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ShareScore release 0.9.0
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21 results for “sequencing depth”
Variation of and associations with the depth and evenness of sequencing coverage in a sample of archived plastid genomes
<p>Depth and evenness of sequencing coverage are considered potential indicators of genome assembly quality. In plastid genomics, where new data generation has outpaced the development of suitable assembly quality indicators, these coverage metrics could offer insights into the quality of plastomes of different sizes, structures, or taxonomic origins. However, the typical variation of sequencing depth and evenness among archived plastid genomes, their variability between plastome partitions, and any association with methodological factors have yet to be evaluated. This study explores the variation of sequencing depth and evenness across a sample of publicly accessible plastid genomes and their potential associations with plastome structure, assembly accuracy, and the methodological provenance of the genome data using statistical tests. Our results indicate significant differences in sequencing depth across the four structural partitions as well as between the coding and non-coding sections of the genomes, a significant correlation between sequencing evenness and the number of ambiguous nucleotides, and a significant difference in sequencing evenness between several DNA sequencing platforms. These findings highlight that many publicly accessible plastid genomes are based on sequence data with highly variable sequencing depth and evenness and that this variation is influenced, at least partially, by genome structure and methodological factors.</p>
Combined high-depth Illumina+PacBio Sequencing of several samples from FDA-ARGOS
<p>The (real) sequencing data is compiled from a concatenation of sequencing runs from Database for Reference Grade Microbial Sequences (FDA-ARGOS). Specifically, the following samples were sequenced with both Illumina and PacBio. The sample accessions are shown below.</p> <pre><code> BioSample Run Platform Organism bases source <chr> <chr> <chr> <chr> <dbl> <chr> 1 SAMN06173354 SRR5409204 ILLUMINA Bacillus anthracis 1778000000 Colorado Serum Co., Anthrax Spore Vaccine 2 SAMN06173354 SRR5409205 PACBIO_SMRT Bacillus anthracis 2420000000 Colorado Serum Co., Anthrax Spore Vaccine 3 SAMN06173356 SRR5448657 ILLUMINA Bacillus circulans 2311000000 swab with brown-gray powder 4 SAMN06173356 SRR5448656 PACBIO_SMRT Bacillus circulans 242000000 swab with brown-gray powder 5 SAMN04875535 SRR4123920 ILLUMINA Elizabethkingia anophelis 1357000000 blood 6 SAMN04875535 SRR4123919 PACBIO_SMRT Elizabethkingia anophelis 2173000000 blood 7 SAMN06173306 SRR5413253 ILLUMINA Escherichia coli O157 3051000000 clinical isolate 8 SAMN06173306 SRR5413252 PACBIO_SMRT Escherichia coli O157 915000000 clinical isolate 9 SAMN06173318 SRR5413272 ILLUMINA Mycobacterium avium subsp. paratuberculosis 1032000000 feces 10 SAMN06173318 SRR5413271 PACBIO_SMRT Mycobacterium avium subsp. paratuberculosis 462000000 feces 11 SAMN07312468 SRR5879398 ILLUMINA Mycobacterium tuberculosis 1054000000 human 12 SAMN07312468 SRR5879396 PACBIO_SMRT Mycobacterium tuberculosis 1854000000 human 13 SAMN04875542 SRR4123931 ILLUMINA Neisseria gonorrhoeae 1053000000 ATCC strain 14 SAMN04875542 SRR4123930 PACBIO_SMRT Neisseria gonorrhoeae 1117000000 ATCC strain </code></pre> <p>Samples were selected with the SRA Run selector. The SraRunTable.txt file was exported containing the metadata for each sample, and fastq-dump from the SRA toolkit was used to write out fastq files for each run, with paired Illumina data being split into separate _1.fastq.gz and _2.fastq.gz files. </p>
variational-depth-from-focus: devCam sequences
<p>The 3 self-generated focal stack images datasets made using devCam.</p>
A confidence interval analysis of sampling effort, sequencing depth, and taxonomic resolution of fungal community ecology in the era of high-throughput sequencing.
Open the record for dataset details and reuse information.
Analysis of the RDR6-dependent small RNA profile in ein5 ski2 in Arabidopsis with biological replications and increased sequencing depth
GEO Series GSE57936. Arabidopsis thaliana. 12 samples. Type: Non-coding RNA profiling by high throughput sequencing.
RNA seq analysis of murine whole colon using Takara SMART-Seq Stranded kit. Libraries were sequenced on an Illumina NovaSeq 6000 to an approximate sequencing depth of 60 million total reads
GEO Series GSE181502. Mus musculus. 28 samples. Type: Expression profiling by high throughput sequencing.
High-depth RNA sequencing of isogenic wild-type, PIK3CA-WT/H1047R and PIK3CA-H1047R/H1047R human iPSCs
GEO Series GSE134076. Homo sapiens. 12 samples. Type: Expression profiling by high throughput sequencing.
Evaluating the Impact of Sequencing Depth on Transcriptome Profiling in Human Adipose
GEO Series GSE46323. Homo sapiens. 2 samples. Type: Expression profiling by high throughput sequencing.
Prospective, Multi-center, Non-interventional, Open Label, Randomized (Depth of Focus Testing Sequences), Clinical Study
ClinicalTrials.gov study NCT06767319. IPD Sharing: YES. Countries: 1. Publications: 0.
In-Depth Patient-specific Analysis of Tumor Heterogeneity in Melanoma Brain Metastasis: Insights from Spatial Transcriptomics and Multi-Region Bulk Sequencing
GEO Series GSE275731. Homo sapiens. 12 samples. Type: Expression profiling by high throughput sequencing.
Whole genome transcription profiling of the L5 spinal nerve transection model of neuropathic pain in the rat, at different sequencing depths (RNA-Seq)
GEO Series GSE53762. Rattus norvegicus. 18 samples. Type: Expression profiling by high throughput sequencing.
High depth sequencing of BrU-labeled nascent RNA.
GEO Series GSE92565. Homo sapiens. 4 samples. Type: Expression profiling by high throughput sequencing.
Whole genome transcription profiling of the L5 spinal nerve transection model of neuropathic pain in the rat, at different sequencing depths
GEO Series GSE53861. Rattus norvegicus. 30 samples. Type: Expression profiling by array; Expression profiling by high throughput sequencing.
Whole genome transcription profiling of the L5 spinal nerve transection model of neuropathic pain in the rat, at different sequencing depths (Affymetrix transcript-level)
GEO Series GSE53764. Rattus norvegicus. 6 samples. Type: Expression profiling by array.
In depth sequencing of the siRNAs associated with peach latent mosaic viroid infection
GEO Series GSE18764. Prunus persica; Prunus persica var. nucipersica. 2 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Characterisation of CD4+ T-cell subtypes using single cell RNA sequencing and the impact of cell number and sequencing depth
GEO Series GSE147928. Homo sapiens. 2 samples. Type: Expression profiling by high throughput sequencing.
Whole genome transcription profiling of the L5 spinal nerve transection model of neuropathic pain in the rat, at different sequencing depths (Affymetrix exon-level)
GEO Series GSE53860. Rattus norvegicus. 6 samples. Type: Expression profiling by array.
Low read depth whole genome sequencing of mouse Cre-loxP-induced Ewsr1-Atf1 translocation tumors
GEO Series GSE158719. Mus musculus. 5 samples. Type: Other.
In depth mechanistic analysis including high-throughput RNA sequencing in the prediction of functional and structural cardiotoxicants using hiPSC cardiomyocytes
GEO Series GSE244740. Homo sapiens. 3072 samples. Type: Expression profiling by high throughput sequencing.
Limited depth in bone defect-combining computational fluid dynamics and genes sequence analysis due to osteogenic effect under negative pressure wound therapy
GEO Series GSE216691. Mus musculus. 5 samples. Type: Expression profiling by high throughput sequencing.
ScienceDex guides
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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.