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97 results for “DNA variants”
Data and software supporting the manuscript 'The population frequency of human mitochondrial DNA variants is highly dependent upon mutational bias'
<p>Next-generation sequencing can quickly reveal genetic variation potentially linked to heritable disease. As databases encompassing human variation continue to expand, rare variants have been of high interest, since the frequency of a variant is expected to be low if the genetic change leads to a loss of fitness or fecundity. However, the use of variant frequency when seeking genomic changes linked to disease remains very challenging. Here, we explore the role of selection in controlling human variant frequency using the HelixMT database, which encompasses hundreds of thousands of mitochondrial DNA (mtDNA) samples. We find that a substantial number of synonymous substitutions, which have no effect on protein sequence, were never encountered in this large study, while many other synonymous changes are found at very low frequencies. Further analyses of human and mammalian mtDNA datasets indicate that the population frequency of synonymous variants is predominantly determined by mutational biases rather than by strong selection acting upon nucleotide choice. Our work has important implications that extend to the interpretation of variant frequency for non-synonymous substitutions. </p> <p> </p>
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>
Phase I trial of CX-5461, a first-in-class G-quadruplex stabilizer in patients with advanced solid tumors enriched for DNA-repair deficiencies (CCTG IND.231) - Variant Calls
<p>Variant Calls from Phase I trial of CX-5461, a first-in-class G-quadruplex stabilizer in patients with advanced solid tumors enriched for DNA-repair deficiencies (CCTG IND.231)</p> <p>See publication for methodology.</p>
Data for publication: A pipeline for in-depth analysis of DNA virus populations by profiling the low abundant virus variants and partial genomic components
<p>Raw and processed sequence data from Oxford Nanopore and BGI short read sequencing platforms used in the publication: "A pipeline for in-depth analysis of DNA virus populations by profiling the low abundant virus variants and partial genomic components".</p>
Multiple full-length variants of the Mitochondrial COI DNA Barcode Region are prevalent in North European Sawflies
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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>
Quartet DNA benchmark sets for germline small variants and structural variants
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A method to investigate Pathological Variant load of Mitochondrial DNA in single human Mesenchyma stem cells
<p>Mesenchymal stem cells (MSCs) are the parent cells to many cells of the musculoskeletal system including osteoblasts. Previous work has shown that in mouse models mitochondrial DNA (mtDNA) pathological variants lead to dysfunction of the respiratory chain of these osteoblasts and the premature development of age related osteoporosis. An increased rate of respiratory chain deficiency has also been observed in human osteoblasts. mtDNA mutates at an enhanced rate compared to nuclear DNA and has been linked to the ageing process in humans. </p> <p>We have developed and optimised an experimental pipeline to isolate single MSCs using flow cytometry before performing next generation sequencing to analyse the pathogenic variant load of 13 patients aged 22-88 to assess if pathogenic variants exist in mesenchymal stem cells and if there are age related changes.</p> <p>Across all patients and all cells mtDNA pathological variants were present at similarly low levels. As per previous studies we found increased pathogenic variants within the mtDNA control region (D-Loop). However overall, there was no significant difference in the distribution of variants across the rest of the genome in all patients. Although a higher proportion of non-synonymous variants were seen this was not statistically significant.</p> <p>We have shown that it is possible to isolate and sequence individual MSCs and observe mtDNA pathological variants. This gives a snapshot in time of the variant load for each patient. Due to low sample numbers compared to other studies investigate mtDNA in other cell types, we did not observe any age related increase in pathological variants. However this adds further evidence that clonally expanded, somatic mtDNA variants are common and could contribute to age related disease including osteoporosis.</p>
The 'dark matter' of protein variants carries a distinct DNA signature and predicts damaging variant effects
<p>Data generated for the manuscript "The 'dark matter' of protein variants carries a distinct DNA signature and predicts damaging variant effects".</p> <p> </p> <p>Please consult the README file for detailed description of data files included in this dataset.</p>
Data from: Mitochondrial DNA variants help monitor the dynamics of Wolbachia invasion into host populations
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Elimination of mitochondrial DNA variants by nuclear genome transfer in human oocytes
GEO Series GSE42077. Homo sapiens. 11 samples. Type: Expression profiling by array.
The histone H3 variant H3.3 regulates gene body DNA methylation [ChIP-seq]
GEO Series GSE96834. Arabidopsis thaliana. 20 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Elimination of mitochondrial DNA variants by nuclear genome transfer in human oocytes.
GEO Series GSE42271. Homo sapiens. 15 samples. Type: Genome variation profiling by SNP array.
DNA variants affecting the expression of numerous genes in trans have diverse mechanisms of action and evolutionary histories
GEO Series GSE134169. Saccharomyces cerevisiae. 25 samples. Type: Expression profiling by high throughput sequencing.
EZH2 alters aggressive variant prostate cancer subtype evolution, but is not required for neuroendocrine prostate cancer. [DNA methylation]
GEO Series GSE297193. Mus musculus. 20 samples. Type: Methylation profiling by genome tiling array.
Androgen receptor splicing variant 7 (ARv7) promotes DNA damage response in prostate cancer cells
GEO Series GSE277204. Homo sapiens. 12 samples. Type: Expression profiling by high throughput sequencing.
Segregation of naturally occurring mitochondrial DNA variants in a mini-pig model
GEO Series GSE73276. Sus scrofa. 24 samples. Type: SNP genotyping by SNP array; Genome variation profiling by SNP array.
Mycobacterial DNA binding protein 1 (MDP1) mediates gene regulation in Mycobacterium tuberculosis variant Bacillus Calmette-Guerin
GEO Series GSE222247. Mycobacterium tuberculosis variant bovis. 27 samples. Type: Expression profiling by high throughput sequencing.
The functional impact of BRCA1 BRCT domain variants using multiplexed DNA double-strand break repair assays
GEO Series GSE188426. Homo sapiens. 66 samples. Type: Other.
Compartmentalization of DNA damage response between heterochromatin and euchromatin is mediated by distinct H2A histone variants
GEO Series GSE95557. Arabidopsis thaliana. 3 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
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Allen Brain Atlas
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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.