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102
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ShareScore release 0.9.0
Dataset results
102 results for “Dual RNA-seq”
External RNA-seq dataset for manuscript entitled "Downregulated dual-specificity protein phosphatase 1 in ovarian carcinoma: a comprehensive study with multiple methods"
<p>RNA-seq dataset of ovarian cancer from TCGA and normal ovary from GTEx database</p>
Data from: Challenges and solutions for analyzing dual RNA-seq data for non-model host/pathogen systems
1. Dual RNA-seq simultaneously profiles the transcriptomes of a host and pathogen during infection and may reveal the mechanisms underlying host-pathogen interactions. Dual RNA-seq is inherently a mixture of transcripts from at least two species (host and pathogen), so this mixture must be computationally sorted into host and pathogen components. Sorting relies on aligning reads to respective reference genomes, which may be unavailable for both species in non-model host-pathogen pairs. This lack of genomic resources may present challenges to applying dual RNA-seq to non-model systems. 2. We assessed the accuracy of alignments of dual RNA-seq when using the genomic resources of a closely-related species to the species of interest by simulating datasets of mixed transcripts from a host and pathogen. Specifically, we compared how different aligners performed across different proportions of pathogen to host transcripts and across variation in the genetic distance between the pathogen genome and reference genome. We performed extensive analyses for a host plant with fungal pathogen, and then we extended the plant-fungus results by repeating key analyses in vertebrate (human)-fungus and vertebrate-bacterium systems. 3. Aligners that were able to map pathogen transcripts to the reference genome of a species closely related to the pathogen (a "related reference genome") also mismapped transcripts originating from the host to the pathogen's related reference genome, which results in regions where this occurred being quantified as overexpressed. If a host reference genome was available, we show that to minimize host transcript mismapping while retaining the ability to map pathogen transcripts, one could concatenate it with the pathogen's related reference genome, then map transcripts to the concatenated genomes. If a host genome was unavailable, assembling reads de novo prior to aligning substantially decreased host read mismapping, while retaining the ability to map pathogen transcripts to a related reference genome. 4. The application of dual RNA-seq to organisms without reference genomes is currently limited. We propose an analytical workflow that leverages the genomic resources of species closely related to species of interest to facilitate application of dual RNA-seq to reveal the mechanisms of host-pathogen interactions across a wider array of systems.
Data from: Challenges and solutions for analyzing dual RNA-seq data for non-model host/pathogen systems
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A dual role for PSIP1/LEDGF in T-cell acute lymphoblastic leukemia [RNA-seq]
GEO Series GSE253138. Homo sapiens; Mus musculus. 42 samples. Type: Expression profiling by high throughput sequencing.
Dual RNA-seq – sRNA profiling in various cell types
GEO Series GSE67947. Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344; Homo sapiens; Sus scrofa; Mus musculus. 89 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.
Rapid CRISPR/Cas12a-based dual-crRNA library screening in high fidelity reveals novel genetic interactions during hepatocarcinogenesis [RNA-Seq]
GEO Series GSE236826. Mus musculus. 12 samples. Type: Expression profiling by high throughput sequencing.
H4K20me1 plays a dual role in transcriptional regulation during regeneration and axis patterning of Hydra [RNA-seq]
GEO Series GSE205916. Hydra vulgaris. 30 samples. Type: Expression profiling by high throughput sequencing.
PALI1 Promotes Tumor Growth through Competitive Recruitment of PRC2 to G9A-target Chromatin for Dual Epigenetic Silencing [RNA-Seq II]
GEO Series GSE182144. Homo sapiens. 12 samples. Type: Expression profiling by high throughput sequencing.
RNA-seq on dual-FACS sorted Drosophila Intestinal stem cell and Enteroblast, and effect of SPEN loss of function on gene expression
GEO Series GSE84367. Drosophila melanogaster. 11 samples. Type: Expression profiling by high throughput sequencing.
Dual RNA-seq – Comparative RNA-seq (in vitro medium shift experiment)
GEO Series GSE67949. Salmonella enterica subsp. enterica serovar Typhimurium. 18 samples. Type: Expression profiling by high throughput sequencing.
Enhancing Precise Genome Editing in Human Pluripotent Stem Cells through Dual Inhibition of DNA Damage Response and Repair Pathways [RNA-seq]
GEO Series GSE247589. Homo sapiens. 5 samples. Type: Expression profiling by high throughput sequencing.
Dual RNA-seq – Dual RNA-seq of further sRNA mutants
GEO Series GSE67952. Homo sapiens; Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344. 42 samples. Type: Expression profiling by high throughput sequencing.
Granuloma Dual RNA-Seq Reveals Composite Transcriptional Programs Driven by Neutrophils and Necrosis within Tuberculous Granulomas
GEO Series GSE289727. Danio rerio; Mycobacterium marinum. 17 samples. Type: Expression profiling by high throughput sequencing.
Dual RNA-Seq Analysis of Trichophyton rubrum and HaCat Keratinocyte Co-Culture Highlights Important Genes for Fungal-Host Interaction
GEO Series GSE110073. Trichophyton rubrum; Homo sapiens. 9 samples. Type: Expression profiling by high throughput sequencing.
Dual RNA-seq – Comparative Dual RNA-seq in pig macrophages
GEO Series GSE67948. Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344; Sus scrofa. 33 samples. Type: Expression profiling by high throughput sequencing.
Genome-wide profiling reveals a dual role for histone H2A monoubiquitylation at Polycomb-repressed and enhancer chromatin [RNA-seq]
GEO Series GSE222473. Caenorhabditis elegans. 8 samples. Type: Expression profiling by high throughput sequencing.
Dual RNA-seq of chlamydial and host cell transcriptomes during nutritional stress
GEO Series GSE179003. Homo sapiens; Chlamydia trachomatis L2/434/Bu. 18 samples. Type: Expression profiling by high throughput sequencing.
Rejuvenation of mesenchymal stem cells by human peripheral blood lymphocytes: A dual-mechanism for targeting senescent cell clearance and promoting cell proliferation in a coculture system [RNA-Seq]
GEO Series GSE307002. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
CBX4 in Lung Adenocarcinoma: A Dual-Edged Sword in Transcriptional Regulation and Tumor Progression [RNA-seq]
GEO Series GSE252181. Homo sapiens. 3 samples. Type: Expression profiling by high throughput sequencing.
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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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.