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ShareScore release 0.7.1
Dataset results
49 results for “pseudogenization”
The Pseudogene RPS27AP5 Reveals Novel Ubiquitin and Ribosomal Protein Variants Involved in Specialised Ribosomal Functions.
GEO Series GSE254888. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
Positive natural selection of N6-methyladenosine on the RNAs of processed pseudogenes
GEO Series GSE172219. Homo sapiens. 18 samples. Type: Expression profiling by high throughput sequencing.
Pseudogenes limit the identification of novel common transcripts generated by their parent genes
GEO Series GSE215459. Homo sapiens. 2 samples. Type: Expression profiling by high throughput sequencing.
Exhaustive profiling in Arabidopsis reveals abundant polysome-associated 24-nt small RNAs including hitherto undescribed AGO5-associated pseudogene-derived siRNAs (psiRNAs) [sRNA]
GEO Series GSE99827. Arabidopsis thaliana. 6 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Systematic functional interrogation of human pseudogenes
GEO Series GSE155510. Homo sapiens. 12 samples. Type: Other.
Pseudogene INTS6P1 regulates its cognate gene INTS6 through competitive binding of miR-17-5p in hepatocellular carcinoma
GEO Series GSE64633. Homo sapiens. 12 samples. Type: Expression profiling by array; Non-coding RNA profiling by array.
Long-read cDNA sequencing identifies functional pseudogenes in the human transcriptome
GEO Series GSE160383. Homo sapiens. 19 samples. Type: Expression profiling by high throughput sequencing.
Knockdown of pseudogene lncRNA UBE2CP3 in gastric cancer cells
GEO Series GSE163813. Homo sapiens. 9 samples. Type: Expression profiling by high throughput sequencing.
A FTH1 gene:pseudogene:miRNA network regulates tumorigenesis in prostate cancer
GEO Series GSE101837. Homo sapiens. 24 samples. Type: Expression profiling by array.
A pseudogene lncRNA at the interface of inflammation and anti-inflammatory therapeutics
GEO Series GSE47494. Mus musculus. 6 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
Data from: Annotation of pseudogenic gene segments by massively parallel sequencing of rearranged lymphocyte receptor loci
Background: The adaptive immune system generates a remarkable range of antigen-specific T-cell receptors (TCRs), allowing the recognition of a diverse set of antigens. Most of this diversity is encoded in the complementarity determining region 3 (CDR3) of the β chain of the αβ TCR, which is generated by somatic recombination of noncontiguous variable (V), diversity (D), and joining (J) gene segments. Deletion and non-templated insertion of nucleotides at the D-J and V-DJ junctions further increases diversity. Many of these gene segments are annotated as non-functional owing to defects in their primary sequence, the absence of motifs necessary for rearrangement, or chromosomal locations outside the TCR locus. Methods: We sought to utilize a novel method, based on high-throughput sequencing of rearranged TCR genes in a large cohort of individuals, to evaluate the use of functional and non-functional alleles. We amplified and sequenced genomic DNA from the peripheral blood of 587 healthy volunteers using a multiplexed polymerase chain reaction assay that targets the variable region of the rearranged TCRβ locus, and we determined the presence and the proportion of productive rearrangements for each TCRβ V gene segment in each individual. We then used this information to annotate the functional status of TCRβ V gene segments in this cohort. Results: For most TCRβ V gene segments, our method agrees with previously reported functional annotations. However, we identified novel non-functional alleles for several gene segments, some of which were used exclusively in our cohort to the detriment of reported functional alleles. We also saw that some gene segments reported to have both functional and non-functional alleles consistently behaved in our cohort as either functional or non-functional, suggesting that some reported alleles were not present in the population studied. Conclusions: In this proof-of-principle study, we used high-throughput sequencing of the TCRβ locus of a large cohort of healthy volunteers to evaluate the use of functional and non-functional alleles of individual TCRβ V gene segments. With some modifications, our method has the potential to be extended to gene segments in the α, γ, and δ TCR loci, as well as the genes encoding for B-cell receptor chains.
Role of Pseudogene in Incontinentia Pigmenti, and Its Potential Treatment
ClinicalTrials.gov study NCT00976586. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Data from: Annotation of pseudogenic gene segments by massively parallel sequencing of rearranged lymphocyte receptor loci
Open the record for dataset details and reuse information.
Gene expression profile of MDA-MB-231 breast cancer cells with BRCA1 pseudogene (BRCA1P1) knockout (KO)
GEO Series GSE112573. Homo sapiens. 4 samples. Type: Expression profiling by array.
Hybrid sequencing characterizes expression and function of mouse pseudogenes
GEO Series GSE176018. Mus musculus. 35 samples. Type: Expression profiling by high throughput sequencing.
Pseudogene repair driven by selection pressure applied in experimental evolution
GEO Series GSE122779. Escherichia coli K-12. 16 samples. Type: Expression profiling by high throughput sequencing.
Differentially Expressed Pseudogenes in HIV-1 Infection
GEO Series GSE70785. Homo sapiens. 2 samples. Type: Expression profiling by high throughput sequencing.
Pseudogene INTS6P1 regulates its cognate gene INTS6 through competitive binding of miR-17-5p in hepatocellular carcinoma [miRNA]
GEO Series GSE64632. Homo sapiens. 6 samples. Type: Non-coding RNA profiling by array.
Exhaustive profiling in Arabidopsis reveals abundant polysome-associated 24-nt small RNAs including hitherto undescribed AGO5-associated pseudogene-derived siRNAs (psiRNAs) [RNA]
GEO Series GSE99826. Arabidopsis thaliana. 4 samples. Type: Expression profiling by high throughput sequencing.
Enrichment of processed pseudogene transcripts in L1-ribonucleoprotein particles
GEO Series GSE43801. Homo sapiens. 5 samples. Type: Expression profiling by high throughput sequencing; 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.