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Data released on July 08, 2013

Stress responsive proteins are actively regulated during rice (Oryza sativa) embryogenesis as indicated by quantitative proteomics analysis

Fu, X; Lin, L; Liu, S; Qiu, X; Wang, Q; Wen, B; Zhang, C; Zhang, J; Zhang, S; Zhong, J; Zhou, B; Zi, J (2013): Stress responsive proteins are actively regulated during rice (Oryza sativa) embryogenesis as indicated by quantitative proteomics analysis GigaScience Database. http://dx.doi.org/10.5524/100053 RIS BibTeX Text

Embryogenesis is the beginning of a plant’s life, and the molecular changes that occur during embryonic development are largely unknown. To explore the relevant molecular events, we used the isobaric tags for relative and absolute quantification (iTRAQ) coupled with shotgun proteomics technique (iTRAQ/Shotgun) to study the proteomic changes of rice embryos during embryogenesis. For the first time, a total of 2,165 unique proteins were identified in rice embryos by using the Q-Exactive Mass spectrometry, and the abundances of 867 proteins were actively changed based on statistical evaluation towards the quantitative MS/MS signals. The quantitative data were then confirmed by using multiple reactions monitoring (MRM) conducted on Qtrap 5500 Mass spectrometry. To make the study reproducible by others, all of the raw Q-Exactive and Qtrap 5500 data had been deposited in the GigaScience database (GigaDB).
By using the WENGO software, we further analyze the GO distribution of the identified embryo proteins. In the molecular functional group, the identified proteins that work as metabolic enzymes, binding (protein binding, nucleotide binding) and transporter are ranked at the top of the category. In the biological process categorization, the proteins that participate in metabolic and response to stimulus process are at the top ratio in the identified embryo proteins.

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Related manuscripts:

doi:10.1371/journal.pone.0074229 (PubMed: 24058531)

Accessions (data included in GigaDB):

PeptideAtlas: PASS00265
ProteomeCentral: PXD000313

Proteomic

http://gigadb.org/images/data/cropped/100063_RicePlant.jpg

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
RICEEMBRYO_12DAP4530RicericeOryza sativa Altitude:40
Amount or size of sample collected:0.5
Collection date:autumn 2009
...
+
RICEEMBRYO_18DAP4530RicericeOryza sativa Altitude:40
Amount or size of sample collected:0.5
Collection date:autumn 2009
...
+
RICEEMBRYO_24DAP4530RicericeOryza sativa Altitude:40
Amount or size of sample collected:0.7
Collection date:autumn 2009
...
+
RICEEMBRYO_30DAP4530RicericeOryza sativa Altitude:40
Amount or size of sample collected:0.8
Collection date:autumn 2009
...
+
RICEEMBRYO_6DAP4530RicericeOryza sativa Altitude:40
Amount or size of sample collected:0.3
Collection date:autumn 2009
...
+
Displaying 1-5 of 5 Sample(s).

Files: (FTP site) Table Settings

Columns:

File Description
Sample ID
File Type
File Format
Size
Release Date
Download Link
File Attributes

File NameSample IDFile TypeFile FormatSizeRelease Date 
RICEEMBRYO_6DAP +Mass Spectrometry dataUNKNOWN-0 KB2013-07-08
RICEEMBRYO_6DAP +Multiple Reaction Monitoring (MRM)UNKNOWN-0 KB2013-07-08
RICEEMBRYO_6DAP +Mass Spectrometry dataUNKNOWN3.79 GB2013-07-08
RICEEMBRYO_6DAP +Mass Spectrometry dataUNKNOWN2.62 GB2013-07-08
RICEEMBRYO_6DAP +Mass Spectrometry dataUNKNOWN2.61 GB2013-07-08
ReadmeTEXT-0 KB2013-07-08
RICEEMBRYO_6DAP +Mass Spectrometry dataUNKNOWN345.16 MB2013-07-08
RICEEMBRYO_6DAP +AnnotationTEXT309.69 MB2013-07-08
RICEEMBRYO_6DAP +Mass Spectrometry dataUNKNOWN310.07 MB2013-07-08
Displaying 1-9 of 9 File(s).

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