Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
33
datasets available to search
ShareScore release 0.9.0
Dataset results
33 results for “Bulk DNA”
Data from: Tropical ancient DNA from bulk archaeological fish bone reveals the subsistence practices of a historic coastal community in southwest Madagascar
Taxonomic identification of archaeological fish bones provides important insights into the subsistence practices of ancient coastal peoples. However, it can be difficult to execute robust morphological identification of fish bones from species-rich fossil assemblages, especially from post-cranial material with few distinguishing features. Fragmentation, weathering and burning further impede taxonomic identification, resulting in large numbers of unidentifiable bones from archaeological sites. This limitation can be somewhat mitigated by taking an ancient DNA (aDNA) bulk-bone metabarcoding (BBM) approach to faunal identification, where DNA from non-diagnostic bone fragments is extracted and sequenced in parallel. However, a large proportion of fishing communities (both past and present) live in tropical regions that have sub-optimal conditions for long-term aDNA preservation. To date, the BBM method has never been applied to fish bones before, or to fossils excavated from an exposed context within a tropical climate. Here, we demonstrate that morphologically indistinct bulk fish bone from the tropics can be identified by sequencing aDNA extracted from 100 to 300 ya archaeological midden material in southwest Madagascar. Despite the biases of the approach, we rapidly obtained family, genus, and species-level assemblage information, and used this to describe a subset of the ichthyofauna exploited by an 18th century fishing community. We identified 23 families of fish, including benthic, pelagic, and coral-dwelling fishes, suggesting a reliance on a variety of marine and brackish habitats. When possible, BBM should be used alongside osteological approaches to address the limitations of both; however, this study highlights how genetic methods can nevertheless be a valuable tool for helping resolve faunal assemblages when morphological identification is hindered by taphonomic processes, lack of adequate comparative collections, and time constraints, and can provide a temporal perspective on fish biodiversity in the context of accelerated exploitation of the marine environment.
Data from: Tropical ancient DNA from bulk archaeological fish bone reveals the subsistence practices of a historic coastal community in southwest Madagascar
Open the record for dataset details and reuse information.
Data from: A critical evaluation of how ancient DNA bulk bone metabarcoding complements traditional morphological analysis of fossil assemblages
Open the record for dataset details and reuse information.
Supplementary material 1 from: Moore MA, Scheible MK, Robertson JB, Meiklejohn KA (2022) Assessing the lysis of diverse pollen from bulk environmental samples for DNA metabarcoding. Metabarcoding and Metagenomics 6: e89753. https://doi.org/10.3897/mbmg.6.89753
Table S1
Supplementary material 2 from: Moore MA, Scheible MK, Robertson JB, Meiklejohn KA (2022) Assessing the lysis of diverse pollen from bulk environmental samples for DNA metabarcoding. Metabarcoding and Metagenomics 6: e89753. https://doi.org/10.3897/mbmg.6.89753
Table S2
Supplementary material 2 from: Majaneva M, Diserud OH, Eagle SHC, Hajibabaei M, Ekrem T (2018) Choice of DNA extraction method affects DNA metabarcoding of unsorted invertebrate bulk samples. Metabarcoding and Metagenomics 2: e26664. https://doi.org/10.3897/mbmg.2.26664
Final species table. :
Supplementary material 5 from: Majaneva M, Diserud OH, Eagle SHC, Hajibabaei M, Ekrem T (2018) Choice of DNA extraction method affects DNA metabarcoding of unsorted invertebrate bulk samples. Metabarcoding and Metagenomics 2: e26664. https://doi.org/10.3897/mbmg.2.26664
Methods (Scripts) :
Supplementary material 3 from: Majaneva M, Diserud OH, Eagle SHC, Hajibabaei M, Ekrem T (2018) Choice of DNA extraction method affects DNA metabarcoding of unsorted invertebrate bulk samples. Metabarcoding and Metagenomics 2: e26664. https://doi.org/10.3897/mbmg.2.26664
Number of reads per sample. :
Supplementary material 4 from: Majaneva M, Diserud OH, Eagle SHC, Hajibabaei M, Ekrem T (2018) Choice of DNA extraction method affects DNA metabarcoding of unsorted invertebrate bulk samples. Metabarcoding and Metagenomics 2: e26664. https://doi.org/10.3897/mbmg.2.26664
Diversity analyses. :
Supplementary material 1 from: Majaneva M, Diserud OH, Eagle SHC, Hajibabaei M, Ekrem T (2018) Choice of DNA extraction method affects DNA metabarcoding of unsorted invertebrate bulk samples. Metabarcoding and Metagenomics 2: e26664. https://doi.org/10.3897/mbmg.2.26664
Fragment and working PCR conditions. :
Multigenerational cell tracking of DNA replication and heritable DNA damage (bulk)
GEO Series GSE288485. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
Combinatorial profiling of multiple histone modifications and transcriptome in single cells using scMTR-seq [bulk_DNA]
GEO Series GSE277776. Homo sapiens. 28 samples. Type: Other.
Precise Gene Editing Preserves Hematopoietic Stem Cell Function Following Transient p53-Mediate DNA Damage Response [bulk RNA-seq]
GEO Series GSE119584. Homo sapiens. 18 samples. Type: Expression profiling by high throughput sequencing.
Placental and Immune Cell DNA Methylation Reference Panel for Bulk Tissue Cell Composition Estimation in Epidemiological Studies
GEO Series GSE271697. Homo sapiens. 93 samples. Type: Methylation profiling by genome tiling array.
Combinatorial genetic strategy accelerates the discovery of cancer genotype-phenotype associations [bulk DNA-Seq]
GEO Series GSE229781. Mus musculus. 10 samples. Type: Other.
HyPR-seq: Single-cell quantification of chosen RNAs via hybridization and sequencing of DNA probes (bulk RNA-seq dataset)
GEO Series GSE158001. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
DNA barcoding reveals ongoing immunoediting of clonal cancer populations during metastatic progression and in response to immunotherapy [Bulk RNAseq]
GEO Series GSE210054. Mus musculus. 20 samples. Type: Expression profiling by high throughput sequencing.
Transcriptional profiling of DNA sensing signal activation of THP-1 cells using bulk RNA-seq and single cell RNA-seq
GEO Series GSE268256. Homo sapiens. 17 samples. Type: Expression profiling by high throughput sequencing.
Single-cell and bulk transcriptional profiling of mouse ovaries reveals novel genes and pathways associated with DNA damage response in oocytes
GEO Series GSE255032. Mus musculus. 28 samples. Type: Expression profiling by high throughput sequencing.
Bulk profiling of genome-wide DNA methylation distributions in mouse embryonic stem cells (mESCs) cultured in different media pulses
GEO Series GSE268814. Mus musculus. 6 samples. Type: Methylation 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.