Dataset Information

Proteogenomics of Gammarus fossarum ovaries

ABSTRACT: This project contributes to the description of the core-proteome of female reproductive tissues from crustacean amphipods.

INSTRUMENT(S): LTQ Orbitrap

ORGANISM(S): Gammarus Fossarum

TISSUE(S): Ovary

SUBMITTER: Jean ARMENGAUD

LAB HEAD: Jean Armengaud

PROVIDER: PXD002253 | Pride | 2015-09-21

REPOSITORIES: Pride

ACCESS DATA

Publications

Data for comparative proteomics of ovaries from five non-model, crustacean amphipods.

Trapp Judith J Almunia Christine C Gaillard Jean-Charles JC Pible Olivier O Chaumot Arnaud A Geffard Olivier O Armengaud Jean J

Data in brief 20150812

Ovaries were taken from five sexually mature amphipods: Gammarus fossarum, Gammarus pulex, Gammarus roeseli, Hyallela azteca and Parhyale hawaiensis. The soluble proteome extracted from individual pair of ovaries from five biological replicates was trypsin digested and the resulting peptides were analyzed by high resolution tandem mass spectrometry. The spectra were assigned with four protein sequence databases with different specificities: a RNAseq-derived G. fossarum database; a RNAseq-derived ...[more]

PMID: 26380837

Similar Datasets

Project description:Organisms were sampled from a field population located in Eastern Central France. Because our focus on proteins involved in reproduction, only sexually mature organisms were chosen by selecting the ones in pre-copulatory mate guarding. We first established a database of nucleic acid-derived protein coding sequences. For this, we extracted total RNAs from four key tissues: the male and female reproductive tissues, the cephalon where several neuroendocrine glands are located and the hepatopancreatic caeca, involved in xenobiotics detoxification and energy acquisition (digestive enzyme secretion, food absorption and nutriment storage). Equal amounts of RNAs from each tissue were pooled together and sequenced in a single run of the Illumina next-generation sequencing approach. The resulting nucleic acid information was used to create a protein database that could be used for proteogenomic identification of proteins. For this, each mRNA contig was systematically translated into the six possible reading frames, thus for considerating all possible putative ORFs. Tandem mass spectrometry data could be assigned with this database. The protein catalogue established from experimental pieces of evidence allows selecting the appropriate reading direction and frame of each protein-coding mRNA contig. We recorded a large dataset on the proteomes from three tissues (reproductive tissues and the cephalon) by resolving each sample by OFFGEL electrophoresis (24 fractions per sample). Each experiment was conducted in triplicates for reproductive tissues and duplicates for the cephalon, resulting in 192 peptide complex mixtures. These samples were analyzed by nanoLC-MS/MS with a high resolution LTQ-Orbitrap XL hybrid mass spectrometer (ThermoFisher). We also focused our attention on the proteome dynamics of the male reproductive tissue analyzed at seven different spermatogenesis stages (pre-copulatory mate guarding, Day 0, Day 1, Day 2, Day 3, Day 4 and Day7) on five biological replicates. Protein extracts from the testis samples were subjected to a short SDS-PAGE electrophoresis in order to get a single polyacrylamide band per proteome. The 35 samples were in-gel trypsic digested and the resulting peptide mixtures were analyzed by nanoLC-MS/MS.

Dataset Information

Proteogenomics of Gammarus fossarum ovaries

Publications

Data for comparative proteomics of ovaries from five non-model, crustacean amphipods.

Similar Datasets

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