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12 results for “Pre-miRNA”
Automatic learning of pre-miRNAs from different species – Supplemental Material
<p>In this study we investigated to which degree the features used to represent the sequences, the learning algorithm and the training and test species impacted the performance of pre-miRNA classification.</p> <p>The folder <em>multispecies.tar.xz </em>contains the data and the scripts necessary to reproduce the results in the publication in BMC Bioinformatics.</p>
Guppy pre-miRNAs (unfiltered set)
<p>Initial (pre-filtered) set of pre-miRNAs from three tissues - brain, ovary and testis.</p>
The loop position of shRNAs and pre-miRNAs is critical for the accuracy of Dicer processing in vivo
GEO Series GSE41292. Mus musculus; Homo sapiens. 20 samples. Type: Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing.
The effect of 22-bulge of pre-miRNAs on DICER cleavage in human cells
GEO Series GSE183552. Homo sapiens. 9 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Intramolecular ligation method (iLIME) for pre-miRNA quantification and sequencing
GEO Series GSE185524. Homo sapiens; synthetic construct. 11 samples. Type: Non-coding RNA profiling by high throughput sequencing.
The effect of 22-bulge of pre-miRNAs on DICER cleavage in human cells.
GEO Series GSE192613. Homo sapiens. 7 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Lung adenocarcinoma subtypes definable by lung development-related miRNA expression profiles in association with clinicopathologic features [pre-miRNA analysis - Whole Human Genome 4 x 44K Microarray]
GEO Series GSE51854. Homo sapiens. 4 samples. Type: Expression profiling by array.
A sliding-bulge structure at the Dicer processing site of pre-miRNA regulates alternative Dicer processing to generate 5’-isomiRs (miR-203)
GEO Series GSE80772. Homo sapiens. 2 samples. Type: Non-coding RNA profiling by high throughput sequencing.
A sliding-bulge structure at the Dicer processing site of pre-miRNA regulates alternative Dicer processing to generate 5’-isomiRs (pre-miR-203)
GEO Series GSE80771. Homo sapiens. 2 samples. Type: Non-coding RNA profiling by high throughput sequencing.
An ARF6-Exportin-5 Axis Delivers pre-miRNA Cargo to Tumor Microvesicles.
GEO Series GSE130316. Homo sapiens. 6 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Structural basis for pre-miRNA-31 biogenesis
GEO Series GSE230167. Homo sapiens. 3 samples. Type: Other.
Sequences and secondary structures of mutated pre-miRNAs from CRISPR/Cas9-edited MIR160a, MIR160b and MIR390a genes of potato
<p><strong>Genotypisation of transfected protoplasts</strong> (folder<strong> “Transfected protoplasts”</strong>)</p> <p>Genomic DNA isolated from transfected and non-transfected protoplast of cv. Desiree was used as a template to amplify approximately 800 bp-long region surrounding coding sequence for miR160a-5p, miR160b-5p and miR390a-5p, encoded by <em>MIR160a</em>, <em>MIR160b</em> and <em>MIR390a</em> genes, respectively. To determine types of mutations and polymorphism, PCR products were cloned into pJET, transformed into <em>E. coli</em>, isolated from 9 or 10 colonies per PCR product and Sanger sequenced with primers specific for amplicons from both directions.</p> <p><strong>Genotypisation of transgenic lines</strong> (folder<strong> “Transgenic potato”</strong>)</p> <p>Approximately 800 bp-long region surrounding coding sequence for each miRNA was amplified from genomic DNA isolated from CRISPR-edited <em>MIR160a</em> (cr-<em>MIR160a</em>), <em>MIR160b </em>(cr-<em>MIR160b</em>) and <em>MIR390a</em> (cr-<em>MIR390a</em>) transgenic and non-transgenic plants (NT; cv. Rywal and cv. Desiree). For the screening of transgenic lines with desired mutations, PCR products were Sanger sequenced (subfolder <strong>“PCR amplicons miRNA”</strong>). To determine types of mutations and polymorphism, PCR products were for the selected transgenic lines and NT plants cloned into pJET, transformed into E. coli, isolated from 9 or 10 colonies per PCR product and Sanger sequenced with primers specific for amplicons from both directions (subfolder <strong>“pJET_miRNA”</strong>).</p> <p><strong>Secondary structures of pre-miRNA precursors</strong> (folder <strong>“Secondary structures”</strong>)</p> <p>Precursor sequences of wild-type potato <em>MIR160a</em> and <em>MIR160b</em> were obtained from miRBase (https://www.mirbase.org/; Accession No. MI0025955, MI0025956) and of wild-type potato <em>MIR390a</em> from the study of Križnik <em>et al.</em>, 2017 (Križnik <em>et al.</em>, 2017) (subfolder <strong>“</strong><strong>WT pre-miRNAs</strong><strong>“</strong>). The mutated pre-miRNAs of cr-<em>MIR160a</em>, cr-<em>MIR160b</em> and cr-<em>MIR390a</em> transgenic lines were extracted from Sanger sequencing results (subfolder <strong>“pJET_miRNA”</strong>). The secondary structures were drawn and miRNA/miRNA* duplex regions were highlighted (orange – 5p miRNA coding region, blue – 3p miRNA coding region) using RNA Folding/Annotation tool of The Small RNA Workbench v4.5 (Stocks <em>et al.</em>, 2018) (subfolders <strong>“Desiree” </strong>and<strong> “Rywal”</strong>).</p>
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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.