Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

GNPS - Herbarium samples of Ferula arrigonii plant species collected in Sardinia during the years 1986-2006

ABSTRACT: Data from the LC-MS/MS analysis of herbarium samples of the plant species Ferula arrigonii, collected in Sardinia during the years 1986-2006.

INSTRUMENT(S): 3200 QTRAP

ORGANISM(S): Ferula Arrigonii

SUBMITTER: Julien Paolini

PROVIDER: MSV000081946 | GNPS | Wed Jan 17 12:21:00 GMT 2018

REPOSITORIES: GNPS

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

DNA barcoding of selected UAE medicinal plant species: a comparative assessment of herbarium and fresh samples.

Project description:It is commonly difficult to extract and amplify DNA from herbarium samples as they are old and preserved using different compounds. In addition, such samples are subjected to the accumulation of intrinsically produced plant substances over long periods (up to hundreds of years). DNA extraction from desert flora may pause added difficulties as many contain high levels of secondary metabolites. Herbarium samples from the Biology Department (UAE University) plant collection and fresh plant samples, collected from around Al-Ain (UAE), were used in this study. The three barcode loci for the coding genes matK, rbcL and rpoC1-were amplified. Our results showed that T. terresteris, H. robustum,T. pentandrus and Z. qatarense were amplified using all three primers for both fresh and herbaium samples. Both fresh and herbarium samples of C. comosum, however, were not amplified at all, using the three primers. Herbarium samples from A. javanica, C. imbricatum, T. aucherana and Z. simplex were not amplified with any of the three primers. For fresh samples 90, 90 and 80% of the samples were amplified using matK, rbcL and rpoC1, respectively. In short, fresh samples were significantly better amplified than those from herbarium sources, using the three primers. Both fresh and herbarium samples from one species (C. comosum), however, were not successfully amplified. It is also concluded that the rbcL regions showed real potentials to distinguish the UAE species under investigation into the appropriate family and genus.

| S-EPMC5313416 | biostudies-literature

plant samples

Project description:plant samples Raw sequence reads

| PRJNA604508 | ENA

Plant sequences from fecal samples collected from mice

Project description:Plant sequences from fecal samples collected from mice Metagenome

| PRJNA801232 | ENA

plant species

Project description:Homotypic motifs in the promoters across various plant species

| PRJNA1002881 | ENA

Transcription profiling during rice plant infection

Project description:Study of transcription profiling during rice plant infection

| PRJEB45007 | ENA

Cryptic species of Curvularia in the culture collection of the Queensland Plant Pathology Herbarium.

Project description:Several unidentified specimens of Curvularia deposited in the Queensland Plant Pathology Herbarium were re-examined. Phylogenetic analyses based on sequence data of the internal transcribed spacer region, partial fragments of the glyceraldehyde-3-phosphate dehydrogenase and the translation elongation factor 1-? genes, supported the introduction of 13 novel Curvularia species. Eight of the species described, namely, C. beasleyisp. nov., C. beerburrumensissp. nov., C. eragrosticolasp. nov., C. kenpeggiisp. nov., C. mebaldsiisp. nov., C. petersoniisp. nov., C. platziisp. nov. and C. warraberensissp. nov., were isolated from grasses (Poaceae) exotic to Australia. Only two species, C. lamingtonensissp. nov. and C. sporobolicolasp. nov., were described from native Australian grasses. Two species were described from hosts in other families, namely, C. coatesiaesp. nov. from Litchi chinensis (Sapindaceae) and C. colbraniisp. nov. from Crinum zeylanicum (Amaryllidaceae). Curvularia reesiisp. nov. was described from an isolate obtained from an air sample. Furthermore, DNA sequences from ex-type cultures supported the generic placement of C. neoindica and the transfer of Drechslera boeremae to Curvularia.

| S-EPMC6015126 | biostudies-literature

Comparative analysis of nascent transcription among plant species

Project description:Comparative analysis of nascent transcription among plant species

2023-09-28 | GSE233927 | GEO

DNA damage in plant herbarium tissue.

Project description:Dried plant herbarium specimens are potentially a valuable source of DNA. Efforts to obtain genetic information from this source are often hindered by an inability to obtain amplifiable DNA as herbarium DNA is typically highly degraded. DNA post-mortem damage may not only reduce the number of amplifiable template molecules, but may also lead to the generation of erroneous sequence information. A qualitative and quantitative assessment of DNA post-mortem damage is essential to determine the accuracy of molecular data from herbarium specimens. In this study we present an assessment of DNA damage as miscoding lesions in herbarium specimens using 454-sequencing of amplicons derived from plastid, mitochondrial, and nuclear DNA. In addition, we assess DNA degradation as a result of strand breaks and other types of polymerase non-bypassable damage by quantitative real-time PCR. Comparing four pairs of fresh and herbarium specimens of the same individuals we quantitatively assess post-mortem DNA damage, directly after specimen preparation, as well as after long-term herbarium storage. After specimen preparation we estimate the proportion of gene copy numbers of plastid, mitochondrial, and nuclear DNA to be 2.4-3.8% of fresh control DNA and 1.0-1.3% after long-term herbarium storage, indicating that nearly all DNA damage occurs on specimen preparation. In addition, there is no evidence of preferential degradation of organelle versus nuclear genomes. Increased levels of C?T/G?A transitions were observed in old herbarium plastid DNA, representing 21.8% of observed miscoding lesions. We interpret this type of post-mortem DNA damage-derived modification to have arisen from the hydrolytic deamination of cytosine during long-term herbarium storage. Our results suggest that reliable sequence data can be obtained from herbarium specimens.

| S-EPMC3230621 | biostudies-literature

Evaluation of commercially available small RNA methods for plant samples

Project description:Plant small RNAs are a diverse and complex set of molecules, ranging in length from 21 to 24 nt, involved in a wide range of essential biological processes. Nowadays, high-throughput sequencing is the most commonly used method for the discovery and quantification of small RNAs. However, it is known that several biases can occur during the preparation of small RNA libraries, especially using low input RNA. We used two types of plant biological samples to evaluate the performance of seven commercially available methods for small RNA library construction, using different RNA input amounts. We show that when working with plant material, library construction methods have differing capabilities to capture small RNAs, and that different library construction methods provide better results when applied to the detection of microRNAs, phased small RNAs, or tRNA-derived fragments.

2021-08-01 | GSE156973 | GEO

Rhizosphere-associated metabolites of four wetland plant species

Project description:This dataset contains raw files for metabolites collected from the soil and roots of four wetland plant species under non-sterile conditions, both in soil and hydroponically, during the day and night time periods.

2024-05-01 | MSV000094652 | MassIVE

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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