019_212'

RDF/XML is a standard XML format for linked data.

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1007/7651_2019_212'


 

This table displays all metadata directly associated to this object as RDF triples.

108 TRIPLES      20 PREDICATES      30 URIs      17 LITERALS      6 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1007/7651_2019_212 schema:about anzsrc-for:06
2 anzsrc-for:0601
3 schema:author N9a3f4b9b882444f39d7158cfef8754c1
4 schema:citation sg:pub.10.1186/s40580-016-0082-x
5 https://doi.org/10.1016/j.jmmm.2017.12.070
6 https://doi.org/10.1021/ja026501x
7 https://doi.org/10.1038/msb.2011.74
8 https://doi.org/10.1049/mnl.2017.0574
9 https://doi.org/10.1126/science.1077194
10 schema:datePublished 2019
11 schema:datePublishedReg 2019-01-01
12 schema:description Here, we report our step-by-step protocol for superparamagnetic nanoparticle (SPMNP)-based endosome and lysosome isolation from HeLa. Briefly, we synthesized SPMNP 1.0 with iron oxide (Fe<sub>3</sub>O<sub>4</sub>) core using thermal decomposition method. Further, we performed ligand-exchange strategy for surface functionalization of SPMNP 1.0 with dimercaptosuccinic acid (DMSA). Thus, we generated DMSA-SPMNP 2.0 and used DMSA-SPMNP 2.0 to isolate endosomes and lysosome from HeLa cells. Using our SPMNP subcellular fractionation protocol, we are able to isolate high-pure-high-yield lysosomes using DMSA-SPMNP 2.0 for lysosome proteomics and lipidomics in order to better understand subcellular compartments.
13 schema:genre chapter
14 schema:inLanguage en
15 schema:isAccessibleForFree false
16 schema:name Step-by-Step Protocol for Superparamagnetic Nanoparticle-Based Endosome and Lysosome Isolation from Eukaryotic Cell.
17 schema:productId N0e805b17f1dc431094d848438898c949
18 N64a962dda05243e39a34c71f2654a8cb
19 Nf0ba7ea9cd074b73a97dce916ccb5fb1
20 schema:publisher N52a96e26c60141c59ef6cdc847b44718
21 schema:sameAs https://app.dimensions.ai/details/publication/pub.1112157129
22 https://doi.org/10.1007/7651_2019_212
23 schema:sdDatePublished 2019-04-16T05:13
24 schema:sdLicense https://scigraph.springernature.com/explorer/license/
25 schema:sdPublisher N1311ba8232c2418097ed9774e33c497e
26 schema:url http://link.springer.com/10.1007/7651_2019_212
27 sgo:license sg:explorer/license/
28 sgo:sdDataset chapters
29 rdf:type schema:Chapter
30 N0e805b17f1dc431094d848438898c949 schema:name dimensions_id
31 schema:value pub.1112157129
32 rdf:type schema:PropertyValue
33 N1311ba8232c2418097ed9774e33c497e schema:name Springer Nature - SN SciGraph project
34 rdf:type schema:Organization
35 N1f42d442fdd44dddb638d121decb1f60 schema:affiliation https://www.grid.ac/institutes/grid.412813.d
36 schema:familyName Arumugam
37 schema:givenName Sivakumar
38 rdf:type schema:Person
39 N226db6936c6b4a309524dcf6676c36d9 schema:affiliation https://www.grid.ac/institutes/grid.56046.31
40 schema:familyName Chu
41 schema:givenName Dinh Toi
42 rdf:type schema:Person
43 N38917708c1bd4cc4812c152af33cace9 rdf:first N67c54ac778924a41bca5f0496e37a416
44 rdf:rest Nf50e1aa5f550497b808270e6e1b1af8f
45 N52a96e26c60141c59ef6cdc847b44718 schema:location Berlin, Heidelberg
46 schema:name Springer Berlin Heidelberg
47 rdf:type schema:Organisation
48 N5f68d9ba0df941fbbd2df9f8d649a803 rdf:first N1f42d442fdd44dddb638d121decb1f60
49 rdf:rest rdf:nil
50 N64a962dda05243e39a34c71f2654a8cb schema:name doi
51 schema:value 10.1007/7651_2019_212
52 rdf:type schema:PropertyValue
53 N67c54ac778924a41bca5f0496e37a416 schema:affiliation N9e1f7d4a41654aa28640afe0b390bbfd
54 schema:familyName Khan
55 schema:givenName Niamat Ali
56 rdf:type schema:Person
57 N9a3f4b9b882444f39d7158cfef8754c1 rdf:first Nd54b3e412f4a40098cfd863989e950de
58 rdf:rest N38917708c1bd4cc4812c152af33cace9
59 N9e1f7d4a41654aa28640afe0b390bbfd schema:name Laboratory of Lipid Metabolism and Cancer, Louvain, Belgium.
60 rdf:type schema:Organization
61 Nd54b3e412f4a40098cfd863989e950de schema:affiliation https://www.grid.ac/institutes/grid.55325.34
62 schema:familyName Thimiri Govinda Raj
63 schema:givenName Deepak B
64 rdf:type schema:Person
65 Nd54ba2047196477491b70c7edd540f3a schema:affiliation https://www.grid.ac/institutes/grid.252262.3
66 schema:familyName Venkatachalam
67 schema:givenName Srisaran
68 rdf:type schema:Person
69 Nee8c672f33eb46b5a0827a90e8707cc7 rdf:first N226db6936c6b4a309524dcf6676c36d9
70 rdf:rest N5f68d9ba0df941fbbd2df9f8d649a803
71 Nf0ba7ea9cd074b73a97dce916ccb5fb1 schema:name pubmed_id
72 schema:value 30771190
73 rdf:type schema:PropertyValue
74 Nf50e1aa5f550497b808270e6e1b1af8f rdf:first Nd54ba2047196477491b70c7edd540f3a
75 rdf:rest Nee8c672f33eb46b5a0827a90e8707cc7
76 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
77 schema:name Biological Sciences
78 rdf:type schema:DefinedTerm
79 anzsrc-for:0601 schema:inDefinedTermSet anzsrc-for:
80 schema:name Biochemistry and Cell Biology
81 rdf:type schema:DefinedTerm
82 sg:pub.10.1186/s40580-016-0082-x schema:sameAs https://app.dimensions.ai/details/publication/pub.1005313892
83 https://doi.org/10.1186/s40580-016-0082-x
84 rdf:type schema:CreativeWork
85 https://doi.org/10.1016/j.jmmm.2017.12.070 schema:sameAs https://app.dimensions.ai/details/publication/pub.1099721964
86 rdf:type schema:CreativeWork
87 https://doi.org/10.1021/ja026501x schema:sameAs https://app.dimensions.ai/details/publication/pub.1030318270
88 rdf:type schema:CreativeWork
89 https://doi.org/10.1038/msb.2011.74 schema:sameAs https://app.dimensions.ai/details/publication/pub.1000680459
90 rdf:type schema:CreativeWork
91 https://doi.org/10.1049/mnl.2017.0574 schema:sameAs https://app.dimensions.ai/details/publication/pub.1092622048
92 rdf:type schema:CreativeWork
93 https://doi.org/10.1126/science.1077194 schema:sameAs https://app.dimensions.ai/details/publication/pub.1015841885
94 rdf:type schema:CreativeWork
95 https://www.grid.ac/institutes/grid.252262.3 schema:alternateName Anna University, Chennai
96 schema:name Bannari Amman Institute of Technology, Sathyamangalam, TN, India.
97 rdf:type schema:Organization
98 https://www.grid.ac/institutes/grid.412813.d schema:alternateName Vellore Institute of Technology University
99 schema:name School of Bio Sciences and Technology (SBST), VIT University, Vellore, TN, India.
100 rdf:type schema:Organization
101 https://www.grid.ac/institutes/grid.55325.34 schema:alternateName Oslo University Hospital
102 schema:name EnvirotransgeneĀ® Bio-solutions Global Chennai India and Institute of Cancer Research, Oslo University Hospital, Oslo, Norway. deepak.balaji@bitsaa.org.
103 rdf:type schema:Organization
104 https://www.grid.ac/institutes/grid.56046.31 schema:alternateName Hanoi Medical University
105 schema:name Faculty of Biology, Hanoi National University of Education, Hanoi, Vietnam.
106 Institute for Research and Development, Duy Tan University, Danang, Vietnam.
107 School of Odonto Stomatology, Hanoi Medical University, Hanoi, Vietnam.
108 rdf:type schema:Organization
 




Preview window. Press ESC to close (or click here)


...