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78 results for “fusion transcripts”
Expression of a corA-lacZ transcriptional fusion in Salmonella
<p>A <i>corA-lacZ</i> transcriptional fusion was shown to be activated by RpoS when<i> Salmonella</i> is grown to stationary phase in LB rich medium (Metaane<i> et al</i>. 2022)</p><p>Here, expression of the <i>corA-lacZ</i> fusion was evaluated in <i>Salmonella</i> wild-type strain and <i>rpoS</i> mutant grown to stationary phase in LB medium containing different concentrations of Mg and in minimal medium M63 starved or not for Mg. RpoS was required fort optimal expression of the fusion in these three environmental conditions and level of expression was slightly higher when the extracellular magnesium concentration was low.</p><p>Metaane S, Monteil V, Ayrault S, Bordier L, Levi-Meyreuis C, Norel F. The stress sigma factor sigmaS/RpoS counteracts Fur repression of genes involved in iron and manganese metabolism and modulates the ionome of <i>Salmonella enterica</i> serovar Typhimurium. PloS one 2022, 17(3):e0265511.</p><p><strong>This work was supported by the French National Research Agency (ANR-19-CE44-0005-01, PERIOMET project).</strong></p><p>See also:</p><p>Metaane S, Monteil V, Douché T, Giai Gianetto Q, Matondo M, Maufrais C, Norel F. Loss of CorA, the primary magnesium transporter of <i>Salmonella, </i>is alleviated by MgtA and PhoP-dependent compensatory mechanisms. PloS one 2023, 18(9):e0291736.</p><p>NOREL, MONTEIL, & METAANE. (2023). Towards new elements involved in magnesium and cobalt trafficking in Salmonella serovar Typhimurium. Zenodo. <a href="https://doi.org/10.5281/zenodo.8086417">https://doi.org/10.5281/zenodo.8086417</a></p><p>NOREL, METAANE, & MONTEIL. (2023). Detection of physical interactions between the magnesium transporter CorA and other Cor proteins using the bacterial two hybrid system (BACTH). Zenodo. <a href="https://doi.org/10.5281/zenodo.7994619">https://doi.org/10.5281/zenodo.7994619</a></p><p>NOREL Francoise, MONTEIL Veronique, DOUCHE Thibaut, & MATONDO Mariette. (2023). Global effects of deletions of the sitABCD, mntH, cbiMNQO and corA genes, encoding transporters for manganese, cobalt and magnesium on protein abundance in Salmonella enterica serovar Typhimurium grown to stationary phase in LB. [Data set]. Zenodo. <a href="https://doi.org/10.5281/zenodo.8279780">https://doi.org/10.5281/zenodo.8279780</a></p>
Benchmarking Illumina RNA-seq fusion transcript detection methods - cancer cell lines RNA-seq
<p>Cancer cell line RNA-seq data (reads or names of reads from CCLE data) used for benchmarking Illumina-based fusion detection methods as used in:</p> <p>Haas, B.J., Dobin, A., Li, B. <em>et al.</em> Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods. <em>Genome Biol</em> <strong>20</strong>, 213 (2019). https://doi.org/10.1186/s13059-019-1842-9</p> <p> </p> <p>For CCLE data, direct sharing of fastq files was not possible. CCLE data must be obtained from:</p> <p> https://portals.broadinstitute.org/ccle/home</p> <p>Instead, the identifiers for the reads leveraged as part of our study are made available, and these reads can be extracted from the CCLE fastq files directly once obtained from the primary source.</p> <p><br>For the non-CCLE data, the exact reads leveraged by our study are made directly available here in fastq format.</p>
ScaR — a tool for sensitive detection of known fusion transcripts
<p>Use scaffold re-aligning approach to detect the prevalence and recurrence of known fusion transcripts across samples</p>
Detection of fusion transcripts and their genomic breakpoints from RNA sequencing data - Table S03 - All detected SVs.xlsx
<p>Large concatenated results table on all samples of the Dr. Disco study.</p> <p> </p>
Benchmarking Illumina RNA-seq fusion transcript detection methods - simulated 101 base PE reads
<p>Simulated 101 base paired-end reads used for benchmarking Illumina-based fusion detection methods as used in:</p> <p>Haas, B.J., Dobin, A., Li, B. <em>et al.</em> Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods. <em>Genome Biol</em> <strong>20</strong>, 213 (2019). https://doi.org/10.1186/s13059-019-1842-9</p> <p> </p>
FusionVAC22_01: Fusion Transcript-based Peptide Vaccine Combined with Immune Checkpoint Inhibition
ClinicalTrials.gov study NCT05937295. IPD Sharing: NO. Countries: 1. Publications: 1.
Multimodal single-cell analyses reveal distinct fusion-regulated transcriptional programs in Ewing sarcoma.
<p>All processed data for analysis at <a href="https://github.com/furlan-lab/EwS_multiome">https://github.com/furlan-lab/EwS_multiome</a></p>
Data from: Fusion transcript discovery in formalin-fixed paraffin-embedded human breast cancer tissues reveals a link to tumor progression
The identification of gene fusions promises to play an important role in personalized cancer treatment decisions. Many rare gene fusion events have been identified in fresh frozen solid tumors from common cancers employing next-generation sequencing technology. However the ability to detect transcripts from gene fusions in RNA isolated from formalin-fixed paraffin-embedded (FFPE) tumor tissues, which exist in very large sample repositories for which disease outcome is known, is still limited due to the low complexity of FFPE libraries and the lack of appropriate bioinformatics methods. We sought to develop a bioinformatics method, named gFuse, to detect fusion transcripts in FFPE tumor tissues. An integrated, cohort based strategy has been used in gFuse to examine single-end 50 base pair (bp) reads generated from FFPE RNA-Sequencing (RNA-Seq) datasets employing two breast cancer cohorts of 136 and 76 patients. In total, 118 fusion events were detected transcriptome-wide at base-pair resolution across the 212 samples. We selected 77 candidate fusions based on their biological relevance to cancer and supported 61% of these using TaqMan assays. Direct sequencing of 19 of the fusion sequences identified by TaqMan confirmed them. Three unique fused gene pairs were recurrent across the 212 patients with 6, 3, 2 individuals harboring these fusions respectively. We show here that a high frequency of fusion transcripts detected at the whole transcriptome level correlates with poor outcome (P<0.0005) in human breast cancer patients. This study demonstrates the ability to detect fusion transcripts as biomarkers from archival FFPE tissues, and the potential prognostic value of the fusion transcripts detected.
Data from: Fusion transcript discovery in formalin-fixed paraffin-embedded human breast cancer tissues reveals a link to tumor progression
Open the record for dataset details and reuse information.
The TAZ-CAMTA1 and YAP-TFE3 fusion proteins modulate the basal TAZ/YAP transcriptional program by recruiting the Ada2a-containing histone acetyltransferase complex [rnaseq_3T3]
GEO Series GSE152736. Mus musculus. 24 samples. Type: Expression profiling by high throughput sequencing.
MLL1 and MLL fusion proteins play distinct roles in regulating MLLleukemic transcription program [RNA-Seq]
GEO Series GSE68822. Mus musculus. 10 samples. Type: Expression profiling by high throughput sequencing.
Transcriptional and epigenetic rewiring by the NUP98::KDM5A fusion oncoprotein directly activates CDK12 (nascent RNA-Seq)
GEO Series GSE255805. Mus musculus. 6 samples. Type: Expression profiling by high throughput sequencing; Other.
Hoxblinc lncRNA reprograms CTCF-independent TADs to drive leukemic transcription and HSC dysregulation in NUP98 fusion transformed leukemia [ATAC-Seq]
GEO Series GSE269216. Mus musculus. 10 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
The TAZ-CAMTA1 and YAP-TFE3 fusion proteins modulate the basal TAZ/YAP transcriptional program by recruiting the Ada2a-containing histone acetyltransferase complex [RNA-seq]
GEO Series GSE168205. Homo sapiens. 12 samples. Type: Expression profiling by high throughput sequencing.
MLL1 and MLL fusion proteins play distinct roles in regulating MLLleukemic transcription program
GEO Series GSE68823. Mus musculus. 24 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
Transcriptional properties of estrogen receptor fusion genes.
GEO Series GSE116170. Homo sapiens. 15 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
Seclidemstat blocks the transcriptional function of multiple FET-fusion oncoproteins
GEO Series GSE267611. Homo sapiens. 70 samples. Type: Expression profiling by high throughput sequencing.
Differentiation related tumorigenic potential and transcriptional profile of the fusion reprogrammed mouse cancer cell lines
GEO Series GSE30965. Mus musculus. 5 samples. Type: Expression profiling by array.
Breakpoint analysis of transcriptional and genomic profiles uncovers novel gene fusions spanning multiple human cancer types (exon expression)
GEO Series GSE39287. Homo sapiens. 16 samples. Type: Expression profiling by array.
ERK5 Regulates Muscle Cell Fusion through Klf Transcription Factors
GEO Series GSE25827. Mus musculus. 10 samples. Type: Expression profiling by array.
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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.