Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Mitochondrial genome capture from fecal samples and museum-preserved specimens

ABSTRACT: Whole mitochondrial genome capture from fecal samples and museum-preserved specimens of the endangered Grauer's gorilla and eastern chimpanzee

PROVIDER: PRJEB21370 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR2011990_1.fastq.gz	Fastqsanger.gz
	ERR2011990_2.fastq.gz	Fastqsanger.gz
	ERR2011991_1.fastq.gz	Fastqsanger.gz
	ERR2011991_2.fastq.gz	Fastqsanger.gz
	ERR2011982_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 80

Similar Datasets

Archival chromatin sequencing in eastern water dragon museum specimens

Project description:Formalin induces inter- and intra-molecular crosslinks within exposed cells. This cross-linking can be exploited to characterise chromatin state as in the MNase (micrococcal nuclease) assays. Our team aims to optimise these assays for application in museum preserved formalin-exposed specimens. To do so, we applied an optimised MNase assay to fresh-frozen and archival eastern water dragon specimens, as old as 1905. We found that heavy formalin fixation modulates rather than eliminates signatures of differential chromatin accessibility and that these chromatin profiles are sex-specific and environmental condition dependent.

2024-03-01 | GSE256157 | GEO

Assessing the hidden potential of beeswax specimens in Natural History Museum collections

Project description:Natural history museum specimens of historical honeybees have been successfully used to explore the genomic past of the honeybee, indicating fast and rapid changes between historical and modern specimens, possibly as a response to current challenges. In our study we explore a potential untapped archive from natural history collections - specimens of beeswax. We examine an Apis mellifera mellifera queen cell specimen from the 19th century. The intact and closed cell was analysed by X-ray Computed Tomography (CT) to reveal a perfectly preserved queen bee inside her cell. Subsequently, a micro-destructive approach was used to evaluate the possibility of protein extraction from the cell. Our results show that studies on specimens such as these provide valuable information about the past rearing of queens, their diet and development, which is relevant for understanding current honeybee behaviour. In addition we evaluate the feasibility of using historical beeswax as a biomolecular archive for ancient proteins to study honeybees.

2024-09-05 | PXD034106 | Pride

Screening great ape museum specimens for DNA viruses

Project description:Screening great ape museum specimens for DNA viruses

| PRJEB75038 | ENA

Archival chromatin sequencing in formalin-fixed mouse specimens

Project description:Formalin induces inter- and intra-molecular crosslinks within exposed cells. This cross-linking can be exploited to characterise chromatin state as in the FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) and MNase (micrococcal nuclease) assays. Here, we optimised the FAIRE and MNase assays for application upon heavily-fixed tissues as is typically found in historical formalin-preserved museum specimens. We demonstrate these assays in formalin-fixed mouse specimens and compare the chromatin signatures to specimen-matched fresh tissues. We found that heavy formalin fixation modulates rather than eliminates signatures of differential chromatin accessibility and that these chromatin profiles are reproducible, tissue-specific and sex-specific in vertebrate specimens.

2024-03-01 | GSE256158 | GEO

Archival chromatin sequencing in eastern water dragon museum specimens

Project description:Archival chromatin sequencing in eastern water dragon museum specimens

| PRJNA1078353 | ENA

Archival chromatin sequencing in formalin-fixed mouse specimens [FAIRE and Mnase]

Project description:Formalin induces inter- and intra-molecular crosslinks within exposed cells. This cross-linking can be exploited to characterise chromatin state as in the FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) and MNase (micrococcal nuclease) assays. Here, we optimised the FAIRE and MNase assays for application upon heavily-fixed tissues as is typically found in historical formalin-preserved museum specimens. We demonstrate these assays in formalin-fixed mouse specimens and compare the chromatin signatures to specimen-matched fresh tissues. We found that heavy formalin fixation modulates rather than eliminates signatures of differential chromatin accessibility and that these chromatin profiles are reproducible, tissue-specific and sex-specific in vertebrate specimens.

2024-03-15 | GSE261169 | GEO

Species identification of ivory and bone museum objects using minimally invasive proteomics

Project description:Ivory is a highly prized material in many cultures since it can be carved into intricated designs and have a highly polished surface. Due to its popularity, the animals from which ivory can be sourced have started to come under threat. Identification of the ivory species is not only important for compliance with the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES), it can also provide important information about the context in which the work was created. In this work, we have developed a minimally invasive workflow to remove minimal amounts of material from precious objects, and, using high-resolution mass spectrometry-based proteomics, identified the taxonomy of several ivory and bone objects from the collection of The Metropolitan Museum of Art dating from as early as 4000 B.C. We built an inhouse proteomic databases of underrepresented species based on exemplars obtained from the Mammology American Museum of Natural History collection and proposed alternative data analysis workflows for rare samples containing sparse and inconsistently preserved organic material. This is a first application demonstrating extensive and accurate ivory species identification using proteomics to unlock sequence uncertainties, e.g. Leu/Ile-discrimination.

2024-02-05 | PXD042536 | Pride

Project description:Archival DNA from historical ethanol preserved museum specimens.

| PRJNA837973 | ENA

Apis mellifera

Project description:Apis mellifera Targeted loci from museum preserved specimens

| PRJNA505606 | ENA

Chemical and Molecular Effects of Diffusion-Based Iodine Contrast-Enhancing Stains on Fluid-Preserved Avian Specimens

Project description:House sparrow specimens were stained with four different iodine-based stains to increase contrast in microCT. Proteomic characterization of muscle and bone was performed on contralateral samples (before and after staining). Iodination was detected for all stains. Analysis on samples from the Smithsonian National Museum of Natural History: USNM 657964, USNM 657968, USNM 657963, USNM 657967

2020-02-18 | MSV000084970 | 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