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Dataset results
7 results for “genome re-sequencing”
Whole genome re-sequencing of B. dorsalis in the Indian Ocean
<p>Files containing essential data for the production of the paper: <em>Bactrocera dorsalis </em>in the Indian Ocean: a tale of two invasions (Deschepper et. al, 202X) DOI:####</p>
Whole genome re-sequencing workshop data: fastq files and reference genomes
<p> </p> <p>Whole genome re-sequencing data analysis workshop datasets. The files are necessary inputs for the workshop in https://github.com/PoODL-CES/Genomics_learning_workshop</p> <p>Tools and scripts listed in the https://github.com/PoODL-CES/Genomics_learning_workshop repository.</p> <p> </p> <p>These are subsampled fastq files from:<br><br>Khan, A., Patel, K., Shukla, H., Viswanathan, A., van der Valk, T., Borthakur, U., Nigam, P., Zachariah, A., Jhala, Y.V., Kardos, M. and Ramakrishnan, U., 2021. Genomic evidence for inbreeding depression and purging of deleterious genetic variation in Indian tigers. <em>Proceedings of the National Academy of Sciences</em>, <em>118</em>(49), p.e2023018118.</p> <p>The reference genome is from :</p> <p>Shukla, H., Suryamohan, K., Khan, A., Mohan, K., Perumal, R.C., Mathew, O.K., Menon, R., Dixon, M.D., Muraleedharan, M., Kuriakose, B. and Michael, S., 2023. Near-chromosomal de novo assembly of Bengal tiger genome reveals genetic hallmarks of apex predation. <em>GigaScience</em>, <em>12</em>, p.giac112.</p> <p> </p> <p>The reference has been indexed using:</p> <p>bwa index <a target="_blank" rel="noopener noreferrer">GCA_021130815.1_PanTigT.MC.v3_genomic.fna</a></p> <p> </p>
Xcc BrA1 re-sequenced genome contigs, annotation file and Trinitiy De-nove assembled DEG's
<p>Assembled genome contigs of Xcc strain BrA1 (Behlau et al 2017) which was re-sequenced by our lab and used in a copper stress Transcriptome study. A hybrid RNA-seq analysis pipeline was used and the DEG Trinity De-novo assembled transcripts are also included.</p>
Data from: A survey of genome-wide single nucleotide polymorphisms through genome re-sequencing in the Périgord black truffle (Tuber melanosporum Vittad.)
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PacBio amplicon re-sequencing of 62 P. tricornutum genomic loci – processed datasets
<p>Processed datasets from PacBio amplicon re-sequencing of 62 P. tricornutum genomic loci. Raw data are available at https://www.ncbi.nlm.nih.gov/bioproject/PRJNA658511. </p> <p>Available datasets: </p> <p>- reference file for regions selected for amplicon sequencing: <em>Phaeodactylum_tricornutum_amplicon_sequencing_loci.fa</em></p> <p>- final .bam files containing processed PacBio sequencing reads aligned to the reference:</p> <p><em>PacBio_amplicon_seq_T1.bam</em> and <em>PacBio_amplicon_seq_T6.bam</em> </p> <p>- . table files with the position, reference and alternative allele for reliable biallelic SNPs selected in ILLUMINA sequencing of the culture at T1: </p> <p><em>P_tricornutum_PacBio_amplicon_sequencing_T1_SNPs.table</em> and <em>P_tricornutum_PacBio_amplicon_sequencing_T6_SNPs.table</em></p> <p>Re-sequencing of 62 endogenous P. tricornutum loci selected in a genome-wide analysis of haplotype diversity. The goal was to determine the number of haplotypes per locus and the appearance of new haplotypes over time. The length of the sequenced loci was 2kb (+/- 5%). Loci were amplified by emulsion PCR on the same culture harvested in two time points: five loci were amplified one month (T1) and all loci were amplified 6 months (T6) after the start of the culture from a single cell. Plasmids containing cloned GFP or YFP were amplified separately as a control for random errors. Control reactions for artificial haplotypes detection consisted of mixed CFP with YFP or CFP with GFP. Amplicons were pooled together into two samples. Sample PacBio_AS_T1 contained five P. tricornutum endogenous amplicons from DNA harvested at T1 time point, GFP amplified separately and CFP+YFP amplified in one reaction. Sample PacBio_AS_T6 contained 63 P. tricornutum endogenous amplicons from DNA harvested at T6 time point, YFP amplified separately and CFP+GFP amplified in one reaction. Samples were mixed in 1:9 PacBio_AS_T1: PacBio_AS_T6 ratio before sequencing on one PacBio Sequel SMRT cell.</p>
Whole genome re-sequencing of mother and offspring D. magna genotypes
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Genome re-sequencing of Arabidopsis epiRILs and epiHybrids
GEO Series GSE99481. Arabidopsis thaliana. 18 samples. Type: Other.
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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.