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Application of in-house virtual protein database performed in genomic-proteomic combined research on heavy-metal stressed onion roots

Björn, Lars Olof LU ; Ning, Chanjuan; Qin, Rong; Chen, Da and Li, Shaoshan (2016) In Biotechnology Letters 38(8). p.1293-1300
Abstract
Objectives To establish an in-house virtual protein database that can be employed in proteomic research on non-model plants. Results A total of 87,430 unigenes were obtained through transcriptome sequencing from onion roots. Of these, 24,305 unigenes were annotated and their nucleotide sequences of coding regions were translated into amino acid sequences. The corresponding 24,305 amino acid sequences were considered as an in-house virtual protein database. Thirty-two protein spots with significant differential abundance were selected. Their MS data were submitted to a restriction enzyme map which was converted from the in-house virtual protein database. A total of 27 proteins were finally matched.
Conclusions The in-house protein... (More)
Objectives To establish an in-house virtual protein database that can be employed in proteomic research on non-model plants. Results A total of 87,430 unigenes were obtained through transcriptome sequencing from onion roots. Of these, 24,305 unigenes were annotated and their nucleotide sequences of coding regions were translated into amino acid sequences. The corresponding 24,305 amino acid sequences were considered as an in-house virtual protein database. Thirty-two protein spots with significant differential abundance were selected. Their MS data were submitted to a restriction enzyme map which was converted from the in-house virtual protein database. A total of 27 proteins were finally matched.
Conclusions The in-house protein database is a
feasible and innovative strategy for proteomic
research on non-model plants. (Less)
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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
In-house database , Non-model plants, Proteomic research , Restriction enzyme map, Unigenes
in
Biotechnology Letters
volume
38
issue
8
pages
8 pages
publisher
Springer
external identifiers
  • Scopus:84966270821
ISSN
1573-6776
DOI
10.1007/s10529-016-2114-3
language
English
LU publication?
yes
id
3ed6a6b6-e29c-47a3-b92b-4b2dbf0ccdc3
date added to LUP
2016-06-06 17:11:55
date last changed
2016-10-13 05:09:51
@misc{3ed6a6b6-e29c-47a3-b92b-4b2dbf0ccdc3,
  abstract     = {Objectives To establish an in-house virtual protein database that can be employed in proteomic research on non-model plants. Results A total of 87,430 unigenes were obtained through transcriptome sequencing from onion roots. Of these, 24,305 unigenes were annotated and their nucleotide sequences of coding regions were translated into amino acid sequences. The corresponding 24,305 amino acid sequences were considered as an in-house virtual protein database. Thirty-two protein spots with significant differential abundance were selected. Their MS data were submitted to a restriction enzyme map which was converted from the in-house virtual protein database. A total of 27 proteins were finally matched.<br/>Conclusions The in-house protein database is a<br/>feasible and innovative strategy for proteomic<br/>research on non-model plants.},
  author       = {Björn, Lars Olof and Ning, Chanjuan and Qin, Rong and Chen, Da and Li, Shaoshan},
  issn         = {1573-6776},
  keyword      = {In-house database      ,Non-model plants,Proteomic research ,Restriction enzyme map,Unigenes},
  language     = {eng},
  number       = {8},
  pages        = {1293--1300},
  publisher    = {ARRAY(0xd41a028)},
  series       = {Biotechnology Letters},
  title        = {Application of in-house virtual protein database performed in genomic-proteomic combined research on heavy-metal stressed onion roots},
  url          = {http://dx.doi.org/10.1007/s10529-016-2114-3},
  volume       = {38},
  year         = {2016},
}