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.
215
datasets available to search
ShareScore release 0.9.0
Dataset results
215 results for “cDNA”
Dataset: CareDx, Inc (CDNA) Stock Performance
This dataset provides historical stock market performance data for specific companies. It enables users to analyze and understand the past trends and fluctuations in stock prices over time. This information can be utilized for various purposes such as investment analysis, financial research, and market trend forecasting.
Microbial 16S rRNA gene (DNA) and transcripts (cDNA) along a boreal soil-freshwater-estuary continuum
<p>This repository stores the processed files of the 16S rRNA sequencing reads (DNA and cDNA) of the La Romaine project, which were processed through the DADA2 pipeline. Files are '.rds' files and/or '.csv' files readable by the open statistical software R. The project is part of the Industrial Research Chair in Carbon Biogeochemistry in Boreal Aquatic systems (CarBBAS Chair) led by Paul A. del Giorgio.</p> <p>Samples were pooled by plate ID and season to be processed by DADA2. The number before each '*_seqtab.rds' file corresponds to a pool. ID details are in "splitdf_new.rds".</p> <p>Raw sequences can be found on SRA under the Bioproject number: PRJNA693020. Intermediate processing files are stored here. And scripts are available on <a href="https://github.com/CarBBAS/Paper_Stadler-delGiorgio_ISMEJ_2021">Github</a>.</p> <p>Files are being uploaded as manuscripts are published.</p> <p>Currently available files:</p> <ul> <li>2015-2017: 16S rRNA gene and transcripts (DNA and cDNA) in spring, summer, autumn (shallow sequencing) <ul> <li>Part of the manuscript: "Terrestrial connectivity, upstream aquatic history and seasonality shape bacterial community assembly within a large boreal aquatic network". The ISME Journal. 2021.</li> </ul> </li> </ul>
Supplementary materials for "High-Throughput Discovery of Substrate Peptide Sequences for E3 Ubiquitin Ligases Using a cDNA Display Method."
<p>The next-generation sequencing (NGS) data of the 5th rounds' samples for LX9 library and p53deg library. The csv files contain DNA sequences read out, amino acid sequences and their read counts in descending order. </p>
Data from: Comprehensive cDNA cloning and putative feature analysis of endogenous cellulases possessed by the Pacific oyster, Crassostrea gigas
Open the record for dataset details and reuse information.
cDNA sequence of E2 gene family in Arabidopsis thaliana and data of statistical analysis
<p>E2 ubiquitin-conjugating enzymes act as a heart role in the ubiquitination process and are responsible for catalysis ubiquitin transfer. Although the function of ubiquitin-protein ligases (E3s) in plant response to diverse abiotic stress by targeting specific substrates has been well studied, the E2s' involvement in environmental responses and their downstream targets are not well understood. Here, we demonstrated that the E2 ubiquitin-conjugating enzyme 18 (UBC18) regulates the stability of FREE1 to modulate iron deficiency stress. UBC18 affects the ubiquitination of FREE1 and promotes its degradation, overexpression of<em> UBC18</em> in plants decreases their sensitivity to iron deficiency by reducing the level of FREE1, and high accumulation of FREE1 in<em> </em>the<em> ubc18</em> mutant resulted in sensitivity to iron deficiency. In addition, we demonstrated the lysine residues K227, K295, K315, and K540 are required for FREE1 ubiquitination and stability regulation, and mutation of these lysines of FREE1 residues resulted in sensitivity to iron starvation in plants. Taken together, our findings reveal a mechanism of UBC18 in response to iron deficiency stress by altering the abundance of FREE1, and further elucidate the role of ubiquitination sites in FREE1 stability regulation and the plant iron deficiency response.</p>
Supplementary Data - Nanopore cDNA With and Without mtDNA
<p>Update (v1.5.8-SUPcaller): added scripts and data files for mt-Nd1 comparisons for different basecaller versions:</p> <ul> <li>LAST_gci_*.csv - gap-compressed identity statistics</li> <li>compStats_*.csv - called base-level statistics</li> <li>process.txt - script example file demonstrating how to generate statistics</li> <li>smealgol.r - R script to generate gap-compressed identities from LAST output</li> <li>est_vs_actual.png - density plots comparing gap-compressed identity with mean estimated accuracy from the caller</li> <li>GCI_albacore_guppy.png - violin plots comparing gap-compressed identity with different callers</li> <li>BaseQ_vs_GCI.png - scatter plots comparing gap-compressed identity with mean estimated accuracy from the caller</li> </ul> <p>Update (v1.5.7-Nd1Reads): added mt-Nd1 read subset from CGDec2017 run:</p> <ul> <li>4T1-WT_reads_CGDec2017_singlePlusMulti.tar</li> </ul> <p>Update (v1.5.6-countAnalysis): added / updated a script to convert transcript mappings to a count table:</p> <ul> <li>count_analysis.r</li> </ul> <p>Update (v1.5.5-Int): added intermediate (post-demultiplexing) demonstration dataset:</p> <ul> <li>SampleDESet_60k_demultiplexed.tar.gz</li> </ul> <p>Also updated count tables and DESeq2 results:</p> <ul> <li>raw_counts_2019-Nov-29.csv</li> <li>DE_orig_VST_GRCm38_CG_GL261_2019-Nov-29.csv.gz</li> <li>DE_shrunk_VST_GRCm38_CG_GL261_2019-Nov-29.csv.gz</li> </ul> <p>Update (v1.5.4-MT): updated demonstration dataset (now 40Mb) to include mitochondrial transcripts, and exclude non-target sequences from chimeric reads:</p> <ul> <li>reads_SampleDESet_sampled_60k.fastq.gz</li> <li>Mm_subset.GRCm38.ensembl_v98.fa</li> </ul> <p>Update (v1.5.3-Ensembl): added/updated Ensembl reference transcripts, including non-coding RNA:</p> <ul> <li>ensembl_mm10_geneFeatureLocations.txt.gz - genome annotation</li> <li>Mus_musculus.GRCm38.ensembl_v98.fa.gz - transcript sequences</li> </ul> <p>Update (v1.5.2-Demo): added 60Mb demonstration dataset for teaching / learning purposes (<em>reads_SampleDESet_sampled_60k.fastq.gz</em>). This dataset can be used for testing demultiplexing, or carrying out differential expression analysis on nanopore reads. There are 15k reads sampled from each run (subset on ~300 genes), plus 7.5k chimeric reads from the Dec17 run, plus 7.5k reads sampled from from CG009/BC08. The gene subset includes ~100 genes differentially-expressed between 4T1WT and 4T1ρ<sup>0</sup> cell lines, plus an additional ~200 genes with minimal differential expression observed between any 4T1 cell lines (i.e. a housekeeping gene set):</p> <ul> <li>BC01, BC02, BC04, BC06 - 4T1 cell line reads from three sequencing runs (005, 005, 004, Dec17)</li> <li>BC03, BC05, BC07 - 4T1ρ<sup>0</sup> (without mtDNA) cell line reads from three sequencing runs (005, 004, Dec17)</li> <li>BC08 - 4T1ρ<sup>0</sup>SC (from subcutaneous tumour) cell line reads from one sequencing run (009)</li> </ul> <p>[note: v1.5.1-Demo has the wrong sequence ID for BC08 reads]</p> <p>Update (v1.5.0-Called): added full 4T1 call set (called using guppy high-accuracy v3.2.2), gene transcript count tables, and differential expression results</p> <p>Update (v1.4.1-Chimeric): added more example called chimeric reads of various [unclassified] categories</p> <p>Update (v1.4.0-Chimeric): added example chimeric reads, one formed [presumably] during sample prep ["conjugation"], another formed in-silico ["double read"]</p> <p>Update (v1.3.0-DESeq2): added count table and metadata file for DESeq2 analysis</p> <p>Update (v1.2.1-10k): added 10k of FASTQ reads from a more recent run (part of the same differential expression project).</p> <p>Supplementary data to go with David Eccles' poster about nanopore cDNA sequencing with and without mitochondrial DNA.</p> <p>Reference mouse mtDNA and mtDNA reads from 4T1 cells (from MinION cDNA sequencing, and from SRA run SRR6747859).</p> <ul> <li>fwd_4T1_BC06.correctedReads.uniqueOnly.fasta.gz -- Canu-corrected cDNA reads from Wildtype 4T1 strain, filtered as transcript-forward orientation</li> <li>rev_4T1_BC06.correctedReads.uniqueOnly.fasta.gz -- Canu-corrected cDNA reads from Wildtype 4T1 strain, filtered as transcript-reverse orientation</li> <li>fwd_4T1_BC07.correctedReads.uniqueOnly.fasta.gz -- Canu-corrected cDNA reads from 4T1ρ0 strain (no mitochondrial DNA), filtered as transcript-forward orientation</li> <li>rev_4T1_BC07.correctedReads.uniqueOnly.fasta.gz -- Canu-corrected cDNA reads from 4T1ρ0 strain (no mitochondrial DNA), filtered as transcript-reverse orientation</li> </ul> <p>Other intermediate data files are also included, see `4way_mapping_process.txt` for more details.</p> <p>The mpileup differential coverage script can be found <a href="https://github.com/gringer/bioinfscripts/blob/master/mpileupDC.pl">here</a>.</p>
The cDNA sequence data of hox genes in Daphnia similoides sinensis
<p><span><span><span><span><span><span><span><span><span><span><span>Hox genes are important regulatory factors of transcription in metazoans, and are involved in the growth and development of organisms. In this study, the effects of <i><span>Microcystis aeruginosa </span></i>on Hox gene expression in the mothers and offspring of <i><span>Daphnia similoides sinensis</span></i> were investigated using a mixed diet of <i><span>M. aeruginosa</span></i> and <i><span>Scenedesmus obliquus</span></i><i> </i>in two clones. The 14 Hox genes sequence were identified in D<i><span>. similoides sinensisare </span></i>through the previous transcriptome data (Zhang et al., 2016. DOI: 10.1038/srep34241).</span></span></span></span></span></span></span></span></span></span></span></p>
Ebbert Lab Nanopore PCS111 brain cDNA discovery (12 samples - AD vs Controls)
<p>For more information about this data see the publication: https://doi.org/10.1038/s41587-024-02245-9</p> <p>The publication GitHub is a good source of information: https://github.com/UK-SBCoA-EbbertLab/brain_cDNA_discovery</p> <p>There are also README files in the data that provide more information about what is contained in each directory.</p> <p> </p> <p>Basic information about main directory structure and files:</p> <p>reproducing_RNA_figures - Contains all references/annotations necessary for reproducing the stats, analysis, and figures for the RNA isoform analysis in the article.</p> <p>reproducing_nextflow_pipeline - Contains all references/annotations necessary for reproducing the NextFlow pipeline.</p> <p>proteomics - Fasta reference files files used for proteomics analysis with FragPipe and results output by FragPipe.</p> <p>transcriptomic_analysis_output - Contains output from transcriptomic analysis including: quality control, counts matrices, new RNA isoform annotations, and the Bambu R object.</p> <p>counts_transcript.txt - Transcript level counts (does not include any intronic reads).</p>
Camponotus fellah cDNA lists for: Social isolation shortens lifespan through oxidative stress in ants
<p>Social isolation negatively affects health, induces detrimental behaviors, and shortens lifespan in social species. Little is known about the mechanisms underpinning these effects because model species are typically short-lived and non-social. Using colonies of carpenter ant <em>Camponotus</em> <em>fellah</em>, we show that social isolation induces hyperactivity, alters space-use, and reduces lifespan via changes in the expression of genes with key roles in oxidation-reduction and an associated accumulation of reactive oxygen species. These physiological effects are localized to the fat body and oenocytes, which perform liver-like functions in insects. We use pharmacological manipulations to demonstrate that the oxidation-reduction pathway causally underpins the detrimental effects of social isolation on behavior and lifespan. These findings have important implications for our understanding of how social isolation affects behavior and lifespan in general.</p>
The coenzyme A precursor pantethine restrains sarcoma growth through promotion of type 1 immunity - Run 1 cDNA 1
<p><strong>Dataset from article</strong> : The coenzyme A precursor pantethine restrains sarcoma growth through promotion of type 1 immunity</p> <p>10X Single-cell RNA-sequencing dataset (1/5).<br> RUN 1(/2), cDNA 1(/2).</p> <p>This repository contains results and necessary files for reproducing the analyses in Miallot et al. (2023). The instructions for reproducing the analysis are given in github (https://github.com/CIML-bioinformatic/PNlab_Sarcoma) and extra files are available in GEO/SRA (GSE221164).</p>
The coenzyme A precursor pantethine restrains sarcoma growth through promotion of type 1 immunity - Run 2 cDNA 2
<p><strong>Dataset from article</strong> : The coenzyme A precursor pantethine restrains sarcoma growth through promotion of type 1 immunity</p> <p>10X Single-cell RNA-sequencing dataset (4/5).<br> RUN 2(/2), cDNA 2(/2).</p> <p>This repository contains results and necessary files for reproducing the analyses in Miallot et al. (2023). The instructions for reproducing the analysis are given in github (https://github.com/CIML-bioinformatic/PNlab_Sarcoma) and extra files are available in GEO/SRA (GSE221164).</p>
The coenzyme A precursor pantethine restrains sarcoma growth through promotion of type 1 immunity - Run 2 cDNA 1
<p><strong>Dataset from article</strong> : The coenzyme A precursor pantethine restrains sarcoma growth through promotion of type 1 immunity</p> <p>10X Single-cell RNA-sequencing dataset (3/5).<br> RUN 2(/2), cDNA 1(/2).</p> <p>This repository contains results and necessary files for reproducing the analyses in Miallot et al. (2023). The instructions for reproducing the analysis are given in github (https://github.com/CIML-bioinformatic/PNlab_Sarcoma) and extra files are available in GEO/SRA (GSE221164).</p>
The coenzyme A precursor pantethine restrains sarcoma growth through promotion of type 1 immunity - Run 1 cDNA 2
<p><strong>Dataset from article</strong> : The coenzyme A precursor pantethine restrains sarcoma growth through promotion of type 1 immunity</p> <p>10X Single-cell RNA-sequencing dataset (2/5).<br> RUN 1(/2), cDNA 2(/2).</p> <p>This repository contains results and necessary files for reproducing the analyses in Miallot et al. (2023). The instructions for reproducing the analysis are given in github (https://github.com/CIML-bioinformatic/PNlab_Sarcoma) and extra files are available in GEO/SRA (GSE221164).</p>
Treatment of SCID Due to ADA Deficiency With Autologous Transplantation of Cord Blood or Hematopoietic CD 34+ Cells After Addition of a Normal Human ADA cDNA by the EFS-ADA Lentiviral Vector
ClinicalTrials.gov study NCT02022696. IPD Sharing: Not stated. Countries: 1. Publications: 3.
Impact of Raltegravir on HIV-1 cDNA Slope Following Antiretroviral Therapy (ART) Initiation
ClinicalTrials.gov study NCT01168167. IPD Sharing: Not stated. Countries: 1. Publications: 1.
The cDNA sequence data of hox genes in Daphnia similoides sinensis
Open the record for dataset details and reuse information.
Camponotus fellah cDNA lists for: Social isolation shortens lifespan through oxidative stress in ants
Open the record for dataset details and reuse information.
cDNA sequence of E2 gene family in Arabidopsis thaliana and data of statistical analysis
Open the record for dataset details and reuse information.
Data from: Characterization of leukemia-inducing genes using a proto-oncogene/homeobox gene retroviral human cDNA library in a mouse in vivo model
The purpose of this research is to develop a method to screen a large number of potential driver mutations of acute myeloid leukemia (AML) using a retroviral cDNA library and murine bone marrow transduction-transplantation system. As a proof-of-concept, murine bone marrow (BM) cells were transduced with a retroviral cDNA library encoding well-characterized oncogenes and homeobox genes, and the virus-transduced cells were transplanted into lethally irradiated mice. The proto-oncogenes responsible for leukemia initiation were identified by PCR amplification of cDNA inserts from genomic DNA isolated from leukemic cells. In an initial screen of ten leukemic mice, the MYC proto-oncogene was detected in all the leukemic mice. Of ten leukemic mice, 3 (30%) had MYC as the only transgene, and seven mice (70%) had additional proto-oncogene inserts. We repeated the same experiment after removing MYC-related genes from the library to characterize additional leukemia-inducing gene combinations. Our second screen using the MYC-deleted proto-oncogene library confirmed MEIS1and the HOX family as cooperating oncogenes in leukemia pathogenesis. The model system we introduced in this study will be valuable in functionally screening novel combinations of genes for leukemogenic potential in vivo, and the system will help in the discovery of new targets for leukemia therapy.
gRNAs, cdna, and code used in High-throughput tagging of endogenous loci for rapid characterization of protein function
<p>Contains code and sequences used to analyze NGS reads sequencing junctions between tagged genes and linker sequences.</p>
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.