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800 results for “RNA methylation”
DATA for manuscript entitled "Integrating Transcriptomes and Somatic Mutations to Identify RNA Methylation Regulators as a Prognostic Marker in Hepatocellular Carcinomas"
<p><strong>Raw data of TCGA dataset and 7-meta data.</strong></p>
Molecular simulations to investigate the impact of N6-methylation in RNA recognition: Improving accuracy and precision of binding free energy prediction
<p>Dataset relative to Molecular dynamics simulation performed for the work "Molecular simulations to investigate the impact of N6-methylation in RNA recognition: Improving accuracy and precision of binding free energy prediction".<br><br>The dataset contains data of 42 alchemical simulations and is subdivided in 4 zip files.<br><br>Folders are named following the scheme: system_configuration_forcefield.<br>Zip file C1 contains .mdp files used for all the simulations.<br><br>Folders corresponding to simulations performed with the fit5_AC ff contains:<br>- topology files (topol.top, topol_RNA_chain_A.itp, topol_RNA_chain_B.itp)<br>- index files needed to reconstruct the demuxed trajectories (replica_index.xvg , replica_index.xvg)<br>- 16 folders, one for each replica (lam0 ... lam15), containing:<br> - final configuration (confout.gro)<br> - log file (md.log)</p> <p> - input file for md run (md.tpr)<br> - energies for the concatenated trajectories recomputed for the realtive replica hamiltonian (ener_trj_conc.edr)<br><br>Folders corresponding to simlations performed with fit_A parametrization only contains .edr files corresponding to energies for the concatenated trajectory computed for 14 set of DeQs drawn from a gaussian distribution, with the relative topologies.<br><br>Supplementary materials relative to simlations performed with fit_A parametrizationcan be found in: https://zenodo.org/records/6498021</p>
Data from: Cancer mutations rewire the RNA methylation specificity of METTL3-METTL14
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RNA m6A methylation in unilateral ureteral ligations model
<p>Chronic kidney disease (CKD) is a high incidence disease. Renal fibrosis is the ultimate pathological pathway for chronic kidney diseases leading to end-stage renal failure. There is currently no effective treatment to prevent the renal fibrosis. Renal EMT is a key mechanism of renal fibrosis. Recent evidence suggests m<sup>6</sup>A modification in RNA can regulate EMT in tumor cells. However, a role of m<sup>6</sup>A RNA modification in renal fibrosis has not been reported. Therefore, we investigate whether m<sup>6</sup>A RNA methylation plays an important role in the epithelial-to-mesenchymal transition (EMT) process of renal fibrosis. Unilateral ureteral ligations were performed in C57BL/6 mice to establish a mouse model of renal fibrosis and TGF-b intervention was used in HK2 cells to establish a cellular model of renal fibrosis. The effects of m<sup>6</sup>A and the role of <i>Mettl14 </i>on kidney disease and HK2 cells were studied. </p>
Data from: Changes in melanocyte RNA and DNA methylation favor pheomelanin synthesis and may avoid systemic oxidative stress after dietary cysteine supplementation in birds
Cysteine plays essential biological roles, but excessive amounts produce cellular oxidative stress. Cysteine metabolism is mainly mediated by the enzymes cysteine dioxygenase and γ-glutamylcysteine synthetase, respectively coded by the genes CDO1 and GCLC. Here we test a new hypothesis posing that the synthesis of the pigment pheomelanin also contributes to cysteine homeostasis in melanocytes, where cysteine can enter the pheomelanogenesis pathway. We conducted a experiment in the Eurasian nuthatch Sitta europaea, a bird producing large amounts of pheomelanin for feather pigmentation, to investigate if melanocytes show epigenetic lability under exposure to excess cysteine. We increased systemic cysteine levels in nuthatches by supplementing them with dietary cysteine during growth. This caused in feather melanocytes the downregulation of genes involved in intracellular cysteine metabolism (GCLC), cysteine transport to the cytosol from the extracellular medium (Slc7a11) and from melanosomes (CTNS), and regulation of tyrosinase activity (MC1R and ASIP). These changes were mediated by increases in DNA m5C in all genes excepting Slc7a11, which experienced RNA m6A depletion. Birds supplemented with cysteine synthesized more pheomelanin than controls, but did not suffer higher systemic oxidative stress. These results suggest that excess cysteine activates an epigenetic mechanism that favors pheomelanin synthesis and may protect from oxidative stress.
2'O-ribose methylation of ribosomal RNA (rRNA 2'Ome) in primary human T cells from septic shock and COVID-19 patients
<h2>Abstract</h2> <p>T cell exhaustion plays a central role in sepsis-induced immunosuppression. Deciphering the precise mechanism of this cellular dysfunction could lead to new therapies. In several pathophysiological contexts, the 2’O-ribose methylation of ribosomal RNA (rRNA 2’Ome) has emerged as a level of epitranscriptomic regulation. Here, we report for the first time site-specific alterations of rRNA 2’Ome epitranscriptomic marks in T cells after sepsis, associated with impaired functionality. Using primary human T cells from septic shock and COVID-19 patients, we identified a subset of sites with high inter-individual variability, the levels of which correlated with lymphocyte effector functions. This was recapitulated in an ex vivo model of stimulated T lymphocytes from healthy donors. Finally, 2’Ome signature discriminated samples from septic patients from those of healthy donors. We describe rRNA 2’Ome regulation as a new molecular mechanism that controls T lymphocyte effector function in sepsis with high potential as biomarker and therapeutic target. </p> <p>---------------------------------------------------</p> <h2>Description of the data and file structure</h2> <p>Each folder contains the read-end counts in the sub-directory <strong>RiboMethSeq_ReadEnd_Counts</strong> and the metadata file. The metadata file describe each file contained in this sub-directory.</p> <p></p> <p>The read-end count file structure:</p> <ol> <li> <p>The <strong>name of the RNA</strong> on which the read end counting was performed.</p> </li> <li> <p>The <strong>number of the position</strong> on the RNA.</p> </li> <li> <p>The <strong>value of the read end counts</strong> at the position.</p> </li> </ol> <h2>Code/Software</h2> <p>Using <a href="https://github.com/RibosomeCRCL/ribomethseq-nf">ribomethseq-nf</a> pipeline, fastq were used to align reads on the human rRNA sequence (NR_046235), compute 5’/3’-end read counts.</p> <p>These files can be the input of <a href="https://github.com/RibosomeCRCL/rRMSAnalyzer">rRMSAnalyzer package</a> to adjust batch effect (ComBat-seq method) and calculate C-score corresponding to the end read count at the genomic position of interest normalized to the median of end read counts of the local environment (6 upstream and 6 downstream nucleotides).</p>
Data from: Changes in melanocyte RNA and DNA methylation favor pheomelanin synthesis and may avoid systemic oxidative stress after dietary cysteine supplementation in birds
Open the record for dataset details and reuse information.
RNA m6A methylation in unilateral ureteral ligations model
Open the record for dataset details and reuse information.
Contribution of differential cell-specific methylation to schizophrenia [RNA-seq]
GEO Series GSE107638. Homo sapiens. 96 samples. Type: Expression profiling by high throughput sequencing.
Integrative analysis of DNA methylation and microRNA expression reveals mechanisms of disparity in hepatocellular carcinoma [RNA-Seq]
GEO Series GSE176271. Homo sapiens. 32 samples. Type: Expression profiling by high throughput sequencing.
The DNA methylation landscape of human melanoma [RNA-Seq]
GEO Series GSE71747. Homo sapiens. 20 samples. Type: Expression profiling by high throughput sequencing.
m6A RNA methylation orchestrates transcriptional dormancy during paused pluripotency [SLAM-seq]
GEO Series GSE228734. Mus musculus. 14 samples. Type: Expression profiling by high throughput sequencing; Other.
Methylation and Transcriptomic Profiling Reveals Short Term and Long Term Regulatory Responses in Polarized Macrophages [RNA-Seq]
GEO Series GSE273627. Homo sapiens. 27 samples. Type: Expression profiling by high throughput sequencing.
De novo DNA methylation suppresses aberrant fate trajectory during epiblast transition [RNA-seq]
GEO Series GSE158310. Mus musculus. 4 samples. Type: Expression profiling by high throughput sequencing.
H3K36 methylation maintains cell identity by regulating opposing lineage programs [RNA-seq II]
GEO Series GSE203370. Mus musculus. 28 samples. Type: Expression profiling by high throughput sequencing.
Microglia isolated from juvenile offspring of dams with allergic asthma exhibit methylation and transcriptional alterations to autism risk genes [RNA-Seq]
GEO Series GSE94525. Mus musculus. 8 samples. Type: Expression profiling by high throughput sequencing.
An siRNA-guided AGO protein recruits Polymerase V to initiate RNA-directed DNA methylation (smallRNA-seq dataset)
GEO Series GSE165574. Arabidopsis thaliana. 45 samples. Type: Non-coding RNA profiling by high throughput sequencing.
RNA-seq profiling and DNA methylation of human somatic, primed and naïve induced Pluripotent Stem cells
GEO Series GSE110377. Homo sapiens. 23 samples. Type: Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing.
Crosstalk between the polycomb repressive complex 2 and DNA methylation mediates neuroendocrine prostate cancer lineage plasticity [RNA-Seq]
GEO Series GSE289248. Mus musculus. 2 samples. Type: Expression profiling by high throughput sequencing.
Unique cell-type specific patterns of DNA methylation in the root meristem (RNA-seq)
GEO Series GSE79709. Arabidopsis thaliana. 6 samples. Type: Expression profiling by high throughput sequencing.
ScienceDex guides
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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)
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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.