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313 results for “Polyadenylation”
Polyadenylation landscape of in vivo long-term potentiation in the rat brain
<h3><strong>This repository contains data published along our corresponding manuscript and additional data resources generated/used throughout this work. <br>______________________________________________________________________________</strong></h3> <h2><strong>Source data accompanying the manuscript:<br></strong></h2> <p><strong>Supplementary Table 1. Key resource table. (A) </strong>Characteristics of analyzed material (e.g. sample identifiers, number of animals used, reads produced, accession numbers). <strong>(B)</strong> Key resources (antibodies, reagents, software).<strong><br><br>Supplementary Table 2. Summary of dentate gyri DRS data per gene. (A)</strong> Differential expression and differential adenylation data for 10 min timepoint. <strong>(B)</strong> Differential expression and differential adenylation data for 60 min timepoint. <strong>(C)</strong> GO-terms for genes with significantly elongated poly(A) tails in 10 min timepoint. <strong>(D)</strong> GO-terms for genes with significantly elongated poly(A) tails in 60 min timepoint. <strong>(E)</strong> GO-terms for upregulated genes in 10 min timepoint. <strong>(F)</strong> GO-terms for upregulated genes in 60 min timepoint. <strong>(G)</strong> GO-terms for upregulated genes with CPEB-binding motifs in 10 min timepoint. <strong>(H)</strong> GO-terms for upregulated genes with CPEB-binding motifs in 60 min timepoint.</p> <p><strong>Supplementary Table 3. Summary of dentate gyri cDNA data per gene. (A)</strong> Differential expression and differential adenylation data for 10 min timepoint. <strong>(B)</strong> Differential expression and differential adenylation data for 60 min timepoint. <strong>(C)</strong> GO-terms for genes with significantly elongated poly(A) tails in 10 min timepoint. <strong>(D)</strong> GO-terms for genes with significantly elongated poly(A) tails in 60 min timepoint. <strong>(E)</strong> GO-terms for upregulated genes in 10 min timepoint. <strong>(F)</strong> GO-terms for upregulated genes in 60 min timepoint. <strong>(G)</strong> GO-terms for upregulated genes with CPEB-binding motifs in 10 min timepoint. <strong>(H)</strong> GO-terms for upregulated genes with CPEB-binding motifs in 60 min timepoint.</p> <p><strong>Supplementary Table 4.</strong> <strong>High-confidence PASs.</strong> <strong>(A)</strong> PASs predicted for datasets obtained 10 min after LTP induction by TAPAS. <strong>(B)</strong> High confidence poly(A) clusters predicted by LAPA for datasets obtained 10 min after LTP induction. <strong>(C)</strong> PASs predicted for datasets obtained 60 min after LTP induction. <strong>(D)</strong> High confidence poly(A) clusters predicted by LAPA for datasets obtained 60 min after LTP induction.</p> <p><strong>Supplementary Table 5.</strong> <strong>Nonadenosine profiling upon LTP induction. (A)</strong> Summary of Ninetails pipeline for dentate gyrus. <strong>(B)</strong> List of genes containing semi-templated poly(A) tails with their adjacent nucleotide contexts.</p> <p><strong>Supplementary Table 6. Summary of synaptoneurosomal DRS/cDNA data per gene.</strong> <strong>(A)</strong> Differential expression and differential adenylation data for unfractionated synaptoneurosomes DRS sequencing. (B) <strong> </strong>Summary of Ninetails pipeline for unfractionated synaptoneurosomes DRS sequencing. (C) Differential expression and differential adenylation data for monoribosome-bound mRNA synaptoneurosomes cDNA sequencing. (D) Differential expression and differential adenylation data for polyribosome-bound mRNA synaptoneurosomes cDNA sequencing. (E) Differential expression and differential adenylation data for unfractionated synaptoneurosomes cDNA sequencing.<br><br><strong>Supplementary Information</strong> - supplementary figures and captions.<br><br><strong>______________________________________________________________________________</strong></p> <h2><strong>Additional data resources:</strong></h2> <p><strong>CPEB1_motif.meme </strong>- CPE1 motif sequence represented as position-dependent letter-probability matrice required by FIMO to make predictions.<br><strong><br>CPEB2_4_motif.meme</strong> - CPE2,4 motif sequence represented as position-dependent letter-probability matrice required by FIMO to make predictions.<strong><br></strong></p> <p><strong>mRatBN7.2_TAPAS_ref_flat.txt</strong> - mRatBN7.2 reference annotation in format required by TAPAS<br><br><strong>mRatBN7.2_LAPA.gtf </strong>- mRatBN7.2 reference annotation in format required by LAPA</p> <p><strong>FIMO_output.zip</strong> - compressed folder with motif predictions provided by FIMO software.<strong><br><br>LAPA_output_dentate_gyrus.zip </strong>- compressed folder with poly(A) clusters predicted by LAPA software. Each timepoint is represented by separate output. <br><strong><br>TAPAS_output_dentate_gyrus.zip </strong>- compressed folder with raw outputs produced by TAPAS software. Each timepoint is represented by separate output. <strong><br><br>Ninetails_output_dentate_gyrus.zip </strong>- compressed folder with raw outputs produced by Ninetails software for samples from dentate gyrus. Subfolders are named according to the sample identifiers provided in Supplementary Table 1. For each sequencing run, 2 tsv files are produced: read classification and nonadenosine residue classification.<br><strong><br>Ninetails_output_synaptoneurosomes.zip </strong>- compressed folder with raw outputs produced by Ninetails software for samples from synaptoneurosomes. Subfolders are named according to the sample identifiers provided in Supplementary Table 1. For each sequencing run, 2 tsv files are produced: read classification and nonadenosine residue classification.<strong><br><br>PolyA_clusters_high_confident.bed </strong>- High-confidence poly(A) clusters annotation in bed format.<strong><br></strong></p>
Multiplexed single-cell characterization of alternative polyadenylation regulators (HEK293FT & K562 Perturb-seq data)
<p>This site provides access to datasets from the CPA-Perturb-seq <a href="https://www.biorxiv.org/content/10.1101/2023.02.09.527751v1">manuscript</a> Kowalski*, Wessels*, Linder* et al., including processed Perturb-seq datasets from HEK293FT and K562. We release these data as Seurat objects, where each object contains single-cell quantifications of gene expression (RNA assay), and in addition, quantifications of polyA site usage (polyA site assay). To explore these data, please install the <a href="https://github.com/satijalab/PASTA">PASTA</a> (PolyA Site analysis using relative Transcript Abundance) package, which provides infrastructure and analytical tools to explore alternative polyadenylation at single-cell resolution. For each dataset, we also include a fragment file which enables visualization of read coverage plots across groups of cells. </p> <p>The files include:</p> <p>1. CPA_K562.Rds : Seurat object containing the K562 CPA-Perturb-seq dataset </p> <p>2. CPA_K562_fragments.tsv.gz : Fragment file for the K562 dataset </p> <p>3. CPA_K562_fragments.tsv.gz.tbi : Fragment file index for the K562 dataset </p> <p> </p> <p>R code below:</p> <pre><code>library(PASTA) k562 <- readRDS("CPA_K562.Rds") # Add fragments for plotting Fragments(k562) <- CreateFragmentObject(path = "download/CPA_K562_blocks.tsv.gz", cells = Cells(k562)) # visualize polyA site usage PolyACoveragePlot(k562, region ="chr7-26212195-26213351")</code></pre>
Magnaporthe oryzae polyadenylation sites for wild-type and delta-rbp35 mutant
<p>Magnaporthe oryzae polyadenylation sites for wild-type and delta-rbp35 mutant, in 4 media: CM, MM, MM-N and MM-C</p>
The 3'-RACE data (InPACT: A computational method for accurate characterization of intronic polyadenylation from RNA sequencing data)
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Supplementary tables for manuscript Dynamics of alternative polyadenylation in single root cells of Arabidopsis thaliana
<p>Supplementary tables for manuscript Dynamics of alternative polyadenylation in single root cells of Arabidopsis thaliana</p>
Data from: Enhanced stability and polyadenylation of select mRNAs support rapid thermogenesis in the brown fat of a hibernator
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Widespread intronic polyadenylation inactivates tumor suppressor genes in leukemia
GEO Series GSE111793. Homo sapiens. 28 samples. Type: Expression profiling by high throughput sequencing; Other.
Genome-wide CRISPR screen for comprehensive identification of human factors involved in alternative polyadenylation based on differential localization of CD47 protein
GEO Series GSE288919. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
Regulation of alternative polyadenylation by the C2H2-zinc finger protein Sp1
GEO Series GSE165772. Homo sapiens. 30 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
DNA Methylation Regulates Alternative Polyadenylation via CTCF and the Cohesin Complex
GEO Series GSE131606. Homo sapiens. 16 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
ALS-Associated TDP-43 Dysfunction Compromises UPF1-Dependent mRNA Metabolism Pathways Including Alternative Polyadenylation and 3’UTR Length
GEO Series GSE304550. Homo sapiens. 16 samples. Type: Expression profiling by high throughput sequencing.
Elevated pre-mRNA 3' end processing activity in cancer cells renders vulnerability to inhibition of cleavage and polyadenylation [ChrRNA-seq]
GEO Series GSE218545. Homo sapiens. 8 samples. Type: Expression profiling by high throughput sequencing.
Next Generation Sequencing of Wild-Type C57BL/6J Mouse Cardiac Polyadenylated RNA
GEO Series GSE55788. Mus musculus. 4 samples. Type: Expression profiling by high throughput sequencing.
Multiplexed single-cell characterization of alternative polyadenylation regulators (3PRACE)
GEO Series GSE269594. Homo sapiens. 28 samples. Type: Other.
Ataxin-2, Twenty-four and Dicer-2 are components of a non-canonical cytoplasmic polyadenylation complex
GEO Series GSE189868. Drosophila melanogaster. 17 samples. Type: Expression profiling by high throughput sequencing.
Transcriptional Pause Sites Delineate Stable Nucleosome-Associated Premature Polyadenylation Suppressed by U1 snRNP [2P-seq]
GEO Series GSE100536. Mus musculus. 12 samples. Type: Other.
Next Generation Sequencing of Wild-Type FVB/NJ Mouse Primary Cardiomyocyte and Cardiac Nonmyocyte Polyadenylated RNA and small RNA
GEO Series GSE58453. Mus musculus. 12 samples. Type: Expression profiling by high throughput sequencing.
An integrin α3β1-CSTF3 signaling axis regulates alternative polyadenylation of Mmp9 mRNA
GEO Series GSE318492. Mus musculus. 6 samples. Type: Expression profiling by high throughput sequencing.
Quant-seq analysis of differential gene expression and polyadenylation site usages in caused by inhibition of CDK12 and CDK13 using THZ531 in THP-1 cells (3’ Quant-seq)
GEO Series GSE141376. Homo sapiens. 4 samples. Type: Expression profiling by high throughput sequencing; Other.
Next Generation Sequencing of Wild-Type C57BL/6J and FVB/NJ Mouse Cardiac Polyadenylated RNA and Small RNA
GEO Series GSE55792. Mus musculus. 111 samples. Type: Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing.
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Allen Brain Atlas
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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.