Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Proteomics analysis of Echis carinatus venom from Sri Lanka

ABSTRACT: In order to study the proteome of Echis carinatus venom from Sri Lanka (SL ECV), crude SL ECV was subjected to 12.5% SDS-PAGE analysis. The resulting SDS-PAGE bands were subjected to in-gel trypsin digestion and subsequent tandem mass spectrometry analysis. The raw data were then analysed using PEAKS 8.5 software to finally decipher the complex venom proteome.

INSTRUMENT(S): LTQ Orbitrap Elite

ORGANISM(S): Echis Carinatus

TISSUE(S): Venom

SUBMITTER: Aparup Patra

LAB HEAD: Ashis K Mukherjee

PROVIDER: PXD018130 | Pride | 2020-06-12

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	26072019_ReqID_962_Sample1.raw	Raw
	26072019_ReqID_962_Sample10.raw	Raw
	26072019_ReqID_962_Sample11.raw	Raw
	26072019_ReqID_962_Sample2.raw	Raw
	26072019_ReqID_962_Sample3.raw	Raw

Items per page:

1 - 5 of 30

Publications

Proteomic Analysis of Sri Lanka Echis carinatus Venom: Immunological Cross-Reactivity and Enzyme Neutralization Potency of Indian Polyantivenom.

Patra Aparup A Mukherjee Ashis K AK

Journal of proteome research 20200623 8

The saw-scaled viper (Echis carinatus carinatus) is a major venomous snake in Sri Lanka (SL) responsible for massive numbers of snakebites on the island; nevertheless, its venom proteome composition has never been explored. The proteome composition of SL E. c. carinatus venom (SL ECV), revealed by tandem mass spectrometry analysis, showed that it is composed of 42 enzymatic and nonenzymatic proteins belonging to 12 snake venom protein families. Snake venom metalloproteases (SVMP) a ...[more]

PMID: 32501701

Similar Datasets

Echis carinatus carinatus (India) venom proteomics

Project description:In order to study the proteome of Echis carinatus carinatus venom of Indian origin, crude venom was fractionated on a Shodex KW-803 gel filtration column coupled to Dionex Ultimate 3000 UHPLC system. The resulting peaks were pooled and subjected to in-solution trypsin digestion and subsequent tandem mass spectrometry analysis. The raw data were then analysed using PEAKS 8.5 software to finally decipher the complex venom proteome.

2017-12-15 | PXD007980 | Pride

Proteomic analysis of Daboia russelli venom samples from Burdwan and Nadia districts of West Bengal, eastern India

Project description:Russell’s viper (Daboia russelii) (RV), a category I medically important snake as well as a member of the “Big Four”, is responsible for a heavy toll of snake bite mortality and morbidity in Indian sub-continent. Epidemiological studies suggest highest incidence of RV envenomation in eastern India (EI). In this study the RV venom proteomes from Burdwan and Nadia, the two districts of West Bengal, eastern India was deciphered for the first time using tandem mass spectrometry analysis.

2018-07-16 | PXD008607 | Pride

Comparative single cell RNA seq of gastruloids from mESCs grown in 3 distinct media conditions facilitating distinct pluripotent states at 3 different developmental time points

Project description:Comparative single cell transcriptomic study (using 10x Genomics v3.1 kits) of gastruloids, aggregates of mESCs, at different developmental timepoints. mESCs, corresponding to the 0h timepoint, were also sequenced. The source mESCs were grown in 2 distinct media conditions: DMEM-based Serum-LIF (SL), SL + 0.3uM PD03 (SL + 1i) and SL + 1.5uM CGP77 + 3uM CHIR99 (SL + a2i). The following sets of timepoints were compared: 0hpa (hours post-aggregation) SL, 0hpa SL + 1i, 0hpa SL + a2i (corresponding to the mESC timepoint; 48hpa SL, 48hpa SL + 1i, 72hpa SL + a2i (corresponding to the pre-CHIR99 timepoint); 72hpa SL, 72hpa SL + 1i, 96hpa SL + a2i (corresponding to the post-CHIR99 timepoint); 120hpa SL, 120hpa SL + 1i, 144hpa SL + a2i (corresponding to the maximum elongation timepoint). The aim of this study was to delineate whether mESC pluripotent state influences cell and tissue fate acquisition dynamics. Gastruloids used in this study were generated from a transgenic G4 mESC line (George et al., PNAS 2007) modified via CRISPR-Cas9 mediated heterozygous knock-in of a Bra/T reporter allele (p2a-H2B-eGFP) as well as a ubiquitous nuclear marker allele (CAG::H2B-mKO2).

2024-11-13 | E-MTAB-13643 | biostudies-arrayexpress

Proteomic profile of BxPC3 cells after RAD51 inhibition by treatment with BRC4

Project description:RAD51 protein is an evolutionarily conserved recombinase that plays a central role in homologous recombination (HR) and DNA double strand break (DSB) repair. RAD51 inactivation by small molecules has been proposed as a strategy to impair the BRCA2/RAD51 binding and, ultimately, the HR pathway, with the aim to make cancer cells more sensitive to PARP inhibitors (PARPi). This strategy, which mimics a synthetic lethality (SL) approach, has been successfully assayed in vitro by using myr-BRC4, a peptide derived from the fourth BRC repeat of BRCA2, being the strongest reported natural RAD51 binder. The present study applies a method to obtain a proteomic fingerprint for RAD51 inhibition by the myr-BRC4 peptide (designed for a more efficient cell entry) using a mass spectroscopy (MS) proteomic approach. We performed a comparative proteomic profiling of the myr-BRC4 treated vs. untreated BxPC-3 pancreatic cancer cells and evaluated the differential expression of proteins. Among the identified proteomic hits, we focused our attention on proteins shared by both the RAD51 and the BRCA2 interactomes, and on those whose reduction showed high statistical significance. Three downregulated proteins were identified (FANCI, FANCD2, and RPA3) and protein downregulation was confirmed through immunoblotting analysis, validating the MS approach. Our results suggest that, being a direct consequence of RAD51 inhibition, the detection of FANCD2, FANCI, and RPA3 downregulation could be used as an indicator for monitoring HR impairment.

2023-08-15 | PXD042696 | Pride

Transcription profiling by high throughput sequencing of 7 tissues of maize inbred line Zheng 58

Project description:RNA-sequencing of 5 tissues of maize inbred line Zheng 58: mature silk (MS), mature pollen (MP), mature ovary (MO), and 6-days old seedling (SL), immature silk (IMS)

2013-01-26 | E-MTAB-964 | biostudies-arrayexpress

Foxd3 promotes the exit from naïve pluripotency and prevents germline specification through enhancer decommissioning [RNA-Seq]

Project description:Following implantation, mouse epiblast cells transit from a naïve to a primed state in which they are competent for both somatic and primordial germ cell (PGC) specification. Using mouse embryonic stem cells (mESC) as an in vitro model to study the transcriptional regulatory principles orchestrating peri-implantation development, here we show that the transcription factor Foxd3 is necessary for the exit from naïve pluripotency and the progression to a primed pluripotent state. During this transition, Foxd3 acts as a repressor that dismantles a significant fraction of the naïve pluripotency expression program through the decommissioning of active enhancers associated with key naïve pluripotency and early germline genes. Subsequently, Foxd3 needs to be silenced in primed pluripotent cells to allow the reactivation of relevant genes required for proper PGC specification. Our findings uncover a wave of activation-deactivation of Foxd3 as a crucial step for the exit from naïve pluripotency and subsequent PGC specification. mRNA profiles were generated by RNA-seq in duplicates for each of the following mESC lines: Foxd3fl/fl;Cre-ER mESC maintained in "Serum+LIF" (SL) treated with TM for three days (SL Foxd3-/-); untreated Foxd3fl/fl;Cre-ER SL mESC (SL Foxd3fl/fl); tetON Foxd3 SL mESC treated with Dox for three days; WT SL mESC treated with Dox for three days; Foxd3fl/fl;Cre-ER mESC maintained in "2i+LIF" (2i) treated with TM for three days (2i Foxd3-/-); untreated Foxd3fl/fl;Cre-ER 2i mESC (2i Foxd3fl/fl).

2015-09-14 | E-GEOD-70546 | biostudies-arrayexpress

Age-associated DNA methylation increases in mouse pancreatic islets suggest an epigenetic drift toward the exocrine pancreas epigenome

Project description:Early postnatal overnutrition causes persistent dysregulation of endocrine pancreas function. We used genome-scale DNA methylation profiling in the suckling-period small litter (SL) mouse model to test whether this occurs via persistent epigenetic changes in pancreatic islets. Although SL islets showed DNA methylation changes directly after weaning and in adulthood, few of these were present at both ages, contrary to our hypothesis. Most interestingly, we discovered that genomic regions that are hypermethylated in exocrine relative to endocrine pancreas tend to gain methylation in islets during aging. Focusing on a subset of genes relevant to β cell function, we showed that these methylation differences are strongly correlated with expression. Together, our results provide the novel insight that DNA methylation changes that occur as islets age indicate an overall epigenetic drift toward the exocrine pancreas epigenome. These concerted shifts in the islet methylome could contribute to the age-associated decline in endocrine pancreas function. Pancreatic islets were isolated from P21/P180 SL or C mice. To ensure purity of islets, 3 rounds of manual picking were performed in each samples. Whole pancreas samples, ~98% of which is exocrine pancreas, were used as exocrine pancreas. There are 5 mice per group.

2014-12-03 | E-GEOD-63811 | biostudies-arrayexpress

Label-free quantitative SWATH-MS proteomic analysis of adult myocardial slices in vitro after biomimetic electromechanical stimulation

Project description:Conventional in vitro cell cultures are relatively available and have been widely used in explaining many mechanisms, but their simple construction is not directly applied to the in vivo environment. A possible solution to overcome this problem is special in vitro model maintained with cardiac slices. Slices show a preserved architecture, multi-cellularity and physiology of the heart tissue. This approach creates a bridge between the gap in cellular and in vivo studies. This study demonstrated that it is possible to find protein biomarkers between rat myocardial slices which were stretched to sarcomere lengths (SL) within the physiological range of 1.8–2.4μm and slices cultured without electromechanical stimulation and with fresh myocardial slices.

2022-08-25 | PXD034891 | Pride

RNA-seq comparing WT to HDAC3 and Dax1 knock-out clones in cell-sorted populations in 2iLIF and SL(RA) differentiation conditions

Project description:In order to determine the transcriptomic profiles of PrE-induced cells following HDAC3 or Dax1 knock-out in SL(RA) differentiation conditions, RNA-seq was performed on Gata6+ or Nanog+ sort-selected cells. Profiles are contrasted with WT cells in the same differentiation conditions as well as to mock-sorted populations of the three genotypes in 2iLIF conditions.

2021-03-15 | E-MTAB-10150 | biostudies-arrayexpress

A comparison of physiological and transcriptome responses to water deprivation and salt loading in the rat supraoptic nucleus

Project description:Salt loading (SL) and water deprivation (WD) are experimental challenges that are often used to study the osmotic circuitry of the brain. Central to this circuit is the supraoptic nucleus (SON) of the hypothalamus, which is responsible for the biosynthesis of the hormones, vasopressin (AVP) and oxytocin (OXT), and their transport to terminals that reside in the posterior lobe of the pituitary. Upon osmotic challenge evoked by a change in blood volume or osmolality, the SON undergoes a function related plasticity that creates an environment that allows for an appropriate hormone response. Here, we have described the impact of SL and WD compared to euhydrated (EU) controls in terms of drinking and eating behaviour, body weight and recorded physiological data including circulating hormone data and plasma and urine osmolality. We have also used microarrays to profile the transcriptome of the SON following SL Microarrays were interrogated with RNA extracted from the supraoptic nucleus of either euhydrated (n=5) or 7-days salt loaded (2% w/v; n=5) rats. Each microarray represented an independent pool of 5 animals, and for each condition, 5 microarrays were performed.

2015-02-05 | E-GEOD-65663 | biostudies-arrayexpress