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503
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Dataset results
503 results for “small RNA-seq”
RNA-Seq data from: Hox genes modulate physical forces to differentially shape small and large intestinal epithelia
<p>Hox genes are highly conserved, master regulators of spatial patterning in the embryo, but how these factors trigger regional morphogenesis has largely remained a mystery. In the developing gut, Hox genes help demarcate identities of the small and large intestines early in embryogenesis, which ultimately leads to their specialization in both form and function. While the midgut forms villi, the hindgut develops flat, brain-like sulci that resolve into heterogeneous outgrowths. Combining mechanical measurements and mathematical modeling, we demonstrate that the posterior Hox gene Hoxd13 regulates biophysical phenomena that shape the hindgut lumen. We further show that Hoxd13 acts through the TGFβ pathway to thicken, stiffen, and promote isotropic growth of the subepithelial mesenchyme; together, these features lead to hindgut surface buckling. TGFβ, in turn, promotes collagen deposition to affect mesenchymal geometry and growth. We thus identify a cascade of events downstream of positional genetic identity that direct posterior intestinal morphogenesis. </p> <p>To identify genes and pathways that are directly or indirectly regulated by Hoxd13 to affect posterior gut morphogenesis in the chick, we compared mesodermal transcriptomes of wild-type midgut and hindgut intestinal samples, as well as mesodermal samples from a Hoxd13-overexpressing midgut at E12 and E14. Tissues were dissected and endoderm layers were removed manually before RNA extraction and downstream processing. Unbiased clustering was used to identify genes commonly differentially expressed in the hindgut and Hoxd13-misexpressing midgut. This submission contains bulk RNA-seq raw data (fastq.bz2 files) and processed .txt files with read counts. Experiment information is provided in .xlsx Metadata file used for NCBI GEO submission.</p>
Training material for small RNA-seq data analysis (Galaxy Training Network tutorial)
<p>The data provided here are part of a Galaxy Training Network tutorial that analyzes small RNA-seq (sRNA-seq) data from a study published by Harrington et al. (DOI:10.1186/s12864-017-3692-8) to detect differential abundance of various classes of endogenous short interfering RNAs (esiRNAs). The goal of this study was to investigate "connections between differential retroTn and hp-derived esiRNA processing and cellular location, and to investigate the potential link between mRNA 3’ end cleavage and esiRNA biogenesis." To this end, sRNA-seq libraries were constructed from triplicate <em>Drosophila</em> tissue culture samples under conditions of either control RNAi or RNAi knockdown of a factor involved in mRNA 3’ end processing, <em>Symplekin</em>. This dataset (GEO Accession: GSE82128) consists of single-end, size-selected, non-rRNA-depleted sRNA-seq libraries. Because of the long processing time for the large original files, we have downsampled the original raw data files to include only reads that align to a subset of interesting transcript features including: (1) transposable elements, (2) <em>Drosophila</em> piRNA clusters, (3) <em>Symplekin</em>, and (4) genes encoding mass spectrometry-defined protein binding partners of <em>Symplekin</em> from Additional File 2 in the indicated paper by Harrington et al. More details on features 1 and 2 can be found here: https://github.com/bowhan/piPipes/blob/master/common/dm3/genomic_features (piRNA_Cluster, Trn). All features are from the <em>Drosophila</em> genome Apr. 2006 (BDGP R5/<em>dm3</em>) release.</p>
Arabidopsis RNA-seq seedling small training set (chr1 100k)
<p>Arabidopsis seedling small training set for RNA-seq. FastQ files for reads mapping to the first 100k of the first chromosome of Arabidopsis are included. The sequencing was done using Illumina, 100 paired-end mode. </p>
Transcription start sites from capped small RNA-seq of rat nucleus accubmens and prefrontal cortex
<p>Small RNAs of ∼15–60 nt were size selected by denaturing gel electrophoresis starting from total RNA extracted from 14 rat brain tissue dissections. For csRNA libraries, cap selection was followed by decapping, adapter ligation, and sequencing. For input libraries, 10% of small RNA input was used for decapping, adapter ligation, and sequencing. After library quality check by gel electrophoresis, the samples were sequenced using the Illumina NextSeq 500 platform using 75 cycles single end. Sequencing reads were aligned to the rat mRatBN7.2 genome assembly using STAR v2.5.3a aligner with default parameters. Transcriptional start regions were defined using HOMER’s findPeaks tool. </p> <p>Duttke, S.H., Montilla-Perez, P., Chang, M.W., Li, H., Chen, H., Carrette, L.L.G., de Guglielmo, G., George, O., Palmer, A.A., Benner, C., et al. (2022). Glucocorticoid Receptor-Regulated Enhancers Play a Central Role in the Gene Regulatory Networks Underlying Drug Addiction. Front. Neurosci. 16, 858427.</p>
Training material for analysis small RNA-seq data (Galaxy Training Network tutorial)
<p>The data provided here is part of the Galaxy Training Network tutorial for analysis of small RNA-seq (sRNA-seq) data using mirdeep2 and miranda. This dataset is provided by INRA (Le Rheu, France).</p>
polyA mRNA RNA-seq from small intestine (ENCSR000BZD)
GEO Series GSE90191. Mus musculus. 2 samples. Type: Expression profiling by high throughput sequencing.
Rapid and synchronous chemical induction of replicative-like senescence via a small molecule inhibitor [bulk RNA-seq]
GEO Series GSE238252. Homo sapiens. 14 samples. Type: Expression profiling by high throughput sequencing.
small RNA-seq in HEK-293t cells
GEO Series GSE132335. Homo sapiens. 6 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Small RNA-seq from FPLC-fractionated leaf and flower crude extracts
GEO Series GSE130431. Arabidopsis thaliana. 16 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Small RNA-seq from ENCODE/Cold Spring Harbor Lab
GEO Series GSE24565. Homo sapiens. 87 samples. Type: Non-coding RNA profiling by high throughput sequencing.
small RNA-seq from prostate gland (ENCSR332RHR)
GEO Series GSE88197. Homo sapiens. 1 samples. Type: Non-coding RNA profiling by high throughput sequencing.
small RNA-seq from A375 (ENCSR376XXO)
GEO Series GSE78382. Homo sapiens. 2 samples. Type: Expression profiling by high throughput sequencing.
Small molecule-induced epigenomic reprogramming of APL blasts leading to antiviral-like response and c-MYC downregulation [RNA-seq]
GEO Series GSE205345. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
small RNA-seq from SK-MEL-5 (ENCSR571FTT)
GEO Series GSE78411. Homo sapiens. 2 samples. Type: Expression profiling by high throughput sequencing.
Small-molecule Inhibition of METTL3 Suppresses Tumor Growth and Promotes Neuroblastoma Differentiation [RNA-Seq Decay]
GEO Series GSE240581. Homo sapiens. 48 samples. Type: Expression profiling by high throughput sequencing.
Integrative analyses of human reprogramming reveal dynamic nature of induced pluripotency [small RNA-Seq]
GEO Series GSE62776. Homo sapiens. 24 samples. Type: Non-coding RNA profiling by high throughput sequencing.
small RNA-seq from spleen (ENCSR917CQJ)
GEO Series GSE88644. Homo sapiens. 1 samples. Type: Non-coding RNA profiling by high throughput sequencing.
small RNA-seq from fibroblast of arm (ENCSR489KNQ)
GEO Series GSE78395. Homo sapiens. 2 samples. Type: Expression profiling by high throughput sequencing.
small RNA-seq from bipolar spindle neuron (ENCSR603RPC)
GEO Series GSE78416. Homo sapiens. 2 samples. Type: Expression profiling by high throughput sequencing.
Small molecule activation of a pseudoexon triggers huntingtin-lowering (RNA-Seq)
GEO Series GSE162813. Homo sapiens. 12 samples. Type: Expression profiling by high throughput sequencing; Other.
ScienceDex guides
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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.