Mainland tiger snake genome project
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB27871 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| ERR2714264_1.fastq.gz | Fastqsanger.gz | |||
| ERR2714264_2.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 3 of 3 |
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Project description:This DATASET collection includes the mass spectrometry files for proteomics venom investigation of island and mainland V. ammodytes populations from North Macedonia.
Sample list:
1. Island - adult - male
2. Island - adult - female
3. Island - juvenile
4. Island - subadult
5. Mainland - adult
6. Mainland - subadult
7. Mainland - juvenile
Folders 01-07 - BOTTOM-UP PROTEOMICS: The venom pools were investigated by the bottom-up "snake venomics" (labelled as SVX) approach and in short: separated by RP-HPLC, followed by SDS-PAGE separation and the single bands were in-gel processed by DTT, IAC and finally o/n tryptic digested. Samples submitted to HPLC-MS/MS. Early peptidic fractions of the first HPLC run were directly submitted to HPLC-MS/MS analytic w/o further gel procession. Folders 01 to 07 include the MS and MS/MS spectra of the V. ammodytes sample pools from different populations. Files are included as RAW and MZML format.
Used instrument: LTQ Orbitrap XL mass spectrometer (Thermo, Bremen, Germany) with an Agilent 1260 HPLC system (Agilent Technologies, Waldbronn, Germany) using a reversed-phase Grace Vydac 218MS C18 (2.1 x 150 mm; 5 um particle size) column.
Modifications: UNIMOD:4 - \"Iodoacetamide derivative.\"
Used protein database: Uniprot_8750_serpentes_CanNIso_2674_entries_220210_cRAP_220210.fasta
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Project description:Notechis scutatus Transcriptome or Gene expression
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Project description:We used gene expression accompanied by physical characteristics and gill Na+/K+-ATPase activity to analyze physiological differences associated with two life history variations of juvenile fall Chinook Salmon in the Snake River basin. Subyearlings originating in the Snake River typically migrate seaward as subyearlings, whereas many subyearlings from the Clearwater River delay seaward migration during summer and complete seaward migration the following spring as yearlings. We examined gill Na+/K+-ATPase activity and gene expression of subyearlings at different times during rearing and seaward emigration. Natural-origin Snake River subyearlings rearing under an increasing photoperiod and seasonally increasing temperatures showed a typical increasing pattern of parr to smolt gill Na+/K+-ATPase activity development, which then declined into autumn. In contrast, Clearwater River subyearlings that had experienced cooler temperatures showed no pattern of increasing gill Na+/K+-ATPase activities and were not different from parr. Liver transcription of genes involved in DNA repair and binding, the cell cycle, metabolism (steroid, fatty acid and other metabolic pathways) iron homeostasis, heme and oxygen binding, the immune response, and male sexual development were enriched amongst genes differentially expressed between Snake River parr versus smolts. Gene expression results confirmed that Clearwater River subyearlings were parr-like in their physiological status. By autumn, subyearlings had low gill Na+/K+-ATPase activities despite their large size and external smolt characteristics. We suggest that environmental factors like temperature and photoperiod influence subyearling physiological status in each river that ultimately dictates juvenile life history pathways. Non-migrating and migrating natural subyearling fall Chinook salmon were collected from the Snake River. Non-migrating natural subyearling fall Chinook salmon were collected from the Clearwater River. Twelve fish were collected at each of four different time points for a total of 48 fish. Total RNA was extracted from the liver of each fish. Equal amounts of RNA from three fish were pooled to create four pools of RNA per time point. Each RNA pool was hybridized to an array for a total of 16 arrays with four arrays per time point.
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Project description:ORG.one project - Sumatran tiger (Panthera tigris sumatrae)
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