Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Investigation of TOF patient heart specimens

ABSTRACT: The protein BBLN with largely unknown function was identified in human right ventricular heart specimens from patients undergoing repair surgery for Tetralogy of Fallot (TOF). Proteins from heart specimens were solubilized and subjected to immuno-affinity enrichment with anti-CAMK2D-specific antibodies. Co-enriched proteins were separated by SDS-PAGE, and the protein band in the range of 8-14 kDa was cut and subjected to identification by nano-LC-ESI-MS/MS.

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Heart, Electrically Active Cell

DISEASE(S): Cardiovascular System Disease

SUBMITTER: Ursula Quitterer

LAB HEAD: Prof. Dr. Ursula Quitterer

PROVIDER: PXD044695 | Pride | 2023-09-18

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Similar Datasets

Transcriptome changes in response to dDAVP stimulation in CRISPR/Cas9 mediated Camk2d knock-out mpkCCD cells

Project description:The Ca2+/CaM-dependent protein kinase 2-delta (CAMK2D) has been proposed to be involved in vasopressin signaling in the renal collecting duct, which controls water and salt excretion by the kidney. RNA sequancing and quantitative proteomics analyses identified the expression of multiple CAMK2 isoforms, with CAMK2D being the most abundant in collecting duct cells. To investigate the role of CAMK2D in regulating RNA expression in response to vasopressin signaling, the transcriptome of CRISPR/Cas9-mediated Camk2d knock-out mpkCCD cells was profiled using RNA-Seq in the presence of vasopressin analogue dDAVP.

2023-06-01 | GSE228762 | GEO

Using CRISPR-Cas9/Phosphoproteomics to Identify Kinase Substrates: Calmodulin Kinase 2 Delta

Project description:The Ca2+/CaM-dependent protein kinase 2 (CAMK2) family of protein kinases are key protein kinases involved in regulation of cellular processes in a variety of tissues including brain, smooth muscle and kidney. One member, CAMK2-delta (CAMK2D), has been proposed to be involved in vasopressin signaling in the renal collecting duct, which controls water and salt excretion by the kidney. To identify CAMK2D target proteins in renal collecting duct cells (mpkCCD), we deleted Camk2d in mpkCCD cells and carried out LC-MS/MS-based quantitative phoshoproteomics analysis. Using CRISPR/Cas9 with two different gRNAs targeting the CAMK2D catalytic domain, we created multiple CAMK2D knock-out cell lines. Using these cells and control cell lines, we carried out large-scale quantitative phosphoproteomic analysis (TMT-labeling) in the presence of the vasopressin analog dDAVP (0.1 nM, 30 min). Of the 11,570 phosphopeptides quantified, 206 were significantly increased and 169 were decreased. These data are available for browsing or download at https://esbl.nhlbi.nih.gov/Databases/CAMK2D-proteome/. Motif analysis of the decreased phosphorylation sites revealed a target preference of –(R/K)-X-X-p(S/T)-X-(D/E), matching the motif identified in previous in vitro studies using recombinant CAMK2D. Thirty-five of the significantly down-regulated phosphorylation sites in CAMK2D knock-out cells had exactly this motif and are judged to be sites that are most likely direct CAMK2D targets. These targets include Ser256 of aquaporin-2 (AQP2), a site known to regulate AQP2 trafficking to the plasma membrane, controlling water excretion by the kidney. The other changes, including phosphorylation sites that increased in response to CAMK2D deletion, are likely phosphorylated by other protein kinases that are regulated by CAMK2D in kinase cascades.

2023-11-06 | PXD040159 | Pride

CaMK2D is a critical regulator of coactivation of leukemia stem cell factors in acute myeloid leukemia.

Project description:Relapse is one of the biggest challenges in treating acute myeloid leukemia (AML) due to leukemia stem cells (LSCs) resisting chemotherapy, providing a cellular reservoir to form the basis for relapse. Here, we identify CaMK2D is a critical regulator of stemness and leukemogenesis of AML. Transcriptionally, loss of CaMK2D was associated with down-regulation kinds of metabolic pathway of AML.

2021-11-08 | GSE161032 | GEO

Heart RNA-seq of therapeutic RBM20 antisense oligonucleotide (ASO) treatment in a mouse model of heart failure with preserved ejection fraction (HFpEF)

Project description:We report the heart RNA-sequencing of control animals and animals of a mouse model of heart failure treated or not with RBM20 antisense oligonucleotide. This study aims to investigate the therapeutic effect of antisense oligonucleotide (ASO)-mediated downregulation of the cardiac splice factor RBM20 in a mouse model of heart failure with preserved ejection fraction. 8-week old wild type and titin N2B KO mice with increased wall stiffness were subcutaneously injected with 50 mg/kg/week RBM20 ASO for 8 weeks. RNA from 4 left ventricles per group were isolated using TRIzol followed by a clean-up with the QIAGEN RNA micro kit. The cDNA libraries were generated using the Illumina TruSeq Stranded mRNA LT Sample Prep Kit and 2x150 paired end sequenced on HiSeq4000. The RNA-Sequencing analysis confirms that RBM20 ASO treatment increased the expression of compliant titin isoforms and improved impaired ventricular filling and cardiac function. RNA-seq confirmed RBM20 dependent isoform changes of known targets such as Titin, Ldb3, Camk2d, and Ank3, and served as a sensitive indicator of potential side effects, largely limited to genes related to the immune response.

2021-12-06 | E-MTAB-9361 | biostudies-arrayexpress

Identification of ELC interacting proteins in zebrafish heart

Project description:The essential myosin light chain (ELC) is part of the cardiac myosin motor regulating the contractility of the heart. Recently, we have demonstrated ELC phosphorylation to be responsible not only for basal maintenance of cardiac contractility, but also for the adaptation of sarcomere function to increased demands in adult zebrafish (Scheid et al. Cardiovascular Research, 2016). However, the direct interacting kinases, phosphatases as well as the signaling pathway mediating the ELC phosphorylation are mostly unknown. Here, we aim to identify ELC interacting proteins in zebrafish heart tissue using an ELC-specific precipitation assay followed by mass spectrometry. In brief, ELC specific co-immunoprecipitation was performed by using the Dynabeads Co-immunoprecipitation Kit (Invitrogen, #14321D). Custom-specific polyclonal ELC antibodies (Eurogentec, peptide for immunization: NH2-CAPVPETPKEPEVDLK-CONH2) against zebrafish ELC were covalently coupled to DynabeadsTM M-270 Epoxy (Invitrogen, #14302D) and whole zebrafish heart protein was used as input. All steps were carried out according to the manufacturer's instructions.

2022-07-24 | PXD016357 | Pride

Cardiac transcriptome analysis of right and left ventricular heart specimens of BBLN-transgenic mice by NGS

Project description:The study performed NGS to investigate the cardiac transcriptomes of right and left ventricular heart specimens of 3-4-month-old BBLN-transgenic mice with FVB/N background in comparison to those of non-transgenic FVB/N mice. BBLN-transgenic (Tg-BBLN) mice with myocardium-specific BBLN expression were generated to investigate the cardiac phenotype of increased cardiac BBLN transcript levels because the function of BBLN (Bublin coiled-coil protein), which is the chromosome 9 open reading frame(C9orf16), is largely unknown. Tg-BBLN mice with increased cardiac BBLN levels developed features of heart failure with increasing age. Pathomechanisms of heart failure induced by BBLN were investigated by NGS of right and left ventricular heart specimens of male, BBLN-transgenic mice (age: 3-4 months). NGS data reveal transcriptome changes in right and left ventricular heart specimens induced by increased expression of BBLN in the heart.

2023-09-18 | GSE241022 | GEO

TCR sequencing of peripheral blood mononuclear cells (PBMC) and prostate biopsies from prostate cancer patients undergoing cryoimmunotherapy

Project description:This dataset includes a total of 18 prostate cancer patients undergoing cryoimmunotherapy (cryoIT). The clinical trial is registered at ClinicalTrials.gov under the identifier NCT02423928. PBMC specimens obtained before and after cryoIT and prostate biopsies at the time of cryoablation are included in this dataset. The specific time points of sampling can be found in the table provided with the dataset. Both visit number and study week are provided for this purpose, with study week 0 corresponding to the time of cryoablation (cryoIT).

2022-10-30 | E-MTAB-10998 | biostudies-arrayexpress

Development and systematic evaluation of decellularization protocols for rat diaphragms

Project description:We decellularized rat diaphragms with the main detergents 1% or 0.1% sodium dodecyl sulfate (SDS) and 4% sodium deoxycholate (SDC) by orbital shaking (OS) or retrograde perfusion (RP) through the vena cava. Our systematic comparison entails evaluation of decellularized diaphragmatic samples by (1) quantitative analysis including DNA quantification and biomechanical testing, (2) qualitative and semi-quantitative analysis by proteomics, as well as (3) qualitative assessment with macroscopic and microscopic evaluation by histological staining, immunohistochemistry and scanning electron microscopy.

2024-05-07 | PXD042219 | Pride

Human Normal & Diseased Cardiovascular Tissue

Project description:Fewer than 50% of patients develop vascular and valvular calcification, implying differential pathogenesis. Disease stage-specific proteomics (normal/non-diseased/fibrotic/calcified areas) was performed on human carotid artery specimens from autopsy, carotid endarterectomy specimens, aortic valves from heart transplant recipients, and stenotic aortic valves.

2023-07-10 | PXD035555 | Pride

Environmental Enrichment and Rat Liver Proteomics

Project description:We aimed to address the challenge of accommodating an increasing demand for aged laboratory animals in the context of rising elderly population and research on aging-related diseases. We developed a cost-effective environmental enrichment method and assessed its impact on metabolic changes in Sprague Dawley rats' livers as a proof-of-concept organ. Twenty-four male rats were divided into four groups, with two kept in standard cages and two in modified rabbit cages. Half of each type of cage group received additional enrichment through weekly playtime in a larger cage. Over six months, the rats' weight gain was consistent across all groups, and corticosterone levels did not significantly differ. However, the control group had significantly lower DHEA and Testosterone levels at the study's end. Rats in enriched environments exhibited less distress during inspections and were more resistant to accepting treats. Animals accustomed to playpen time left their cages more easily. Overall, the study demonstrated that refining husbandry for aging rats is both simple and cost-effective, without detrimental effects on stress levels, development, or liver metabolism.

2024-01-22 | PXD046110 | Pride

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