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Dataset results
313 results for “Polyadenylation”
Evolutionary dynamics of polyadenylation signals and their recognition strategies in protist
GEO Series GSE260731. Giardia muris; Entamoeba histolytica; Naegleria gruberi; Giardia duodenalis; Trichomonas vaginalis; Tritrichomonas foetus. 20 samples. Type: Expression profiling by high throughput sequencing.
mRNA polyadenylation profile analysis in control and U1 AMO treated HeLa cells
GEO Series GSE125397. Homo sapiens. 4 samples. Type: Other.
Extensive alternative polyadenylation during zebrafish development
GEO Series GSE37453. Danio rerio. 14 samples. Type: Expression profiling by high throughput sequencing.
DNA Methylation Regulates Alternative Polyadenylation via CTCF and the Cohesin Complex
GEO Series GSE86178. Homo sapiens. 8 samples. Type: Other; Non-coding RNA profiling by high throughput sequencing.
TLDR (True Length of Diverse capped RNAs)-seq: a method for 5’-to-3’ end sequencing of capped full-length RNAs with or without 3’ polyadenylation [R10]
GEO Series GSE289428. Homo sapiens. 3 samples. Type: Expression profiling by high throughput sequencing.
TDP-43 loss induces cryptic polyadenylation in ALS/FTD [sknbe2-curve-kd-1-vs-ctl]
GEO Series GSE296711. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
POS-1 protects posterior gut specification by blocking GLD-3/2 polyadenylation of anterior factor neg-1
GEO Series GSE57993. Caenorhabditis elegans. 12 samples. Type: Expression profiling by high throughput sequencing.
Quant-seq analysis of differential polyadenylation site usages in caused by different Pol II mutants with slow elongation rates in Flp-In-293 cells and dual inhibition of CDK12 and CDK13 by THZ531 HE
GEO Series GSE141375. Homo sapiens. 10 samples. Type: Expression profiling by high throughput sequencing; Other.
Alternative polyadenylation sites in rats
<p>A total of 83 WTTS-seq (whole transcriptome termini site sequencing) libraries were constructed individually using total RNA samples derived from several brain tissues of rats. Library sequencing produced a total of 312,092,803 raw reads, but the mapped reads were 240,225,046 (76.97%) on Rnor6.0, while 251,188,567 (80.49%) on mRatBN7.2, respectively. Using 25 reads per clustered site as a cutoff, we identified 173,124 APA sites mapped to the new reference genome, while 167,136 APA sites were assigned to the old reference genome. For Rnor6.0, only 127,460 (76.26%) APA sites were assigned to the genome regions with 18,177 annotated genes. In contrast, 141,399 (81.67%) APA sites were mapped to the 20,102 annotated genes on mRatBN7.2. In brief, our results provide evidence that mRatBN7.2 has improved qualities of both genome assembly and gene annotation in rat. </p> <p>Zhou, X., Li, R., Michal, J.J., Wu, X.-L., Liu, Z., Zhao, H., Xia, Y., Du, W., Wildung, M.R., Pouchnik, D.J., et al. (2016). Accurate Profiling of Gene Expression and Alternative Polyadenylation with Whole Transcriptome Termini Site Sequencing (WTTS-Seq). Genetics 203, 683–697.</p> <p> </p> <p>This work was supported by the National Institute of Food and Agriculture, United States Department of Agriculture under Award Numbers 2016-67015-24470/2020-67015-31733/2022-51300-38058/2023-67015-39566/2023-67015-40080 to ZJ.</p> <p> </p>
CPA-Perturb-seq: Multiplexed single-cell characterization of alternative polyadenylation regulators (PBMC data)
<p>This site provides access to datasets from the CPA-Perturb-seq manuscript Kowalski*, Wessels*, Linder* et al., including PBMC data to replicate analyses in Figure 6. We release these data as Seurat objects, where each object contains single-cell quantifications of gene expression (RNA assay), and in addition, quantifications of polyA site usage (polyA site assay). To explore these data, please install the <a href="https://github.com/satijalab/PASTA">PASTA</a> (PolyA Site analysis using relative Transcript Abundance) package which provides infrastructure and analytical tools to explore alternative polyadenylation at single-cell resolution. For each dataset, we also include a fragment file which enables visualization of read coverage plots across groups of cells. </p> <p> </p> <p>To replicate the analysis in Figure 6, in which we analyze a dataset of circulating human peripheral blood mononuclear cells, we provide a vignette available <a href="http://www.satijalab.org/seurat/articles/pasta_vignette.html">here</a>. To following files are used:</p> <p> </p> <ol> <li> <p>matrix.mtx: 10X file containing RNA for PBMC dataset</p> </li> <li> <p>barcodes.tsv: 10X file containing barcodes for PBMC dataset</p> </li> <li> <p>genes.tsv: 10X file containing genes for PBMC dataset</p> </li> <li> <p>PBMC_meta_data.csv: meta data for PBMC dataset</p> </li> <li> <p>PBMC_pA_counts.tab.gz: Counts file containing polyA quantification for PBMC dataset</p> </li> <li> <p>PBMC_fragments.tsv.gz: Fragment file to visualize the PBMC dataset.</p> </li> <li> <p>PBMC_fragments.tsv.gz.tbi: Fragment file index for the PBMC dataset. </p> </li> <li> <p>PBMC_polyA_peaks.gff: Gff file containing location of polyA site read regions.</p> </li> <li> <p>human_PAS_hg38.txt: Text file containing information from polyAdbv3 resource. </p> </li> </ol>
Alternative Polyadenylation by Sequential Activation of Distal and Proximal PolyA Sites
GEO Series GSE165742. Homo sapiens. 18 samples. Type: Expression profiling by high throughput sequencing; Other.
Nuclear m6 A reader YTHDC1 suppresses proximal alternative polyadenylation sites by interfering with the 3' processing machinery
GEO Series GSE198143. Homo sapiens. 6 samples. Type: Other.
Regulation of alternative polyadenylation by the C2H2-zinc finger protein Sp1 [ChIP-Seq]
GEO Series GSE165683. Homo sapiens. 4 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Abundant polyadenylation of transcripts and precursor tRNAs in Mycobacterium tuberculosis upon depletion of Rv3907c, the mycobacterial CCA-adding enzyme
GEO Series GSE220711. Mycolicibacterium smegmatis MC2 155; Mycobacterium tuberculosis H37Rv. 24 samples. Type: Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing.
Premature polyadenylation-mediated loss of stathmin-2 is a hallmark of TDP-43-dependent neurodegeneration
GEO Series GSE122069. Homo sapiens. 10 samples. Type: Expression profiling by high throughput sequencing.
Coupling between alternative polyadenylation and alternative splicing is limited to terminal introns
GEO Series GSE79157. Homo sapiens. 4 samples. Type: Expression profiling by high throughput sequencing.
Polyadenylation of mRNAs encoding secreted proteins by TENT5 family of enzymes is essential for gametogenesis in mice
GEO Series GSE239661. Mus musculus. 5 samples. Type: Expression profiling by high throughput sequencing.
The polyadenylation factor FIP1 is important for plant development and root responses to abiotic stresses
GEO Series GSE127972. Arabidopsis thaliana. 4 samples. Type: Expression profiling by high throughput sequencing.
TDP-43 loss induces cryptic polyadenylation in ALS/FTD [shsy5y-curve-kd-075-vs-ctl]
GEO Series GSE296712. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
TDP-43 loss induces cryptic polyadenylation in ALS/FTD [humphrey-i3-cortical]
GEO Series GSE296714. Homo sapiens. 12 samples. Type: Expression profiling by high throughput sequencing.
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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.