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119 results for “Interferon stimulation”
Transcriptome analysis of the effect of over-expressing H2A.J mutants in proliferating WI38 fibroblasts for the paper entitled: The H2A.J histone variant contributes to Interferon-Stimulated Gene expression in senescence by its weak interaction with H1 and the derepression of repeated DNA sequences
<p>Abstract for overall study:</p> <p>The histone variant H2A.J was previously shown to accumulate in senescent human fibroblasts with persistent DNA damage to promote inflammatory gene expression, but its mechanism of action was unknown. We show that H2A.J accumulation contributes to weakening the association of histone H1 to chromatin and increasing its turnover. Decreased H1 in senescence is correlated with increased expression of some repeated DNA sequences, increased expression of STAT/IRF transcription factors, and transcriptional activation of Interferon-Stimulated Genes (ISGs). The H2A.J-specific Val-11 moderates the transcriptional activity of H2A.J, and H2A.J-specific Ser-123 can be phosphorylated in response to DNA damage with potentiation of its transcriptional activity by the phospho-mimetic S123E mutation. Our work demonstrates the functional importance of H2A.J-specific residues and potential mechanisms for its function in promoting inflammatory gene expression in senescence.</p> <p>Specific description for this dataset:</p> <p>H2A.J differs from canonical H2A only by a valine at position 11 instead of alanine, and the 7 C-terminal amino acids containing a potential minimal phosphorylation site SQ for DNA-damage response kinases. To test the functional importance of these H2A.J-specific sequences, we mutated Val-11 to Ala as is found in all canonical H2A sequences, and we mutated Ser-123 to either Glu to mimic a phospho-serine residue or to Ala to prevent phosphorylation. We also substituted the C-terminus of H2A.J with the C-terminus of H2A. These mutants, WT-H2A.J and canonical H2A-type1 were ectopically expressed in proliferating fibroblasts, and their microarray transcriptomes were compared to that of proliferating and senescent fibroblasts without ectopic histone expression. Genome-wide transcriptome analysis indicated that senescent fibroblasts clustered distinctly from proliferating fibroblasts, and proliferating fibroblasts expressing the H2A.J-V11A and H2A.J-S123E mutants clustered distinctly from fibroblasts expressing the other H2A.J mutants, WT-H2A.J, and H2A. Hallmark gene set enrichment analysis of the transcriptomes of fibroblasts expressing H2A.J-V11A or H2A.J-S123E versus control proliferating fibroblasts indicated that they showed the same highly significant enrichment for the Epithelial-Mesenchyme Transition, TNF-Alpha Signaling Via NF-kB, and Inflammatory Response gene sets. Notable inflammatory genes including IL1A, IL1B, IL6, CXCL8, and CCL2 are contained in these gene sets and are often induced in senescence as part of the senescence-associated secretory phenotype. Heat maps showed that the H2A.J-V11A and H2A.J-S123E mutants were particularly apt at activating the expression of these inflammatory genes in proliferating fibroblasts</p>
Dataset for the stimulator of interferon genes protein (STING1) antibody screening study
<p><strong>This antibody characterization dataset is related to the F1000 research article openly available at F1000Research.</strong></p> <p><em>This dataset contains the following underlying raw data for a study which characterized sixteen antibodies for the stimulator of interferon genes protein (STING1) in western blot, immunoprecipitation and immunofluorescence. The corresponding study is accessible on the YCharOS community on Zenodo (<a href="https://doi.org/10.5281/zenodo.11582350">https://doi.org/10.5281/zenodo.11582350</a>).</em></p> <p><em>The Dataset is in the format of a zip file. Once downloaded, please expand the zip file to access the folders containing the underlying data for Western blot (Wb), immunoprecipitation (IP) and immunofluorescence (IF).</em></p>
Transcriptome analysis of WT versus H2A.J-KO MEFs for the paper entitled: The H2A.J histone variant contributes to Interferon-Stimulated Gene expression in senescence by its weak interaction with H1 and the derepression of repeated DNA sequences
<p>Abstract for overall study:</p> <p>The histone variant H2A.J was previously shown to accumulate in senescent human fibroblasts with persistent DNA damage to promote inflammatory gene expression, but its mechanism of action was unknown. We show that H2A.J accumulation contributes to weakening the association of histone H1 to chromatin and increasing its turnover. Decreased H1 in senescence is correlated with increased expression of some repeated DNA sequences, increased expression of STAT/IRF transcription factors, and transcriptional activation of Interferon-Stimulated Genes (ISGs). The H2A.J-specific Val-11 moderates the transcriptional activity of H2A.J, and H2A.J-specific Ser-123 can be phosphorylated in response to DNA damage with potentiation of its transcriptional activity by the phospho-mimetic S123E mutation. Our work demonstrates the functional importance of H2A.J-specific residues and potential mechanisms for its function in promoting inflammatory gene expression in senescence.</p> <p>Specific description for this dataset:</p> <p>We further tested a role for H2A.J in Interferon-Stimulated Gene expression by analyzing the transcriptome of WT and H2A.J MEFs induced into senescence by etoposide. TruSeq stranded DNA libraries were prepared from polyA-selected RNA and sequenced as 43 bp paired-end reads. The fastq sequences were mapped to Gencode.vM24.transcripts.fa.gz (GRCm38 transcriptome) with salmon. Read counts were then aggregated to the gene level with tximeta, and differential gene expression was analysed with DESeq2, edgeR, and limma-voom. Gene set enrichment analysis was performed with camera.</p> <p>The transciptomes of senescent WT and H2AFJ-KO showed strong separation from proliferating MEFs, and a weaker separation distinguished WT and H2A.J-KO MEFs. Strikingly, gene set enrichment analysis indicated highly significant defects in Interferon Response Gene Expression in the H2A.J-KO MEFs in senescence with significant down-regulation in senescent H2A.J-KO cells of a series of oligoadenylate synthase genes (Oas1g, Oas1a, Oasl1, Oas2, Oasl2) and several ISGs. Thus, H2A.J also contributes to ISG expression in the heterologous context of senescent MEFs.</p>
A Phase I Trial of Recombinant Human Granulocyte-Macrophage Colony Stimulating Factor (rHuGM-CSF), Recombinant Alpha Interferon and Azidothymidine (AZT) in AIDS-Associated Kaposi's Sarcoma
ClinicalTrials.gov study NCT00000694. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Study of Intratumorally Administered Stimulator of Interferon Genes (STING) Agonist E7766 in Participants With Advanced Solid Tumors or Lymphomas - INSTAL-101
ClinicalTrials.gov study NCT04144140. IPD Sharing: YES. Countries: 5. Publications: 0.
Viral Kinetics, Interferon Stimulated Genes (ISGs) and mirRNA Among Subjects Infected With Different Hepatitis C Virus Genotypes During Therapy With Sofosbuvir and GS-5816
ClinicalTrials.gov study NCT02468648. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Restoring PU.1 induces apoptosis and modulates viral transactivation via interferon-stimulated genes in primary effusion lymphoma
GEO Series GSE97318. Homo sapiens. 2 samples. Type: Expression profiling by array.
Next Generation Sequencing Facilitates Quantitative Analysis of interferon stimulated MEFs Transcriptomes [RNA-Seq]
GEO Series GSE89349. Mus musculus. 10 samples. Type: Expression profiling by high throughput sequencing.
Transcriptomic Profiling of Collaborative Cross Founder Mouse Embryonic Fibroblasts stimulated with Type I, II and III Interferons
GEO Series GSE53057. Mus musculus. 71 samples. Type: Expression profiling by array.
Genome-wide analysis of interferon-stimulated genes in primary cells and immortalized cell lines
GEO Series GSE46599. Homo sapiens. 48 samples. Type: Expression profiling by array.
Chronic Interferon Stimulated Gene Transcription Promotes Oncogene Induced Breast Cancer [RNA-Seq]
GEO Series GSE246409. Mus musculus. 21 samples. Type: Expression profiling by high throughput sequencing.
Diversity in Modulation of Interferon Stimulated Genes by Dobrava, Kurkino, and Sochi Genotypes of Dobrava-Belgrade Hantavirus in comparison to Tula Virus
GEO Series GSE73410. Homo sapiens. 10 samples. Type: Expression profiling by array.
Positionally distinct interferon-stimulated dermal immune-acting fibroblasts promote neutrophil recruitment in Sweet’s syndrome [snRNA-seq]
GEO Series GSE299795. Homo sapiens. 2 samples. Type: Expression profiling by high throughput sequencing.
DLEU1 promotes oral squamous cell carcinoma progression through activating interferon-stimulated genes
GEO Series GSE178613. Homo sapiens. 8 samples. Type: Expression profiling by array; Genome binding/occupancy profiling by high throughput sequencing.
Induction of antiviral Interferon-Stimulated Genes (ISGs) by neuronal STING promotes the resolution of pain
GEO Series GSE236865. Mus musculus. 8 samples. Type: Expression profiling by high throughput sequencing.
Human DUX4 and mouse Dux interact with STAT1 and broadly inhibit interferon-stimulated gene induction
GEO Series GSE186244. Homo sapiens. 18 samples. Type: Expression profiling by high throughput sequencing.
DLEU1 promotes oral squamous cell carcinoma progression through activating interferon-stimulated genes [microarray]
GEO Series GSE178608. Homo sapiens. 2 samples. Type: Expression profiling by array.
10x single-cell RNAseq profiling of hiPSC derived WT and ISG15 KO macrophages stimulated with interferon-a and treated with itaconic acid, 4-octyl itaconate and ruxolitinib
GEO Series GSE168816. Homo sapiens. 9 samples. Type: Expression profiling by high throughput sequencing.
Dynamic expression profiling of type I and type III interferon-stimulated hepatocytes.
GEO Series GSE48400. Homo sapiens. 73 samples. Type: Expression profiling by array.
Gene expression profile of Cd45 positive cells in single cell level from KRASLSL.G12D/+P53LSL.R172H/+Pdx-Cre mice (KPC tumor mouse) model treated with stimulator of interferon genes (STING) and lymph
GEO Series GSE275840. Mus musculus. 4 samples. Type: Expression profiling by high throughput sequencing.
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OpenNeuro
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