Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Archaeal diversity

ABSTRACT: Archaeal diversity Raw sequence reads

PROVIDER: PRJNA588367 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR10418164.fastq.gz	Fastqsanger.gz

Items per page:

1 - 1 of 1

Similar Datasets

Archaeal diversity

Project description:Archaeal diversity Raw sequence reads

| PRJNA436179 | ENA

archaeal amoA 454

Project description:archaeal amoA 454 Raw sequence reads

| PRJNA431674 | ENA

Archaeal reads waste contaminated soil

Project description:Archaeal reads waste contaminated soil Raw sequence reads

| PRJNA613158 | ENA

Deep Coverage and Extended Sequence Reads Obtained with a Single Archaeal Protease Expedite de novo Protein Sequencing by Mass Spectrometry

Project description:Label-free protein sequencing is critically enabled by bottom-up, mass spectrometry-based proteomics workflows. Applications such as antibody sequencing or antigen discovery require de novo reconstruction of peptide and protein sequences. While trypsin has long served as the gold-standard protease in proteomics, its restricted C-terminal cleavage specificity constrains peptide diversity, particularly limiting coverage in antibody hypervariable complementarity-determining regions (CDRs). As a result, current workflows yield sparse reads and sequence gaps. Although multi-protease and hybrid-fragmentation strategies can notably improve coverage, they add complexity and compromise scalability and reproducibility. Here, we present a novel approach using HyperThermoacidic Archaeal (HTA) proteases Krakatoa or Vesuvius as powerful single-enzyme solutions for de novo antibody sequencing. Each protease generated over five times more unique peptide reads than trypsin or chymotrypsin with high redundancy across CDRs. Combined with EAciD fragmentation on a ZenoTOF 7600 system, this workflow enabled complete, unambiguous antibody sequencing. Despite most de novo tools being optimized for CID/HCD-tryptic data, analysis using PEAKS/DeepNovo and Stitch softwares showed that HTA-Proteases yielded up to fourfold higher alignment scores and fewer sequence mistakes across variable regions. Redundant reads increased more than threefold compared to standard proteases, boosting confidence in amino acid assignment and reducing ambiguity in final assemblies. Our alternative HTA-EAciD approach offers short digestion times, eliminates extensive cleanup, and enables analysis in a single LC-MS/MS run. This single-protease strategy delivers sequencing performance comparable to multi-enzyme workflows, providing a scalable, efficient, and highly confident approach for de novo sequencing in antibody discovery and beyond.

2026-03-17 | PXD063988 | Pride

Structure of an Archaeal Ribosome Reveals a Divergent Active Site and Hibernation Factor

Project description:Ribosomes translate mRNA into protein. Despite divergence in ribosome structure over the course of evolution, the catalytic site, known as the peptidyl transferase center (PTC), is thought to be nearly universally conserved. Here, we identify clades of archaea that have highly divergent ribosomal RNA sequences in the PTC. To understand how these PTC sequences fold, we determined cryo-EM structures of the 70S and 50S ribosomes to 2.4 Å and 2 Å, respectively, from the hyperthermophilic archaeon Pyrobaculum calidifontis. PTC sequence variation leads to the rearrangement of key base triples and differences between archaeal and bacterial ribosomal proteins enable sequence variation in archaeal PTCs. Finally, we identify a previously undescribed archaeal ribosome hibernation factor, Dri, that differs from known bacterial and eukaryotic hibernation factors and is found in multiple archaeal phyla. Overall, this work identifies factors that regulate ribosome function in archaea and reveals a larger diversity of the most ancient sequences in the ribosome

2025-06-17 | PXD064958 | Pride

Morus alba Raw protein sequence reads

Project description:Morus alba L. Raw protein sequence reads and sequence

2024-02-08 | PXD049451 |

Archaeal community across refuse decomposition

Project description:Archaeal community across refuse decomposition Raw sequence reads

| PRJNA411954 | ENA

Groundwater archaeal communities in China Raw sequence reads

Project description:Groundwater archaeal communities in China Raw sequence reads Raw sequence reads

| PRJNA932609 | ENA

Archaeal diversity coastal environment

Project description:Archaeal diversity of free-living fraction of surface seawater collected in the Bay of Brest and the Iroise Sea.

| PRJEB48467 | ENA

Ammonia oxidizing archaeal community composition in Gulf of Mexico sediments investigated with an amoA functional gene microarray

Project description:Ammonia-oxidizing archaeal (AOA) amoA diversity and relative abundance in Gulf of Mexico sediments (0-2 cm) were investigated using a functional gene microarray; a two color array with a universal internal standard

2013-03-01 | GSE42286 | GEO

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