Dataset Information

Quantitative proteomics study on rice embryo during embryogenesis by using isobaric tags for relative and absolute quantification (iTRAQ)

ABSTRACT: Sample Info.: There are five embryogenesis stages, 6, 12, 18, 24 and 30 days after pollination (DAP). We collect the rice embryos from above five stages. Protein extraction and analysis: Embryos of the five sampling time points were used for protein extraction and One hundred micro gram extracted proteins of each sampling time point was tryptic digested and then labeled with iTRAQ 113, 115, 117, 119 and 121 for 6, 12, 18, 24 and 30 DAP resceptively. The labeled peptides were mixed together and then fractionated via SCX column to 10 fraction (named from 1 to 10). Two microgram peptides of each fraction was loaded onto a nano HPLC mounted with C 18 column and tandermed with a Q-Exactive mass spectrometer. For each fraction, three technical analysis were conducted (e.g., for fraction 5, the three injection raw files were named as 5_1, 5_2 and 5_3). Protein search: Each group of raw files (e.g., 1_1, 2_1, ... , 10_1) were combined and used for Mascot search and the search results were also uploaded in this system. F009646, F009647 and F009648 represent the mascot search result of replication 1, 2 and 3 respectively.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Oryza Sativa (rice)

SUBMITTER: Jin Zi

PROVIDER: PXD000313 | Pride | 2013-08-06

REPOSITORIES: Pride

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

Zi Jin J Zhang Jiyuan J Wang Quanhui Q Zhou Baojin B Zhong Junyan J Zhang Chaoliang C Qiu Xuemei X Wen Bo B Zhang Shenyan S Fu Xiqin X Lin Liang L Liu Siqi S

PloS one 20130918 9

Embryogenesis is the initial step in 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 the 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, and the abundances of 867 ...[more]

PMID: 24058531

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Project description:Human histomonocytic U937 cells exhibit macrophage-like properties after phorbol ester stimulation. Accumulating evidence demonstrated that remarkable number of transcripts changed in their amount at total RNA levels. However, post-transcriptional regulation has not been fully elucidated in this model. Thus, we compared expression profiles between polysomal and cytoplasmic RNAs before and after phorbol 12-myristate 13-acetate stimulation (48h, 32nM). Table 1: Detailed description of the expression data of human histomonocytic cell line U937 cells. Data of total cytoplasmic and polysomal fractions before and after PMA stimulation is shown. This table contains all spot data except: 1) saturated spots, 2) undetectable spots, 3) stained spots, and 4) spots only detected in less than one samples. Column A: Gene symbol (“I_xxxxxx” is corresponding to EST clones) Column B: Genbank accession no. Column C: Description Column D: Average value of expression levels in total cytoplasmic fraction in the absence of PMA Column E: Average value of expression levels in total cytoplasmic fraction in the presence of PMA (32nM, 48h) Column F: Average value of expression levels in polysomal fraction in the absence of PMA Column G: Average value of expression levels in polysomal fraction in the presence of PMA Column H: Expression ratio of polysome, PMA (-) to cytoplasm, PMA(-) Column I: Expression ratio of polysome, PMA (+) to cytoplasm, PMA(+) Column J: Expression ratio of cytoplasm, PMA (+) to cytoplasm, PMA(-) Column K: Expression ratio of polysome, PMA (+) to polysome, PMA(-) Column L: Different expression between polysome, PMA (-) and cytoplasm, PMA(-): different=1 Column M: Different expression between polysome, PMA (+) and cytoplasm, PMA(+): different=1 Column N: Different expression between cytoplasm, PMA (+) and cytoplasm, PMA(-): different=1 Column O: Different expression between polysome, PMA (+) and polysome, PMA(-): different=1 Table 2: Candidates post-transcriptionally regulated by PMA. We extracted 105 transcripts whose expression levels were altered only in either fraction accompanied by changes in polysome/cytoplasm expression ratio. Column A: Gene symbol (“I_xxxxxx” is corresponding to EST clones) Column B: Genbank accession no. Column C: Description Column D: Average value of expression levels in total cytoplasmic fraction in the absence of PMA Column E Average value of expression levels in total cytoplasmic fraction in the presence of PMA Column F: Average value of expression levels in polysomal fraction in the absence of PMA Column G: Average value of expression levels in polysomal fraction in the presence of PMA Column H: Expression ratio of polysome, PMA (-) to cytoplasm, PMA(-) Column I: Expression ratio of polysome, PMA (+) to cytoplasm, PMA(+) Column J: Expression ratio of cytoplasm, PMA (+) to cytoplasm, PMA(-) Column K: Expression ratio of polysome, PMA (+) to polysome, PMA(-) Keywords = phorbol ester Keywords = macrophage Keywords = polysome Keywords = post-transcriptional regulation Keywords: parallel sample

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