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67 results for “transcriptome reference”
Comparing the Transcriptomes of Wild Type (WT) and Gdf9-Cre or Zp3-Cre mediated Mtor Oocyte-Conditional Knockout (referred to as MG and MZ, respectively) Mouse GV-stage fully-grown oocytes (FGO) by RN
GEO Series GSE114126. Mus musculus. 9 samples. Type: Expression profiling by high throughput sequencing.
A reference single-cell regulomic and transcriptomic map of cynomolgus monkeys
GEO Series GSE196794. Macaca fascicularis. 28 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
Identification of reference genes for quantitative Real-Time PCR in Bifidobacterium bifidum PRL2010 based on transcriptome analysis
GEO Series GSE30832. Bifidobacterium bifidum; Bifidobacterium bifidum PRL2010. 4 samples. Type: Expression profiling by array.
Multiple reference genomes and transcriptomes for Arabidopsis thaliana
GEO Series GSE30814. Arabidopsis thaliana. 48 samples. Type: Expression profiling by high throughput sequencing.
Emiliania huxleyi (UNC1419) reference transcriptome
<p>Reference transcriptome and associated annotations for <em>Emiliania huxleyi </em>(UNC1419). </p> <p>A culture was grown into late exponential phase for filtration. Total RNA was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s protocol except for an initial bead beating step and two instead of one chloroform steps to separate proteins and DNA. RNA libraries were created with the KAPA Stranded mRNA-Seq kit for Illumina platforms. The library was sequenced on an Illumina MiSeq (300 bp, paired-end reads) and an Illumina HiSeq 2500 with one lane in high output mode (100 bp, paired-end reads) and another lane in rapid run mode (150 bp, paired-end reads).</p> <p>Raw reads were trimmed for quality with Trimmomatic v0.36 then assembled <em>de novo </em>with Trinity v2.5.1 with the default parameters for paired-reads and a minimum contig length of 90 bp. Contigs were clustered based on 99% similarity using CD-HIT-EST v4.7 and then protein sequences were predicted with GeneMark S-T. Protein sequences were annotated by best-homology (lowest E-value) with the KEGG (Release 86.0), UniProt (Release 2018_03), and PhyloDB (v1.076) databases via BLASTP v2.7.1 (E-value ≤ 10<sup>-5</sup>) and with Pfam 31.0 via HMMER v3.1b2 (Dataset S2). KEGG Ortholog (KO) annotations were assigned from the top hit with a KO annotation from the top 10 hits (<a href="https://github.com/ctberthiaume/keggannot">https://github.com/ctberthiaume/keggannot</a>).</p> <p>Provided here are predicted proteins as nucleotides and peptides. Raw reads are deposited in SRA (SRP234650).</p>
Reference transcriptome and Alignments of candidate gene
<p>Recently diverged taxa with contrasting phenotypes offer opportunities for unravelling the genetic basis of phenotypic variation in nature. Horseshoe bats are a speciose group that exhibit a derived form of high duty cycle echolocation in which the inner ear is finely tuned to echoes of the narrowband call frequency. Here, by focusing on three recently diverged subspecies of the intermediate horseshoe bat (<i>Rhinolophus affinis</i>) that display divergent echolocation call frequencies, we aim to identify candidate loci putatively involved in hearing frequency variation. We used <i>de novo</i> transcriptome sequencing of two mainland taxa (<i>himalayanus</i> and <i>macrurus</i>)<i> </i>and one island taxon (<i>hainanus</i>) to compare expression profiles of thousands of genes. By comparing taxa with divergent call frequencies (around 15 kHz difference), we identified 252 differentially expressed genes (DEGs), of which six have been shown to be involved in hearing or deafness in human/mouse. To obtain further validation of these results, we applied quantitative reverse transcription-PCR to the candidate gene <i>FBXL15</i> and found a broad association between the level of expression and call frequency across taxa. The genes identified here represent strong candidate loci associated with hearing frequency variation in bats.</p>
Reference transcriptome for the siphonophore Marrus claudanielis
<p>Long read--PacBio IsoSeq--reference transcriptome for the siphonophore Marrus claudanielis</p>
Performance of AclarusDx™, a Blood-Based Transcriptomic Test for AD, in US Patients Newly Referred to a Memory Center
ClinicalTrials.gov study NCT01465360. IPD Sharing: Not stated. Countries: 1. Publications: 0.
A reference single-cell regulomic and transcriptomic map of cynomolgus monkeys [RNA-seq]
GEO Series GSE196792. Macaca fascicularis. 20 samples. Type: Expression profiling by high throughput sequencing.
Reference Short-Read Transcriptomes of Human Peripheral Blood Lymphocytes (Illumina RNA-Seq, Matched to PacBio Iso-Seq Data)
GEO Series GSE202328. Homo sapiens. 4 samples. Type: Expression profiling by high throughput sequencing.
Reference transcriptome and Alignments of candidate gene
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A reference single-cell regulomic and transcriptomic map of cynomolgus monkeys [ATAC-seq]
GEO Series GSE196791. Macaca fascicularis. 8 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Comparative transcriptomics among floral organs of the basal eudicot Eschscholzia californica: a reference for comparison with core eudicots and basal angiosperms
GEO Series GSE24237. Eschscholzia californica. 32 samples. Type: Expression profiling by array.
Circulating RNA transcriptome of pregnant women with TSH just above the trimester-specific reference and its correlation with the hypertensive phenotype
GEO Series GSE147527. Homo sapiens. 9 samples. Type: Expression profiling by high throughput sequencing.
Proteome reference map of Haloarcula hispanica and comparative proteomic and transcriptomic analysis of polyhydroxyalkanoate biosynthesis under genetic and environmental perturbations
GEO Series GSE42800. Haloarcula hispanica. 6 samples. Type: Expression profiling by array.
Impact of NAA50 depletion on the transcriptome of rosette leaves from the reference plant Arabidopsis thaliana (Col-0).
GEO Series GSE233192. Arabidopsis thaliana. 8 samples. Type: Expression profiling by array.
Towards a reference human platelet transcriptome: evaluation of inter-individual correlations and of its relationship with a platelet proteome
GEO Series GSE50858. Homo sapiens. 10 samples. Type: Expression profiling by array.
Reference Gene Selection for Expression Analysis of Hepatic Genes Responding to Fasting via Transcriptomic Analysis
<p>Raw date for this manuscript</p>
Performance of AclarusDx® a Blood-Based Transcriptomic Test for AD, in French Patients Newly Referred to a Memory Center
ClinicalTrials.gov study NCT02221661. IPD Sharing: Not stated. Countries: 0. Publications: 0.
Transcriptome profiling of porcine jejunum tissue, its derived organoids over long-term culture, and transformed cell line IPECJ2 as reference model
GEO Series GSE146408. Sus scrofa. 17 samples. Type: Expression profiling by high throughput sequencing.
ScienceDex guides
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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.