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22
datasets available to search
ShareScore release 0.7.1
Dataset results
22 results for “454 sequencing”
454-sequence data of Iron Age cattle from Althiburos – Tunisia
<p>The Maghreb is a key region for understanding the dynamics of cattle dispersal and admixture with local aurochs following their earliest domestication in the Fertile Crescent more than 10,000 years ago. Here, we present data on mitochondrial <em>D-loop</em> sequences obtained for 12 archaeological specimens of Iron Age (~2,800 cal BP–2,000 cal BP) domestic cattle from the Eastern Maghreb, i.e. Althiburos (El Kef, Tunisia). Maternal lineages were assigned to the elusive R and ubiquitous African-T1 haplogroups found in two and ten Althiburos specimens, respectively. Our results corroborate the introgression of aurochs females into the domestic stock of cattle from Althiburos. </p>
454-sequence data of Iron Age cattle from Althiburos – Tunisia
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Data from: Microsatellite markers from the Ion Torrent: a multi-species contrast to 454 shotgun sequencing
The development and screening of microsatellite markers have been accelerated by next-generation sequencing (NGS) technology and in particular GS-FLX pyro-sequencing (454). More recent platforms such as the PGM semiconductor sequencer (Ion Torrent) offer potential benefits such as dramatic reductions in cost, but to date have not been well utilized. Here, we critically compare the advantages and disadvantages of microsatellite development using PGM semiconductor sequencing and GS-FLX pyro-sequencing for two gymnosperm (a conifer and a cycad) and one angiosperm species. We show that these NGS platforms differ in the quantity of returned sequence data, unique microsatellite data and primer design opportunities, mostly consistent with the differences in read length. The strength of the PGM lies in the large amount of data generated at a comparatively lower cost and time. The strength of GS-FLX lies in the return of longer average length sequences and therefore greater flexibility in producing markers with variable product length, due to longer flanking regions, which is ideal for capillary multiplexing. These differences need to be considered when choosing a NGS method for microsatellite discovery. However, the ongoing improvement in read lengths of the NGS platforms will reduce the disadvantage of the current short read lengths, particularly for the PGM platform, allowing greater flexibility in primer design coupled with the power of a larger number of sequences.
Data from: Allele discovery of ten candidate drought-response genes in Austrian oak using a systematically informatics approach based on 454 amplicon sequencing
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Data from: Microsatellite markers from the Ion Torrent: a multi-species contrast to 454 shotgun sequencing
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Data from: Breakdown of phylogenetic signal: a survey of microsatellite densities in 454 shotgun sequences from 154 non model eukaryote species
Microsatellites are ubiquitous in Eukaryotic genomes. A more complete understanding of their origin and spread can be gained from a comparison of their distribution within a phylogenetic context. Although information for model species is accumulating rapidly, it is insufficient due to a lack of species depth, thus intragroup variation is necessarily ignored. As such, apparent differences between groups may be overinflated and generalizations cannot be inferred until an analysis of the variation that exists within groups has been conducted. In this study, we examined microsatellite coverage and motif patterns from 454 shotgun sequences of 154 Eukaryote species from eight distantly related phyla (Cnidaria, Arthropoda, Onychophora, Bryozoa, Mollusca, Echinodermata, Chordata and Streptophyta) to test if a consistent phylogenetic pattern emerges from the microsatellite composition of these species. It is clear from our results that data from model species provide incomplete information regarding the existing microsatellite variability within the Eukaryotes. A very strong heterogeneity of microsatellite composition was found within most phyla, classes and even orders. Autocorrelation analyses indicated that while microsatellite contents of species within clades more recent than 200 Mya tend to be similar, the autocorrelation breaks down and becomes negative or non-significant with increasing divergence time. Therefore, the age of the taxon seems to be a primary factor in degrading the phylogenetic pattern present among related groups. The most recent classes or orders of Chordates still retain the pattern of their common ancestor. However, within older groups, such as classes of Arthropods, the phylogenetic pattern has been scrambled by the long independent evolution of the lineages.
Raw sequencing data of Anaplamsa phagocytophilum loci (ankA, msp4, groEL) obtained from 454 and parameter files to clean these data using MOTHUR
<p>A compressed archive including: i) raw sequences in ssf file; ii) Mothur oligo files to sort out sequences among loci and individual samples.</p>
Data from: "454 sequencing of reduced representation libraries to discover single nucleotide polymorphisms (SNPs) in Megabunus harvestmen" in Genomic Resources Notes accepted 1 December 2013 to 31 January 2014
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Data from: "A reduced representation libraries approach for nuclear marker development via 454 sequencing applied on Tetramorium (Hymenoptera: Formicidae)" in Genomic Resources Notes Accepted 1 February 2015 to 31 March 2015
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Data from: Breakdown of phylogenetic signal: a survey of microsatellite densities in 454 shotgun sequences from 154 non model eukaryote species
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Targeted RT-PCR assays spanning unannotated splice junctions sequenced by Roche 454.
GEO Series GSE38886. Homo sapiens. 3 samples. Type: Expression profiling by high throughput sequencing.
MIRNA Gene Evolution in Arabidopsis lyrata and Arabidopsis thaliana: 454 sequencing
GEO Series GSE20654. Arabidopsis lyrata; Capsella rubella. 8 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Structural and Functional Analysis of Viral siRNAs using 454 sequencing
GEO Series GSE17164. Cymbidium ringspot virus; Nicotiana benthamiana. 2 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Global Changes following N-deprivation in Chlamydomonas: 454 sequencing
GEO Series GSE24366. Chlamydomonas reinhardtii. 2 samples. Type: Expression profiling by high throughput sequencing.
Testing the limits of 454 pyrotag sequencing: reproducibility, quantitative assessment and comparison to T-RFLP fingerprinting of aquifer microbes
GEO Series GSE35631. environmental samples; environmental samples; environmental samples; aquifer metagenome; Aliivibrio fischeri. 21 samples. Type: Expression profiling by high throughput sequencing; Other.
454 Life Sciences/Roche and Illumina sequencing of small RNAs from planarian samples
GEO Series GSE16159. Schmidtea mediterranea. 6 samples. Type: Non-coding RNA profiling by high throughput sequencing.
[E-MTAB-1222] GENCODE Batch VIII a: determining lncRNA transcript 5' and 3'-ends by RACE-PCR / 454 sequencing
GEO Series GSE46635. Homo sapiens. 2 samples. Type: Expression profiling by high throughput sequencing.
Arabidopsis thaliana small RNAs sequences identified using high-throughput 454 sequencing technology
GEO Series GSE6682. Arabidopsis thaliana. 14 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Heart-muscle expression ratios in pig obtained by 454-sequencing, iTRAQ-based proteomics and cDNA microarrays
GEO Series GSE10122. Sus scrofa. 18 samples. Type: Expression profiling by array.
[E-MTAB-1226] GENCODE Batch VIII b: determining lncRNA transcript 5' and 3'-ends by RACE-PCR / 454 sequencing
GEO Series GSE46636. Homo sapiens. 2 samples. Type: Expression profiling by high throughput sequencing.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.