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199 results for “RNA-seq, splicing”
Data for manuscript "rMATS-turbo: an efficient and flexible computational tool for alternative splicing analysis of large-scale RNA-seq data"
<p>Output files generated by rMATS-turbo for the two example datasets described in the manuscript titled "rMATS-turbo: an efficient and flexible computational tool for alternative splicing analysis of large-scale RNA-seq data".</p> <table> <tbody> <tr> <td>File</td> <td>Description</td> <td>Cell lines</td> <td>BioProject</td> </tr> <tr> <td>PC3E-GS689.tar.gz</td> <td>Compressed folder containing all 36 rMATS-turbo output files for Example 1 described in the manuscript</td> <td>PC3E and GS689 cell lines</td> <td>PRJNA438990</td> </tr> <tr> <td>CCLE.tar.gz</td> <td>Compressed folder containing all 36 rMATS-turbo output files for Example 2 described in the manuscript</td> <td>1,019 CCLE human cancer cell lines</td> <td>PRJNA523380</td> </tr> </tbody> </table> <p>A detailed description of the output files is available in the manuscript and the rMATS-turbo software GitHub repository (https://github.com/Xinglab/rmats-turbo).</p>
Simulated RNA-seq data for differential splicing analysis with covariates
<p>The repository includes alignments of simulated RNA-seq data for evaluating differential splicing detection with covariates. Starting from an empirical transcript expression matrix trained on an RNA-seq data set from lung fibroblasts (GenBank A# SRR493366) and using GENCODE v.41 as reference, 11.5 million 100 bp long paired-end reads were generated per sample, from 2,000 genes with two or more expressed isoforms. RNA-seq data was simulated for one ‘condition’, with values ‘control’, ‘disease’ and ‘stage2’, with one covariate, ‘biological sex’, with values ‘M’ and ‘F’. 5 samples each were simulated for each (condition x sex) category. Changes were simulated in the expression (DE) and/or the splicing ratio (DS) of genes as follows. Changes in expression (DE) were simulated by either halving or doubling the expression level of the gene. Changes in splicing ratios (DS) were simulated by swapping the expression levels of the gene’s top two transcript isoforms. All RNA-seq data was mapped to the hg38 genome with the spliced alignment tool STAR v2.7.10a.</p> <p> <em><u>Pairwise comparison alignment set</u></em>: Differences due to ‘condition’ between two states, ‘control’ and ‘disease’, were simulated at 600 genes, including 200 DE, 200 DS and 200 DE+DS genes. Differences in ‘biological sex’ (covariate) were represented as changes in 300 genes, including 100 from each of the DS, DE and DE+DS categories. Hence, the target gene set for differential splicing ratio (DSR)<em> pairwise comparisons </em>consists of the pooled 200 DS and 200 DS+DE genes differentially spliced between the ‘control’ and ‘disease’ states, while for differential splicing abundance (DSA)<em> pairwise comparisons </em>the target gene set is the set of 600 modified genes, 200 in each of the DS, DE and DS+DE categories.</p> <p> <em><u>Multiway (3-way) comparison alignment set:</u></em> Additional changes between ‘disease’ and ‘stage2’ were made to 100 of the previously modified genes, as well as to a set of 200 additional genes not encountered previously, for each of the categories DE, DS and DE+DS. Therefore, for <em>DSR three-way comparisons</em>, the target gene set represents the 800 genes simulated as being DS or DE+DS between any of the ‘control’, ‘disease’ and ’stage2’ categories, while for the <em>multi-way DSA comparisons</em> the target is the full set of 1,200 genes (400 DE, 400 DS and 400 DE+DS) simulated to have changed between any of the 'control', 'disease’ and ‘stage2’ states.</p> <p> <em><u>Further details:</u></em> See the ‘key’ directories in each package for the gene lists.</p>
RNA-seq and RT-qPCR data showing MDF role in RNA splicing and gene expression control in Arabidopsis
<p>Plants respond to environmental stresses through controlled stem cell maintenance and meristem activity. One level of transcriptional control is RNA alternative splicing. However the mechanistic link between stress, meristem function and RNA splicing is poorly understood. The MERISTEM-DEFECTIVE (MDF)/DEFECTIVELY ORGANIZED TRIBUTARIES (DOT2) gene of Arabidopsis encodes a SR-related family protein, required for meristem function and leaf vascularization, and is the likely orthologue of the human SART1 and yeast snu66 splicing factors. MDF is required for the correct splicing and expression of key transcripts associated with root meristem function. We identified RSZ33 and ACC1, both known to regulate cell patterning, as splicing targets required for MDF function in the meristem. MDF expression is modulated by osmotic and cold stress, associated with differential splicing and specific isoform accumulation and shuttling between nucleus and cytosol, and acts in part via a splicing target SR34. We propose a model in which MDF controls splicing in the root meristem to promote stemness and repress stress response and cell differentiation pathways.</p>
RNA-seq and RT-qPCR data showing MDF role in RNA splicing and gene expression control in Arabidopsis
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A total RNA-Seq screen reveals that the splicing inhibitor Isoginkgetin blocks transcription elongation
GEO Series GSE86857. Homo sapiens. 80 samples. Type: Expression profiling by high throughput sequencing.
Variation of C-terminal domain governs RNA polymerase II genomic locations and alternative splicing in eukaryotic transcription (RNA-Seq)
GEO Series GSE252260. Homo sapiens. 4 samples. Type: Expression profiling by high throughput sequencing.
SFSWAP is a negative regulator of OGT intron detention and global pre-mRNA splicing [RNA-seq II]
GEO Series GSE277951. Homo sapiens. 12 samples. Type: Expression profiling by high throughput sequencing.
Alternative splicing of a chromatin modifier alters the transcriptional regulatory programs of embryonic stem cell maintenance and neuronal differentiation [RNA-seq]
GEO Series GSE241377. Mus musculus. 18 samples. Type: Expression profiling by high throughput sequencing.
Mis-splicing of mitotic regulators sensitizes SF3B1-mutated human HSCs to CHK1 inhibition [RNA-seq]
GEO Series GSE263299. Homo sapiens. 10 samples. Type: Expression profiling by high throughput sequencing.
A dual role for the RNA helicase DHX34 in NMD and pre-mRNA splicing and its role in familial AML/MDS (RNA-Seq II)
GEO Series GSE204985. Homo sapiens. 9 samples. Type: Expression profiling by high throughput sequencing.
Expression profiling by RNA-seq of LNCaP cells expressing wild-type androgen receptor (AR-WT), AR-V7 splice variant or mutant AR-Q641X
GEO Series GSE158557. Homo sapiens. 24 samples. Type: Expression profiling by high throughput sequencing.
Androgen Receptor splice variant V7 (AR-V7) mediates AR signalling in castration resistant prostate cancer (CRPC) [RNA-seq]
GEO Series GSE143905. Homo sapiens. 12 samples. Type: Expression profiling by high throughput sequencing.
Multiplexed primer extension sequencing: A targeted RNA-seq method that enables high-precision quantitation of mRNA splicing isoforms and rare pre-mRNA splicing intermediates
GEO Series GSE126583. Schizosaccharomyces pombe. 2 samples. Type: Other.
Aberrant EVI1 splicing contributes to EVI1-rearranged leukemia (RNA-Seq)
GEO Series GSE202208. Mus musculus. 2 samples. Type: Expression profiling by high throughput sequencing.
Filtering of RNA-seq datasets and differences between cell types in global coordination of splicing and proportion of highly expressed genes
GEO Series GSE85458. Mus musculus. 0 samples. Type: Expression profiling by high throughput sequencing; Third-party reanalysis.
SFSWAP is a negative regulator of OGT intron detention and global pre-mRNA splicing [RNA-seq I]
GEO Series GSE277950. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
The histone variant macroH2A1 regulates key genes for myogenic cell fusion in a splice-isoform dependent manner [RNA-Seq]
GEO Series GSE147590. Mus musculus. 9 samples. Type: Expression profiling by high throughput sequencing.
A CLK3-HMGA2 alternative splicing axis impacts human hematopoietic stem cell molecular identity throughout development [HSC and PROG RNA-seq]
GEO Series GSE109089. Homo sapiens. 21 samples. Type: Expression profiling by high throughput sequencing.
Methylation Affects Transposition and Splicing of a Large CACTA Transposable Element From a MYB Transcription Factor Regulating Anthocyanin Synthase (ANS) Genes in Soybean Seed Coats (RNA-Seq)
GEO Series GSE60593. Glycine max. 14 samples. Type: Expression profiling by high throughput sequencing.
LARP6 promotes carcinogenic features of triple negative breast cancer cell line by directly modulating alternative splicing of associated genes [RNA-Seq]
GEO Series GSE248131. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
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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.