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1,760
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ShareScore release 0.9.0
Dataset results
1,760 results for “small RNA”
Characterization of Natural Killer Cell Sensitivity of Circulating Tumor Cells in Non-small Cell Lung Cancer using Bulk RNA-sequencing
GEO Series GSE211830. Homo sapiens. 7 samples. Type: Expression profiling by high throughput sequencing.
modENCODE RNA-Seq of Drosophila S2-DRSC small RNAs
GEO Series GSE18041. Drosophila melanogaster. 8 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Small RNA sequencing of plasma RNA
GEO Series GSE52981. Homo sapiens. 3 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Time-resolved small RNA sequencing unravels molecular principles of microRNA homeostasis [ago2KO s4U TT-SLAMseq]
GEO Series GSE129597. Drosophila melanogaster. 7 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Evolutionary dynamics of small RNA regulation through genomic hybridization in sugarcane
GEO Series GSE116171. Saccharum spontaneum; Saccharum hybrid cultivar SP70-1143; Saccharum hybrid cultivar RB867515; Saccharum robustum; Saccharum barberi; Saccharum hybrid cultivar; Saccharum sinense. 14 samples. Type: Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing.
mRNA gene expression profiling in a human AML cell line treated with small molecule inhibitors that impact different RNA polymerase transcription complexes, or their combination, in comparison to a gl
GEO Series GSE118565. Homo sapiens. 18 samples. Type: Expression profiling by high throughput sequencing.
Asymmetric bulges within hairpin RNA transgenes influence small RNA size, secondary siRNA production and viral defence I
GEO Series GSE243255. Nicotiana tabacum. 19 samples. Type: Expression profiling by high throughput sequencing.
Small RNA-seq files from van Kleeff et al, 2016
<p>Dataset companion of: </p> <p>P.J.M. van Kleeff, M. Galland, R.C. Schuurink, P.M. Bleeker. <strong>Small RNAs from <em>Bemisia tabaci</em> are transferred to <em>Solanum lycopersicum</em> phloem during feeding. </strong>Front Plant Sci, 7 (2016), p. 1759 https://doi.org/10.3389/fpls.2016.01759</p>
Stem trichome small RNA-Seq from the 20 accessions
<p><strong>Total and Small RNA Isolation</strong></p> <p>Total RNA from stem trichomes (n = 1) were isolated using concentrated TRIzol reagent (Life Technologies). Total RNA was isolated using the E.Z.N.A.<sup>®</sup> MicroElute RNA Clean Up Kit (Omega Bio-Tek). Briefly, TRIzol Reagent (Life Technologies) and chloroform was added according to the manufacturer's instructions. After centrifugation, the RNA-containing aqueous phase was collected, mixed with 1.5 volume of 100% ethanol and applied to a MicroElute spin column (Omega Bio-Tek). The column was washed according to the manufacturers's instructions: once with RWT buffer (Qiagen), once with RPE washing buffer (Qiagen) and finally with 80% ethanol. The RNA concentration was measured on a NanoDrop ND-2000 (Thermo Scientific) and RNA integrity was examined using the 2200 TapeStation System with Agilent RNA ScreenTapes (Agilent Technologies).</p> <p>Total RNA was spiked with ERCCs spike-in mix 1 (Life Technologies) as well as a synthetic spike-in set for Size Range Quality Control (SRQC) together with an External Reference for Data Normalization (ERDN; <a href="https://www.frontiersin.org/articles/10.3389/fpls.2016.01759/full#B38">Locati et al., 2015</a>). The total RNA was divided in a large and a small fraction. The large RNA fraction was bound to a mirVana™ spin column (mirVana™ miRNA Isolation Kit, Life Technologies) according to the manufacturer's instructions. Small RNAs (<200 nts) were purified from the flow-through by adding ethanol to a final concentration of 65% (v/v) and bound to an E.Z.N.A.<sup>®</sup> MicroElute spin column. The column was washed once with RWT buffer, once with RPE buffer and once with 80% ethanol (Qiagen). The concentration and integrity of small RNA was examined as described above.</p> <p><strong>Next-Generation Sequencing</strong></p> <p>Bar-coded small RNA libraries were generated according to the manufacturer's protocols using the Ion Total RNA-Seq Kit v2 and the Ion Xpress™ RNA-Seq bar-coding kit (Life Technologies). The size distribution and yield of the bar-coded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes (Agilent Technologies). Sequencing templates were prepared on the Ion Chef™ System using the Ion PI Hi-Q Chef Kit (Life Technologies). Sequencing was performed on an Ion Proton™ System using Ion PI v3 chips (Life Technologies) according to the manufacturer's instructions.</p> <p><strong>References</strong></p> <p>Locati et al. 2015. Improving small RNA-seq by using a synthetic spike-in set for size-range quality control together with a set for data normalization. <a href="https://www.ncbi.nlm.nih.gov/pubmed/25870415#">Nucleic Acids Res.</a> (2015). 43(14):e89. doi: 10.1093/nar/gkv303. </p> <p><strong>Table of genotypes used</strong></p> <pre><code class="language-markdown">| accession | species | accession nr | synonym | origin | |------------|--------------------------------|--------------|---------|-------------| | LA2172 | S. arcanum | TR0009 | - | Peru | | LA1401* | S. cheesmaniae f. minor | EA00652 | - | Ecuador | | LA1840 | S. chmielewskii | - | - | unknown | | LA2695 | S. chmielewskii | EA00759 | - | Peru | | LA0407 | S. habrochaites f. glabratum | EA00558 | - | Ecuador | | LA1777 | S. habrochaites f. hirsutum | EA00703 | - | Peru | | PI134418 | S. habrochaites f. glabratum | TR00015 | LYC38 | unknown | | LYC4 | S. habrochaites f. hirsutum | TR00017 | - | unknown | | LA1718 | S. habrochaites f. glabratum | EA00699 | LYC4934 | Peru | | PI127826 | S. habrochaites f. hirsutum | - | - | Peru | | LA1364 | S. huaylasense | TR00030 | - | Peru | | Moneymaker | S. lycopersicum | - | C32 | Netherlands | | LA4024 | S. lycopersicum | TA209 | - | unknown | | LA2386 | S. lycopersicoides | - | - | Peru | LA2133 | S. neorickii/L. parviflorum | EA00729 | - | Peru | | LA0735 | S. neorickii | TR00025 | LYC140 | unknown | | LA0716 | S. pennellii | EA00585 | - | Peru | | LA1278 | S. peruvianum/pimpinellifolium | TR00005 | - | unknown | | LA1954 | S. peruvianum | EA00713 | - | Peru | | LA1578 | S. pimpinellifolium | EA00674 | - | Peru |</code></pre>
Gel-free library preparation for next-generation RNA sequencing and small RNA quantification
GEO Series GSE313501. Escherichia coli. 12 samples. Type: Non-coding RNA profiling by high throughput sequencing.
small RNA sequencing of two developmental stages of Ciona intestinalis
GEO Series GSE21078. Ciona intestinalis. 2 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Sustained epigenetic reactivation in fragile X neurons with an RNA-binding small molecule [RNA-seq]
GEO Series GSE272192. Homo sapiens. 8 samples. Type: Expression profiling by high throughput sequencing.
Small RNA sequencing of Rice Efficient and Non-Efficient Genotypes to determine uptake of Nitrogen
GEO Series GSE198560. Oryza sativa Indica Group. 8 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Genome-Wide Small RNA Profiling of a Soybean Seed Compartment-Globular Stage
GEO Series GSE57845. Glycine max. 12 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Small RNA sequencing of cerebrospinal fluid exosome fraction in medulloblastoma patients
GEO Series GSE157916. Homo sapiens. 58 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Small RNA profile from Cymbidium mosaic virus (CymMV) and Odontoglossum ringspot virus (ORSV) infected Phalaenopsis amabilis
GEO Series GSE94083. Phalaenopsis amabilis. 10 samples. Type: Non-coding RNA profiling by high throughput sequencing.
SARS-CoV-2 produces a diverse small viral RNA landscape capable of targeting host transcripts
GEO Series GSE197521. Chlorocebus aethiops; Homo sapiens. 99 samples. Type: Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing.
Transcriptomic Analysis Identifies B-Lymphocyte Kinase as a Therapeutic Target for Desmoplastic Small Round Cell Tumor Cancer Stem Cell-Like Cells [RNA-seq]
GEO Series GSE248761. Homo sapiens. 12 samples. Type: Expression profiling by high throughput sequencing.
The effect of MAC3 and MAC5A on small RNA accumulation
GEO Series GSE106110. Arabidopsis thaliana. 6 samples. Type: Non-coding RNA profiling by high throughput sequencing.
RNA-seq of small cell lung cancer [circRNA-Seq]
GEO Series GSE193851. Homo sapiens. 2 samples. Type: Non-coding RNA 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)
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.