Transcriptome Studies in Trypanosoma cruzi Using RNA-seq. View Full Text


Ontology type: schema:Chapter     


Chapter Info

DATE

2019

AUTHORS

Gonzalo Greif , Luisa Berná , Florencia Díaz-Viraqué , Carlos Robello

ABSTRACT

RNA-seq is a powerful method to study in detail transcriptome changes in defined conditions, providing enormous amount of information on RNA stability and gene regulation. In this chapter, we describe a directional and a nondirectional library preparation protocol for RNA-seq in Trypanosoma cruzi, as well as a pipeline for bioinformatic analysis, which includes read trimming, alignment to a reference genome, and differential expression. More... »

PAGES

35-45

Book

TITLE

T. cruzi Infection

ISBN

978-1-4939-9147-1
978-1-4939-9148-8

Author Affiliations

Identifiers

URI

http://scigraph.springernature.com/pub.10.1007/978-1-4939-9148-8_3

DOI

http://dx.doi.org/10.1007/978-1-4939-9148-8_3

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1112730810

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/30868517


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/2008/0604", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Genetics", 
        "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": "Institut Pasteur de Montevideo", 
          "id": "https://www.grid.ac/institutes/grid.418532.9", 
          "name": [
            "Laboratory of Host Pathogen Interactions-UBM, Institut Pasteur de Montevideo, Montevideo, Uruguay."
          ], 
          "type": "Organization"
        }, 
        "familyName": "Greif", 
        "givenName": "Gonzalo", 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Institut Pasteur de Montevideo", 
          "id": "https://www.grid.ac/institutes/grid.418532.9", 
          "name": [
            "Laboratory of Host Pathogen Interactions-UBM, Institut Pasteur de Montevideo, Montevideo, Uruguay."
          ], 
          "type": "Organization"
        }, 
        "familyName": "Bern\u00e1", 
        "givenName": "Luisa", 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Institut Pasteur de Montevideo", 
          "id": "https://www.grid.ac/institutes/grid.418532.9", 
          "name": [
            "Laboratory of Host Pathogen Interactions-UBM, Institut Pasteur de Montevideo, Montevideo, Uruguay."
          ], 
          "type": "Organization"
        }, 
        "familyName": "D\u00edaz-Viraqu\u00e9", 
        "givenName": "Florencia", 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Institut Pasteur de Montevideo", 
          "id": "https://www.grid.ac/institutes/grid.418532.9", 
          "name": [
            "Laboratory of Host Pathogen Interactions-UBM, Institut Pasteur de Montevideo, Montevideo, Uruguay. robello@pasteur.edu.uy.", 
            "Departamento de Bioqu\u00edmica, Facultad de Medicina-UDELAR, Montevideo, Uruguay. robello@pasteur.edu.uy."
          ], 
          "type": "Organization"
        }, 
        "familyName": "Robello", 
        "givenName": "Carlos", 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "https://doi.org/10.1371/journal.ppat.1001090", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1007969467"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1371/journal.ppat.1005511", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1008315421"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/0003-2697(87)90021-2", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1013321498"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/s13059-014-0550-8", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1015222646", 
          "https://doi.org/10.1186/s13059-014-0550-8"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/s13059-014-0550-8", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1015222646", 
          "https://doi.org/10.1186/s13059-014-0550-8"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1112631", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1021102160"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1590/s0074-02761988000100016", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1025665532"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1371/journal.pntd.0003975", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1028743992"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1371/journal.ppat.1001037", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1034156285"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1371/journal.pntd.0002806", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1043656168"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nmeth.1226", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1045381177", 
          "https://doi.org/10.1038/nmeth.1226"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/gb-2009-10-3-r25", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1049583368", 
          "https://doi.org/10.1186/gb-2009-10-3-r25"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.3389/fcell.2017.00008", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1083800454"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1002/jcb.25978", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1084012971"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.7717/peerj.3017", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1084488480"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/s12864-017-4163-y", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1092241348", 
          "https://doi.org/10.1186/s12864-017-4163-y"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1371/journal.pone.0188441", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1093062250"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1371/journal.ppat.1006767", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1099672547"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/279174", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1101524077"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/279174", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1101524077"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/279174", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1101524077"
        ], 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2019", 
    "datePublishedReg": "2019-01-01", 
    "description": "RNA-seq is a powerful method to study in detail transcriptome changes in defined conditions, providing enormous amount of information on RNA stability and gene regulation. In this chapter, we describe a directional and a nondirectional library preparation protocol for RNA-seq in Trypanosoma cruzi, as well as a pipeline for bioinformatic analysis, which includes read trimming, alignment to a reference genome, and differential expression.", 
    "editor": [
      {
        "familyName": "G\u00f3mez", 
        "givenName": "Karina Andrea", 
        "type": "Person"
      }, 
      {
        "familyName": "Buscaglia", 
        "givenName": "Carlos Andr\u00e9s", 
        "type": "Person"
      }
    ], 
    "genre": "chapter", 
    "id": "sg:pub.10.1007/978-1-4939-9148-8_3", 
    "inLanguage": [
      "en"
    ], 
    "isAccessibleForFree": false, 
    "isPartOf": {
      "isbn": [
        "978-1-4939-9147-1", 
        "978-1-4939-9148-8"
      ], 
      "name": "T. cruzi Infection", 
      "type": "Book"
    }, 
    "name": "Transcriptome Studies in Trypanosoma cruzi Using RNA-seq.", 
    "pagination": "35-45", 
    "productId": [
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "30868517"
        ]
      }, 
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1112730810"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1007/978-1-4939-9148-8_3"
        ]
      }
    ], 
    "publisher": {
      "location": "New York, NY", 
      "name": "Springer New York", 
      "type": "Organisation"
    }, 
    "sameAs": [
      "https://doi.org/10.1007/978-1-4939-9148-8_3", 
      "https://app.dimensions.ai/details/publication/pub.1112730810"
    ], 
    "sdDataset": "chapters", 
    "sdDatePublished": "2019-04-16T08:53", 
    "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/v90/0000000368_0000000368/records_78968_00000001.jsonl", 
    "type": "Chapter", 
    "url": "http://link.springer.com/10.1007/978-1-4939-9148-8_3"
  }
]
 

Download the RDF metadata as:  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.10.1007/978-1-4939-9148-8_3'

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

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1007/978-1-4939-9148-8_3'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1007/978-1-4939-9148-8_3'

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

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1007/978-1-4939-9148-8_3'


 

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

147 TRIPLES      23 PREDICATES      45 URIs      20 LITERALS      8 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1007/978-1-4939-9148-8_3 schema:about anzsrc-for:06
2 anzsrc-for:0604
3 schema:author N48cb52d717364be48d01cae813b59125
4 schema:citation sg:pub.10.1038/nmeth.1226
5 sg:pub.10.1186/gb-2009-10-3-r25
6 sg:pub.10.1186/s12864-017-4163-y
7 sg:pub.10.1186/s13059-014-0550-8
8 https://doi.org/10.1002/jcb.25978
9 https://doi.org/10.1016/0003-2697(87)90021-2
10 https://doi.org/10.1101/279174
11 https://doi.org/10.1126/science.1112631
12 https://doi.org/10.1371/journal.pntd.0002806
13 https://doi.org/10.1371/journal.pntd.0003975
14 https://doi.org/10.1371/journal.pone.0188441
15 https://doi.org/10.1371/journal.ppat.1001037
16 https://doi.org/10.1371/journal.ppat.1001090
17 https://doi.org/10.1371/journal.ppat.1005511
18 https://doi.org/10.1371/journal.ppat.1006767
19 https://doi.org/10.1590/s0074-02761988000100016
20 https://doi.org/10.3389/fcell.2017.00008
21 https://doi.org/10.7717/peerj.3017
22 schema:datePublished 2019
23 schema:datePublishedReg 2019-01-01
24 schema:description RNA-seq is a powerful method to study in detail transcriptome changes in defined conditions, providing enormous amount of information on RNA stability and gene regulation. In this chapter, we describe a directional and a nondirectional library preparation protocol for RNA-seq in Trypanosoma cruzi, as well as a pipeline for bioinformatic analysis, which includes read trimming, alignment to a reference genome, and differential expression.
25 schema:editor N89551ac0a78c48489b004202d9799ca4
26 schema:genre chapter
27 schema:inLanguage en
28 schema:isAccessibleForFree false
29 schema:isPartOf N5feb7f5a8b6940fd8b562e5e147ba602
30 schema:name Transcriptome Studies in Trypanosoma cruzi Using RNA-seq.
31 schema:pagination 35-45
32 schema:productId N5d5a41bebba24f9b9546e356b690b128
33 N760d030d24794e5198c3c9f671ba65aa
34 Ne8b8efd53f924c038a02fa0dd2fa5e00
35 schema:publisher N339b67c4d5e948b18643ab33ef23230c
36 schema:sameAs https://app.dimensions.ai/details/publication/pub.1112730810
37 https://doi.org/10.1007/978-1-4939-9148-8_3
38 schema:sdDatePublished 2019-04-16T08:53
39 schema:sdLicense https://scigraph.springernature.com/explorer/license/
40 schema:sdPublisher Nf3a8cce6194b4eff90edb486faea0bdc
41 schema:url http://link.springer.com/10.1007/978-1-4939-9148-8_3
42 sgo:license sg:explorer/license/
43 sgo:sdDataset chapters
44 rdf:type schema:Chapter
45 N0e6d98e9fe974eef8fca42a35cc36b7c rdf:first N40300fd5c81444d5927fb374b7890392
46 rdf:rest rdf:nil
47 N1ab1d30c00204a4a8744d19f554f6770 rdf:first Nb990ea46996b4c5a8e5e8d0f6fcf38fb
48 rdf:rest rdf:nil
49 N339b67c4d5e948b18643ab33ef23230c schema:location New York, NY
50 schema:name Springer New York
51 rdf:type schema:Organisation
52 N40300fd5c81444d5927fb374b7890392 schema:affiliation https://www.grid.ac/institutes/grid.418532.9
53 schema:familyName Robello
54 schema:givenName Carlos
55 rdf:type schema:Person
56 N48cb52d717364be48d01cae813b59125 rdf:first N78d65bedc3b244b19a8cf8745de157c6
57 rdf:rest Nd43cfa8cc09d488ab6f6a177e7efec2e
58 N5d5a41bebba24f9b9546e356b690b128 schema:name pubmed_id
59 schema:value 30868517
60 rdf:type schema:PropertyValue
61 N5feb7f5a8b6940fd8b562e5e147ba602 schema:isbn 978-1-4939-9147-1
62 978-1-4939-9148-8
63 schema:name T. cruzi Infection
64 rdf:type schema:Book
65 N760d030d24794e5198c3c9f671ba65aa schema:name dimensions_id
66 schema:value pub.1112730810
67 rdf:type schema:PropertyValue
68 N7774321ab2bf41fbbc3f07c1000caf96 schema:affiliation https://www.grid.ac/institutes/grid.418532.9
69 schema:familyName Berná
70 schema:givenName Luisa
71 rdf:type schema:Person
72 N78d65bedc3b244b19a8cf8745de157c6 schema:affiliation https://www.grid.ac/institutes/grid.418532.9
73 schema:familyName Greif
74 schema:givenName Gonzalo
75 rdf:type schema:Person
76 N89551ac0a78c48489b004202d9799ca4 rdf:first Nf8c5f9acb5f24e4fa9db5036c96e6f08
77 rdf:rest N1ab1d30c00204a4a8744d19f554f6770
78 Nb990ea46996b4c5a8e5e8d0f6fcf38fb schema:familyName Buscaglia
79 schema:givenName Carlos Andrés
80 rdf:type schema:Person
81 Nd047333460ff4a909a597cc7b924f253 rdf:first Nd26118feed2a4df4bda338451a48379b
82 rdf:rest N0e6d98e9fe974eef8fca42a35cc36b7c
83 Nd26118feed2a4df4bda338451a48379b schema:affiliation https://www.grid.ac/institutes/grid.418532.9
84 schema:familyName Díaz-Viraqué
85 schema:givenName Florencia
86 rdf:type schema:Person
87 Nd43cfa8cc09d488ab6f6a177e7efec2e rdf:first N7774321ab2bf41fbbc3f07c1000caf96
88 rdf:rest Nd047333460ff4a909a597cc7b924f253
89 Ne8b8efd53f924c038a02fa0dd2fa5e00 schema:name doi
90 schema:value 10.1007/978-1-4939-9148-8_3
91 rdf:type schema:PropertyValue
92 Nf3a8cce6194b4eff90edb486faea0bdc schema:name Springer Nature - SN SciGraph project
93 rdf:type schema:Organization
94 Nf8c5f9acb5f24e4fa9db5036c96e6f08 schema:familyName Gómez
95 schema:givenName Karina Andrea
96 rdf:type schema:Person
97 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
98 schema:name Biological Sciences
99 rdf:type schema:DefinedTerm
100 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
101 schema:name Genetics
102 rdf:type schema:DefinedTerm
103 sg:pub.10.1038/nmeth.1226 schema:sameAs https://app.dimensions.ai/details/publication/pub.1045381177
104 https://doi.org/10.1038/nmeth.1226
105 rdf:type schema:CreativeWork
106 sg:pub.10.1186/gb-2009-10-3-r25 schema:sameAs https://app.dimensions.ai/details/publication/pub.1049583368
107 https://doi.org/10.1186/gb-2009-10-3-r25
108 rdf:type schema:CreativeWork
109 sg:pub.10.1186/s12864-017-4163-y schema:sameAs https://app.dimensions.ai/details/publication/pub.1092241348
110 https://doi.org/10.1186/s12864-017-4163-y
111 rdf:type schema:CreativeWork
112 sg:pub.10.1186/s13059-014-0550-8 schema:sameAs https://app.dimensions.ai/details/publication/pub.1015222646
113 https://doi.org/10.1186/s13059-014-0550-8
114 rdf:type schema:CreativeWork
115 https://doi.org/10.1002/jcb.25978 schema:sameAs https://app.dimensions.ai/details/publication/pub.1084012971
116 rdf:type schema:CreativeWork
117 https://doi.org/10.1016/0003-2697(87)90021-2 schema:sameAs https://app.dimensions.ai/details/publication/pub.1013321498
118 rdf:type schema:CreativeWork
119 https://doi.org/10.1101/279174 schema:sameAs https://app.dimensions.ai/details/publication/pub.1101524077
120 rdf:type schema:CreativeWork
121 https://doi.org/10.1126/science.1112631 schema:sameAs https://app.dimensions.ai/details/publication/pub.1021102160
122 rdf:type schema:CreativeWork
123 https://doi.org/10.1371/journal.pntd.0002806 schema:sameAs https://app.dimensions.ai/details/publication/pub.1043656168
124 rdf:type schema:CreativeWork
125 https://doi.org/10.1371/journal.pntd.0003975 schema:sameAs https://app.dimensions.ai/details/publication/pub.1028743992
126 rdf:type schema:CreativeWork
127 https://doi.org/10.1371/journal.pone.0188441 schema:sameAs https://app.dimensions.ai/details/publication/pub.1093062250
128 rdf:type schema:CreativeWork
129 https://doi.org/10.1371/journal.ppat.1001037 schema:sameAs https://app.dimensions.ai/details/publication/pub.1034156285
130 rdf:type schema:CreativeWork
131 https://doi.org/10.1371/journal.ppat.1001090 schema:sameAs https://app.dimensions.ai/details/publication/pub.1007969467
132 rdf:type schema:CreativeWork
133 https://doi.org/10.1371/journal.ppat.1005511 schema:sameAs https://app.dimensions.ai/details/publication/pub.1008315421
134 rdf:type schema:CreativeWork
135 https://doi.org/10.1371/journal.ppat.1006767 schema:sameAs https://app.dimensions.ai/details/publication/pub.1099672547
136 rdf:type schema:CreativeWork
137 https://doi.org/10.1590/s0074-02761988000100016 schema:sameAs https://app.dimensions.ai/details/publication/pub.1025665532
138 rdf:type schema:CreativeWork
139 https://doi.org/10.3389/fcell.2017.00008 schema:sameAs https://app.dimensions.ai/details/publication/pub.1083800454
140 rdf:type schema:CreativeWork
141 https://doi.org/10.7717/peerj.3017 schema:sameAs https://app.dimensions.ai/details/publication/pub.1084488480
142 rdf:type schema:CreativeWork
143 https://www.grid.ac/institutes/grid.418532.9 schema:alternateName Institut Pasteur de Montevideo
144 schema:name Departamento de Bioquímica, Facultad de Medicina-UDELAR, Montevideo, Uruguay. robello@pasteur.edu.uy.
145 Laboratory of Host Pathogen Interactions-UBM, Institut Pasteur de Montevideo, Montevideo, Uruguay.
146 Laboratory of Host Pathogen Interactions-UBM, Institut Pasteur de Montevideo, Montevideo, Uruguay. robello@pasteur.edu.uy.
147 rdf:type schema:Organization
 




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


...