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34 results for “GCA”
Genome, repeat, and functional annotation associated with the naked mole-rat genome assembly, mHetGlaV3 (GCA_964261345.1)
<p>The naked mole-rat (NMR; Heterocephalus glaber) is a eusocial subterranean rodent with a highly unusual set of physiological traits, such as extreme longevity, that has attracted great interest amongst the scientific community. However, the genetic basis of most of these traits has not been elucidated. To facilitate our understanding of the molecular mechanisms underlying NMR physiology and behaviour, we generated a long-read chromosomal-level genome assembly of the NMR. This genome, mHetGlaV2, was subsequently annotated and incorporated into a “91 eutherian mammals” multiple whole genome alignment in Ensembl. </p> <p>We identified intra-chromosomal misassemblies within mHetGlaV2. We fixed these misassemblies by comparing syntenic blocks between this assembly and the Canadian Porcupine (EreDor) genome assembly (https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_028451465.1/) and a FISH-Karyotype of the naked mole-rat completed by Romanenko et al., 2023 (PMID: 380307020) to address any misassemblies and place centromeres. Chromosome numbering was identified from a composite karyogram of karyotypes from over 350 cells. This scaffold-corrected assembly is labelled mHetGlaV3 (https://www.ebi.ac.uk/ena/browser/view/GCA_964261345.1).</p> <p>This repository stores the repeat, genome, and epigenome annotations for HetGlaV3.</p> <p>mHetGlaV3.primary.gtf.gz. Gene structures and gene symbols are transferred from ENSEMBL annotations of mHetGlaV2 using liftOff with default parameters. Additional gene symbols were identified using TOGA and manual curation.</p> <p>mHetGlaV3.primary.gtf.gz. Simple repetitive regions and transposable elements were annotated using EarlGrey (https://github.com/TobyBaril/EarlGrey) using "Rodentia" annotations for RepeatMasker.</p> <p>mHetGlaV3.primary.genesymbol_table.txt.txt.gz. A tab-delimited file where rows are gene IDs and columns are gene symbols generated with each method. "Consensus" shows the best matching gene symbol for each gene ID.</p> <p>mHetGlaV3.primary_annotated_blacklist.bed.gz. Provides an assembly "blacklist" for mHetGlaV3. This blacklist is a bed file annotating assembly breakpoints between HetGlaV2 and HetGlaV3. This blacklist contains additional columns (e.g., closest gene, overlapping TE etc.) and should therefore be filtered to the first column before being incorporated into traditional genomic pipelines.</p> <p>mHetGlaV3.primary_hypothalamus_ABC_enhancer.bedpe.gz. Activity-By-Contact enhancers (https://github.com/broadinstitute/ABC-Enhancer-Gene-Prediction) generated in the female subordinate naked mole-rat hypothalamus using Hi-C-seq, ChIP-seq of H3K27Ac data, ATAC-seq, and RNA-seq information.</p> <p>mHetGlaV3.primary_hypothalamus_chromHMM.bed.gz. Chromatin states (using Chromhmm) annotating the female subordinate naked mole-rat hypothalamus using H3K4me3 (promoter), H4K4me2 (promoter-enhancer), H3K27Ac (active enhancer), H3K36me3 (elongated), H3K27me3 (polycomb repressed), H3K9me3 (heterochromatin), and CTCF (whole brain) ChIP-seq data, as well as ATAC-seq and RNA-seq data.</p> <p>mHetGlaV3.primary.fa.gz. Genome assembly fasta file for the naked mole-rat (V3, primary assembly). This assembly matches the primary assembly stored on ENA, however the chromosome names match these files, rather than have chromosome names processed by ENA (e.g. chr 1 instead of "OZ179169.1 Heterocephalus glaber genome assembly, chromosome: 1").</p> <p> </p> <p>UPDATES:</p> <p>* The 1.2 update fixed unscaffolded contig names from those used in-lab to those compatible with ENA.</p> <p>* The 1.3 update added small (50~100kbp) contigs onto mHetGlaV3.primary.fa.gz that were filtered before the ENA submission.</p> <p>* The 1.4 update fixed a small chromosome naming inconsistency spotted in the 1.3 update.</p>
Data from: Assembly ASM291031v2 (Genbank: GCA_002910315.2) identified as assembly of the Northern Dolly Varden (Salvelinus malma malma) genome, and not the Arctic char (S. alpinus) genome
<p>Here is the data that is a supplementary to the preprint: Shedko S.V. 2019. Assembly ASM291031v2 (Genbank: GCA_002910315.2) identified as assembly of the Northern Dolly Varden (Salvelinus malma malma) genome, and not the Arctic char (S. alpinus) genome // arXiv:1912.02474 <a href="https://arxiv.org/abs/1912.02474">https://arxiv.org/abs/1912.02474</a></p>
Annotation files related to the Telomere-to-Telomere genome assembly of the clubroot pathogen Plasmodiophora brassicae (GCA_036867785.1)
<p>This repository contains annotation files related to the T2T genome aseembly of <em>Plasmodiophora brassicae</em>. Link to the NCBI genome submission- https://www.ncbi.nlm.nih.gov/bioproject/1071157</p> <p><strong>Description of the files :</strong></p> <p><strong>GCA_036867785.1_ULAVAL_Pb3A_genomic.fna</strong> - Soft-masked genome sequence FASTA file representing 20 chromosomes.</p> <p><strong>sequence_report.jsonl</strong> - Detailed information about individual chromosome seqeunce.</p> <p><strong>PBTT_annotation.gtf</strong> - GTF file corresponding to the genomic FASTA file.The GTF file was generated by BRAKER3 and contains information about all possible transcripts.</p> <p><strong>PBTT_CDS_longest_isoform.fasta</strong> - Contains 10521 FASTA sequences representing the CDS of only the longest isoform of the gene models.</p> <p><strong>PBTT_protein_longest_isoform.fasta</strong> - Contains 10521 FASTA sequences representing the amino acid sequences of only the longest isoform of the gene models.</p>
Evaluation of Efficacy and Safety of Sarilumab in Patients With GCA
ClinicalTrials.gov study NCT03600805. IPD Sharing: YES. Countries: 21. Publications: 1.
Tocilizumab Plus a Short Prednisone Taper for GCA
ClinicalTrials.gov study NCT03726749. IPD Sharing: NO. Countries: 1. Publications: 1.
An Efficacy and Safety Study of Tocilizumab (RoActemra/Actemra) in Participants With Giant Cell Arteritis (GCA)
ClinicalTrials.gov study NCT01791153. IPD Sharing: Not stated. Countries: 14. Publications: 6.
A Study to Evaluate the Pharmacokinetics, Pharmacodynamics, and Safety of Tocilizumab (TCZ) Administered to Participants With Giant Cell Arteritis (GCA).
ClinicalTrials.gov study NCT03923738. IPD Sharing: YES. Countries: 1. Publications: 1.
Phase III Study of Efficacy and Safety of Secukinumab Versus Placebo, in Combination With Glucocorticoid Taper Regimen, in Patients With Giant Cell Arteritis (GCA)
ClinicalTrials.gov study NCT04930094. IPD Sharing: YES. Countries: 27. Publications: 0.
GCA
Sin descripcion Source: Objaverse 1.0 / Sketchfab
iMUSH_GCA: Dataset
<p>Contents of this zip file are explosion and earthquake metadata alongside nodal and Texan waveforms used in the local detection of Ground Coupled Acoustic waves with multiple types of seismometers and their potential role in the discrimination of explosions and earthquakes.</p>
The Applanation Tonometry in GCA Pilot
ClinicalTrials.gov study NCT05703763. IPD Sharing: UNDECIDED. Countries: 1. Publications: 2.
Use of Gallium-68 HA-DOTATATE PET/CT in Giant Cell Arteritis (GCA)
ClinicalTrials.gov study NCT03812302. IPD Sharing: NO. Countries: 1. Publications: 2.
Ultra-short Glucocorticosteroids and Tocilizumab Therapy in GCA Patients
ClinicalTrials.gov study NCT05394909. IPD Sharing: NO. Countries: 1. Publications: 3.
Temporal Artery Biopsy vs ULtrasound in Diagnosis of GCA (TABUL)
ClinicalTrials.gov study NCT00974883. IPD Sharing: Not stated. Countries: 5. Publications: 4.
Macular Ganglion Cell Analysis (GCA) of the Cirrus HD-OCT in Glaucoma
ClinicalTrials.gov study NCT01272102. IPD Sharing: Not stated. Countries: 1. Publications: 7.
TocILizumab in aorTitis in GCA (TILT)
ClinicalTrials.gov study NCT06271018. IPD Sharing: UNDECIDED. Countries: 1. Publications: 3.
DATA for GCA
<p>Research Data</p>
Data for GCA
<p>Research Data for GCA</p>
HSE-Se-Te-Os isotopes-major element sulfide data (MONTANINI ET AL. SUBMITTED TO GCA)
Open the record for dataset details and reuse information.
Next-generation sequencing (NGS) analysis of GCA effects on BMSCs
GEO Series GSE180774. Mus musculus. 6 samples. Type: Expression profiling by high throughput sequencing.
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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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.