MinION cDNA sequencing - snake venom glands
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ABSTRACT:
PROVIDER: PRJEB10285 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Hydrophilic interaction liquid chromatography coupled with LC- MS/MS was used to analyze the crude venom extracts of Echis ocellatus (Carpet viper) and Bitis arietans (Puff adder). The gel-free proteomic analysis of the crude venom extracts from E. ocellatus and B. arietans yielded the identification of 86 and 80 proteins, respectively. Seventy- nine proteins were common between the two snake species with a 90.8% similarity. The identified proteins belong to 12 protein families where serine proteases (22.31%) and metalloproteinases (21.06%) were the dominant proteins in the venom of B. arietans. Metalloproteinases (34.84%), phospholipase A 2 s (25.69%) and serine proteases (17.25%) represents the major toxins in the E. ocellatus venom. This study provides some valuable insights into the toxin families to be neutralized in case of envenomation.
2021-03-11 | PXD024638 | Pride
Project description:Portable DNA sequencers such as the Oxford Nanopore MinION device have the potential to be truly disruptive technologies, facilitating new approaches and analyses and, in some cases, taking sequencing out of the lab and into the field. However, the capabilities of these technologies are still being revealed. Here we show that single-molecule cDNA sequencing using the MinION accurately characterises venom toxin-encoding genes in the painted saw-scaled viper, Echis coloratus. We find the raw sequencing error rate to be around 12%, improved to 0-2% with hybrid error correction and 3% with de novo error correction. Our corrected data provides full coding sequences and 5' and 3' UTRs for 29 of 33 candidate venom toxins detected, far superior to Illumina data (13/40 complete) and Sanger-based ESTs (15/29). We suggest that, should the current pace of improvement continue, the MinION will become the default approach for cDNA sequencing in a variety of species.
| S-EPMC4662598 | biostudies-literature
Project description:This project mainly aims to characterize the complex toxic components present in the venom of Trimeresurus malabaricus (Malabar pit viper). Since Trimeresurus malabaricus (Malabar pit viper) species are mainly inhabited to plantation crop areas, its envenomation is a serious threat to the human population thriving in these zones, especially to the plantation workers. Therefore, exploring the venom proteome of Malabar pit viper is decisive to develop and design new antivenom and therapeutics against its envenomation. As described in this study, applying various orthogonal separation strategies helped in dissecting venom constituents of Trimeresurus malabaricus and is the first comprehensive attempt in revealing the complex venom profile of Malabar pit viper through proteomics approaches incorporating multiple database searches. In order to achieve this the crude venom components were resolved on a 12% SDS page. Further each of the bands were subjected to in-gel trypsin digestion. The crude venom was also subjected to ion-exchange chromatography separation. The obtained fractions were subjected to in-solution trypsin digestion. All the digested peptides were then subjected to Q-TOF LC-MS/MS analysis.
2020-01-24 | PXD011673 | Pride
Project description:Both single cell and bulk RNA sequencing was performed on expanding or differentiating snake venom gland organoids (from Aspidelaps Lubricus Cowlesi and Naja Nivea), or tissue (Aspidelaps Lubricus Cowlesi). Bulk RNA sequencing from the snake venom gland, liver and pancreas was performed to construct a de novo transcriptome using Trinity.
2020-02-24 | GSE129581 | GEO
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
Project description:Diachasmimorpha longicaudata parasitoid wasps carry a symbiotic poxvirus, known as DlEPV, within the female wasp venom gland. We sequenced RNA from venom gland tissue to identify DlEPV orthologs for 3 conserved poxvirus core genes. The DlEPV ORFs identified from this transcriptome were used to design primers for downstream RT-qPCR analysis and RNAi knockdown experiments.
2020-02-03 | GSE144541 | GEO
Project description:Background The generalist dipteran pupal parasitoid Nasonia vitripennis injects 79 venom peptides into the host before egg laying. This venom induces several important changes in the host, including developmental arrest, immunosuppression, and alterations to normal metabolism. It is hoped that diverse and potent bioactivities of N. vitripennis venom provide an opportunity for the design of novel acting drugs. However, currently very little is known about the individual functions of N. vitripennis venom peptides and less than half can be bioinformatically annotated. The paucity of annotation information complicates the design of studies that seek to better understand the potential mechanisms underlying the envenomation response. Although the RNA interference system of N. vitripennis provides an opportunity to functionally characterise venom encoding genes, with 79 candidates this represents a daunting task. For this reason we were interested in determining the expression levels of venom encoding genes in the venom gland, such that this information could be used to rank candidate venoms. To do this we carried out deep sequencing of the transcriptome of the venom gland and neighbouring ovary tissue and used RNA-seq to measure expression from the 79 venom encoding genes. The generation of a specific venom gland transcriptome dataset also provides further opportunities to investigate novel features of this highly specialised organ. Results High throughput sequencing and RNA-seq revealed that the highest expressed venom encoding gene in the venom gland was a serine protease called Nasvi2EG007167, which has previously been implicated in the apoptotic activity of N. vitripennis venom. As expected the RNA-seq confirmed that the N. vitripennis venom encoding genes are almost exclusively expressed in the venom gland relative to the neighbouring ovary tissue. Novel peptides appear to perform key roles in N. vitripennis venom function as only four of the highest 15 expressed venom encoding genes are bioinformatically annotationed. The high throughput sequencing data also provided evidence for the existence of an additional 471 novel genes in the Nasonia genome that are expressed in the venom gland and ovary. Finally, metagenomic analysis of venom gland transcripts identified viral transcripts that may play an important part in the N. vitripennis venom function. Conclusions The expression level information provided here for the 79 venom encoding genes provides an unbiased dataset that can be used by the N. vitripennis community to identify high value candidates for further functional characterisation. These candidates represent bioactive peptides that have value in drug development pipelines.
2016-12-31 | GSE76257 | GEO
Project description:Callobius koreanus (C.koreanus) is a wandering spider and a member of the Amaurobiidae family, infraorder Araneae. RNA-sequencing was performend for venom gland tissue and whole body except venom gland.
2020-09-26 | GSE158565 | GEO
Project description:Agelena koreana is indigenous spider in South Korea that lives on piles of trees building webs. RNA-sequencing was performed for venom gland tissue and whole body except venom gland.
2022-02-23 | GSE197102 | GEO
Project description:Viper venom was tested using standard methods, native methods, and zinc addition.
2021-04-14 | MSV000087207 | GNPS