Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Proteomic changes associated with predator induced morphological defenses in Olympia oysters

ABSTRACT: Samples were collected and experiments performed by the laboratories of Tyler Evans and Eric Sanford. Samples represent a single biological replicate processed using an identical procedure, i.e., reduction/ alkylation and trypsin digestion as described in a previously published protocol (https://doi.org/10.1074/mcp.M113.029827). Data for each sample were acquired using regular bottom-up DDA proteomics. Biological mass spectrometry was performed and data analyzed using a workflow consisting of Compass Hystar 4.1, DataAnalysis 4.4, PEAKS Studio 8.5, Mascot 2.2.7, X!Tandem Alanine, and Scaffold 4.8 in the Kültz laboratory.

INSTRUMENT(S): impact HD

ORGANISM(S): Ostrea Lurida (ncbitaxon:627230)

SUBMITTER: Tyler Evans Dietmar Kueltz

PROVIDER: MSV000088386 | MassIVE | Mon Nov 15 19:27:00 GMT 2021

SECONDARY ACCESSION(S): PXD029757

REPOSITORIES: MassIVE

ACCESS DATA

Json Xml

Similar Datasets

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

miRNA profiling in the plasma of patients with in-stent restenosis (ISR)

Project description:Studies of miRNA profiling in the plasma of patients between ISR and non-ISR Venous blood was collected in EDTA in the ward or the cardiac catheterization laboratory before the angiography procedure and heparin administration. Plasma was harvested by centrifugation and stored at -80°C until assayed. Identical volumes of plasma from the 6 patients with ISR and 4 patients with non-ISR were pooled to reach a final volume of 1500µL for each patient. Total RNA was extracted using miRVana isolation kit, dephosphorylated and labeled using miRNA Complete Labeling kit. Scanning was achieved with the illumina iScan System. The result were acquired with the Genome Studio (GenomeStudioV2009.1).

2014-09-02 | E-GEOD-60959 | biostudies-arrayexpress

Transcriptional profiling of clonal INS-1 832/13 beta-cells

Project description:This experiment aimed to measure gene expression in glucose-responsive beta-cells. RNA was extracted using RNeasy Mini kit. Quantity and quality of extracted RNA were assessed by the NanoDrop spectrophotometer ND-1000 and Experion RNA StdSens Analysis Kit, respectively. Background correction, normalization, and probe summarization were performed by the Robust Multichip Average method. More details can be found in J Biol Chem (doi: 10.1074/jbc.M112.422527).

2015-01-30 | E-MTAB-3232 | biostudies-arrayexpress

mRNA-seq data during learning and memory in mice

Project description:RNA was extracted from homogenates (HOM) and synapses (SYN) of mice on days 1, 6, and 20 after Morris water maze (MWM) training. Regular RNA sequencing was performed using the NovaSeq 6000 system (Illumina). Our protocol yielded reliable input for SYN using hippocampal RNA from ten mice. In contrast, we generated input libraries for HOM using hippocampal RNA from three mice per three biological replicates

2024-03-31 | GSE262566 | GEO

RNA-seq of KYAE-1 and OE19 oesophageal adenocarcinoma cells following induction of dominant negative (acidic) FOS

Project description:To identify AP-1 regulated genes in KYAE-1 and OE19 oesophageal adenocarcinoma cells we induced expression of dominant negative (acidic) FOS to inhibit AP-1 activity and then performed RNA-seq. Acidic FOS (aFOS, J Biol Chem. 1997 Jul 25;272(30):18586-94. doi: 10.1074/jbc.272.30.18586) was expressed from the pINDUCER20 vector.

2023-01-05 | E-MTAB-10334 | biostudies-arrayexpress

The transcriptional response of Pasteurella multocida to three classes of antibiotics

Project description:We studied the effects of three classes of antibiotics (amoxicillin, chlortetracycline and enrofloxacin ) on P. multocida transcriptome using custom oligonucleotide microarrays from Nimblegen systems. All the 2015 genes of Pm70 were spotted on the array and hybridizations were carried out with RNA isolated from three independent cultures of Pm70 grown in the presence or absence of sub-minimum inhibitory (sub-MIC) doses of antibiotics. Differentially expressed genes were identified by ANOVA and Dunnett’s test. Biological modeling of the differentially expressed genes (DE) was carried out based on Clusters of Orthologous (COG) groups and network analysis in Pathway Studio. Keywords: Response to sub-MIC antibiotics

2009-09-01 | GSE12779 | GEO

Paenibacillus larvae exoproteins of ERIC I-IV genotypes

Project description:The following strains of Paenibacillus larvae classified as ERIC I-IV genotypes (pl1-pl4) were used in the study: ERIC I - DSM-7030; ERIC II - DSM-25430; ERIC III - LMG-16252; and ERIC IV - DSM-3615. The 7 biological replicates (a-g) of the exoprotein fractions prepared from each ERIC genotype were used in the nanoLC-MS/MS analysis. All 28 samples were consecutively analyzed using an OrbitrapTM FusionTM Tribrid q-OT-IT mass spectrometer. To improve the protein identification and easy exclude contaminants from the medium, we considered the proteins that could originate from the yeast extract and Mueller-Hinton broth (contains beef fusion and casein peptone-acidic hydrolysate) in analyzing the MS data. Thus, we included the sequences related to Saccharomyces cerevisiae and Bos taurus, respectively, to the list of contaminants in MaxQuant. The contaminants.fasta file is provided. Futhermore, we provide the database (uniprot-paenibacillus+larvae.fasta) used for the identification of P. larvae proteins created of different strains of P. larvae. The sequences were downloaded of UniProt on 12.03.2019. Finally, the compressed (zipped) folder "combined" is provided. The data were analyzed in MaxQuant v1.6.3.4.

2019-03-27 | MSV000083636 | MassIVE

Diversity of Human Copy Number Variation and Multicopy Genes

Project description:Copy number variants (CNVs) affect both disease and normal phenotypic variation but those lying within heavily duplicated, highly identical sequence have been difficult to assay. By analyzing short-read mapping depth for 159 human genomes, we demonstrate accurate estimation of absolute copy number for duplications as small as 1.9 kbp, ranging from 0-48 copies. We identified 4.1 million ‘singly unique nucleotide’ (SUN) positions informative in distinguishing specific copies, and use them to genotype the copy and content of specific paralogs within highly duplicated gene families. These data identify human-specific expansions in genes associated with brain development, reveal extensive population genetic diversity, and detect signatures consistent with gene conversion in the human species. Our approach makes ~1000 genes accessible to genetic studies of disease association.

2010-09-24 | GSE24334 | GEO

Identification of O-glycosylation sites in Clostridium botulinum and Geobacillus kaustophilus flagellins

Project description:In this study, we identified the O-glycosylation sites in recombinant Clostridium botulinum flagellin (CbFla) and Geobacillus kaustophilus flagellins, GkFlaA1 and GkFlaA2, expressed from the E. coli strains, EV136 and EV240 (K1:K12 strains engineered by Prof. Eric Vimr’s group to accumulate CMP-sialic acid in the cytosol), EV36 (wildtype K1:K12 strain), and BL21(DE3) (laboratory strain used for protein expression using T7 RNA polymerase). The recombinant flagellins were expressed with or without co-expression of motility associated factor (Maf) (flagellin nonulosonic acid glycosyltransferase) in these strains, purified and subjected to MS/MS analysis at Taplin Biological Mass Spectrometry facility.

2020-09-07 | PXD018167 | Pride

Nitrogen-efficient rice over-expressing alanine aminotransferase

Project description:Oryza sativa cv. Nipponbare was engineered to over-express a barley alanine aminotransferase (alaAT) gene using the promoter (OsANT1) from a rice aldehyde dehydrogenase gene that expresses in roots. We are using biotechnology to improve the nitrogen use efficiency of rice by over-expressing alaAT in a tissue specific (root) manner. The AlaAT enzyme is a reversible aminotransferase that is linked to both C and N metabolism since it uses pyruvate plus glutamate to produce alanine and 2-oxoglutarate, and visa versa.

2012-07-27 | GSE39687 | GEO

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