Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Salinity-dependent proteome dynamics in Nile tilapia gills

ABSTRACT: Experiments and fish acclimations were performed in the laboratory of Prof. Avner Cnaani at the Agricultural Research Organization (ARO) Volcani Center (Israel). Proteomics sample preparation and biological mass spectrometry analyses (DDA) were performed in the laboratory of Prof. Dietmar Kueltz at UC Davis (CA). Samples represent protein extracts from gill epithelium of individual fish. Proteins were extracted, digested, and prepared for online LCMS2 as described previously (Kultz et al., 2013, Molecular & Cellular Proteomics 12/12, 3962-3975). Each sample represents a different biological replicate obtained from a separate fish.

INSTRUMENT(S): impact

ORGANISM(S): Oreochromis Niloticus (ncbitaxon:8128)

SUBMITTER: Avner Cnaani Dietmar Kueltz

PROVIDER: MSV000085639 | MassIVE | Sat Jun 27 22:35:00 BST 2020

SECONDARY ACCESSION(S): PXD020064

REPOSITORIES: MassIVE

ACCESS DATA

Json Xml

Similar Datasets

Salinity-dependent regulation of the kidney proteome of Oreochromis niloticus

Project description:PI: Experiments and fish acclimations were performed in the laboratory of Prof. Avner Cnaani at the Agricultural Research Organization (ARO) Volcani Center (Israel). Proteomics contact: Proteomics sample preparation and biological mass spectrometry analyses were performed in the laboratory of Prof. Dietmar Kueltz at UC Davis (CA). Database for spectral annotation: NCBI-Refseq.

2020-06-27 | MSV000085637 | MassIVE

Effect of water emersion on the gill proteome of Mangrove killifish

Project description:Gill proteome of Mangrove killifish was compared by LC-MS/MS using 6 biological replicates of fish exposed to emersion stress versus 6 biological replicates kept under water that served as controls. PI: Experiments and fish exposures were performed in the laboratory of Prof. Patricia Wright at the University of Guelph (Canada). Proteomics contact: Proteomics sample preparation and biological mass spectrometry were performed in the laboratory of Prof. Dietmar Kueltz laboratory at UC Davis (CA).

2017-03-15 | MSV000080634 | MassIVE

Delayed effect of early-life exposure to 17-alpha-ethinylestradiol on brain proteome of adult mangrove rivulus fish

Project description:PI: Experiments and fish exposures were performed in the laboratory of Frederic Silvestre at the University of Namur (Belgium). Proteomics contact: Proteomics sample preparation and biological mass spectrometry were performed in the laboratory of Prof. Dietmar Kueltz at UC Davis (CA). LC-MS/MS data obtained from brains of 17 adult mangrove rivulus exposed to different doses of 17-alpha-ethinylestradiol during early development.

2018-08-13 | MSV000082814 | MassIVE

The plasma proteome of Rufous-collared sparrows (Zonotrichia capensis) from valleys of the Atacama Desert (Chile)

Project description:The plasma proteome of sparrows from the Atacama desert was identified using bottom up proteomics by online nanoLC tandem mass spectrometry. Seasonal and geographic effects on the plasma proteome were investigated. All experiments and sample collections were performed by the team of Dr. Paulina Gonzalez-Gomez. Proteomics sample preparation and biological mass spectrometry were performed in the laboratory of Prof. Dietmar Kueltz at UC Davis

2018-04-26 | MSV000082313 | MassIVE

The kidney proteome of the rufous-collared sparrow (Andean sparrow, Zonotrichia capensis) from Chile

Project description:Kidney proteomes of Rufous-collared sparrows from two different areas of the Atacama desert (Chile) were identified and compared by bottom-up proteomics utilizing nanoUPLC coupled online to tandem mass spectrometry. All experiments and sample collections were performed by the team of Dr. Paulina Gonzalez-Gomez. Proteomics sample preparation and biological mass spectrometry were performed in the laboratory of Prof. Dietmar Kueltz at UC Davis.

2018-04-26 | MSV000082314 | MassIVE

Integration of time- and dose-dependent effects of salinity stress on the branchial proteome of euryhaline tilapia

Project description:Experiments were performed by Larken Root in the laboratory of Dietmar K&uumlltz at UC Davis. Tilapia were acclimated at different rates from freshwater (FW) to elevated salinity. FW handling controls were included in parallel. Samples represent biological replicates, i.e. each sample was obtained from a different fish processed using an identical procedure. Dataset 1: Acclimation of fish from FW to 35 g/kg, 70 g/kg and 90 g/kg salinity. Sample preparation was based on a previously published protocol (https://doi.org/10.1074/mcp.M113.029827) and total peptide amount on column was 200 ng. Dataset 2: Acclimation of fish from FW to 75, 85, and 105 g/kg salinity. Sample preparation was slightly modified from the protocol above to minimize protein carbamylation during urea incubation. Total peptide amount for each sample was low for preliminary optmization purposes (125 ng on column). Dataset 3: Acclimation of fish from FW to 85 g/kg and 105 g/kg salinity but in a different experiment using other fish and experimental setup than those used for dataset 2. Sample preparation was the same as for dataset 2 above and total peptide amount loaded was 180 ng on column. Dataset 4: Samples represent the same fish acclimated to 105 g/kg as for dataset 2 but sample preparation was performed using the original protocol as for dataset 1 above. Sample amount loaded was 180 ng total peptides on column. Dataset 5: Replicate run of the same samples as in dataset 2 above but at optimal sample loading of 200 ng total peptides on column. Biological mass spectrometry (Bottom-up LCMS2-DDA proteomics) was performed and data analyzed using a workflow consisting of Compass Hystar 4.1, DataAnalysis 4.4, PEAKS Studio X+, Scaffold 4.11, and ScaffoldPTM 3.0 in the K&uumlltz laboratory.

2020-07-14 | MSV000085745 | MassIVE

Gene expression in liver, gill, hypothalamus, pituitary, and olfactory rosettes from Atlantic salmon parr and smolt

Project description:To identify genes involved in the developmental process of Atlantic salmon smoltification, gene expression was compared between smolt and parr in tissues involved in osmoregulation (gill), metabolism (liver), imprinting (olfactory rosettes) and neuroendocrine control (hypothalamus and pituitary). Tissue samples were harvested from laboratory-reared parr and smolts on the same date. Smolts were distinguished from parr by size and appearance; developmental status was confirmed by physiological assays. Eight biological replicates (16 fish) balanced for sex and for dye were used in the liver, gill, olfactory rosette, and hypothalamus comparisons. Four male parr were compared to four male smolts and four female parr were compared to four female smolts; smolts were labeled with Alexa Fluor 555 on four arrays and with Alexa Fluor 647 on four arrays. Six biological replicates (12 fish) were used for the pituitary comparison (two female and four male).

2012-08-20 | E-GEOD-33711 | biostudies-arrayexpress

Global gene expresssion profiling the gills of amoebic gill disease (AGD) affected Atlantic salmon (Salmo salar)

Project description:Amoebic gill disease (AGD) is an ectoparasitic condition of some farm-reared marine fish and is caused by Neoparamoeba perurans. Tanks housing Atlantic salmon (Salmo salar) were inoculated with Neoparamoeba perurans and fish were sampled at 36 days postinoculation (pi.). AGD-affected gill tissue was dissected from N. perurans infected fish, and a DNA microarray was used to compare global gene expression against tissues from AGD-naive fish. To determine whether the changes in gene expression were restricted to AGD-lesions, lesion tissue from AGD-affected fish was also compared with non-lesion gill tissue dissected from the same gill arch. Samples were assessed using a DNA microarray. mRNA from lesion and non-lesion gill tissue was amplified and labeled. Six biological and two technical replicates were utilised to hybridise to 12 arrays using amplified RNA from AGD-affected lesion gill tissue with AGD-naive fish as a control. Four biological and two technical replicates were utilised to hybridise to 8 arrays using amplified RNA from AGD-affected lesion gill tissue with non-lesion tissue from the same gill arch as a control. The assignment of microarrays to treatment groups for hybridization was randomised by using a random number generator.

2010-05-25 | E-GEOD-9595 | biostudies-arrayexpress

Global gene expresssion profiling the gills of amoebic gill disease (AGD) affected Atlantic salmon (Salmo salar)

2007-11-15 | GSE9595 | GEO

Delayed effect of early-life exposure to 17-alpha-ethinylestradiol on the liver proteome of adult mangrove rivulus fish

Project description:LC-MS/MS data obtained from livers of 17 adult mangrove rivulus exposed to different doses of 17-alpha-ethinylestradiol during early development. All fish acclimations, treatments, experimental design, and data anlyses were performed in Frederic Silvestre's laboratory at the University of Namur, Belgium by Anne-Sophie Voisin. LC-MS/MS runs were done in Dietmar Kueltz's laboratory at UC Davis.

2018-08-13 | MSV000082815 | MassIVE

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data