Comprehensive catalog of dendritically localized mRNA isoforms from sub-cellular sequencing of single mouse neurons
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA475141 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7276970_1.fastq.gz | Fastqsanger.gz | |||
| SRR7276970_2.fastq.gz | Fastqsanger.gz | |||
| SRR7276980_1.fastq.gz | Fastqsanger.gz | |||
| SRR7276980_2.fastq.gz | Fastqsanger.gz | |||
| SRR7276990_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 64 |
Similar Datasets
Project description:To compare the RNAs present in dendrites and somas of individual neurons, we manually separated the dendrites and soma of primary mouse hippocampal neurons using a micropipette and performed RNA-sequencing on each subcellular fraction such that we obtained the subcellular transcriptomes of the same cell.
2019-01-07 | GSE115480 | GEO
Project description:BACKGROUND:RNA localization involves cis-motifs that are recognized by RNA-binding proteins (RBP), which then mediate localization to specific sub-cellular compartments. RNA localization is critical for many different cell functions, e.g., in neuronal dendrites, localization is a critical step for long-lasting synaptic potentiation. However, there is little consensus regarding which RNAs are localized and the role of alternative isoforms in localization. A comprehensive catalog of localized RNA can help dissect RBP/RNA interactions and localization motifs. Here, we utilize a single cell sub-cellular RNA sequencing approach to profile differentially localized RNAs from individual cells across multiple single cells to help identify a consistent set of localized RNA in mouse neurons. RESULTS:Using independent RNA sequencing from soma and dendrites of the same neuron, we deeply profiled the sub-cellular transcriptomes to assess the extent and variability of dendritic RNA localization in individual hippocampal neurons, including an assessment of differential localization of alternative 3'UTR isoforms. We identified 2225 dendritic RNAs, including 298 cases of 3'UTR isoform-specific localization. We extensively analyzed the localized RNAs for potential localization motifs, finding that B1 and B2 SINE elements are up to 5.7 times more abundant in localized RNA 3'UTRs than non-localized, and also functionally characterized the localized RNAs using protein structure analysis. CONCLUSION:We integrate our list of localized RNAs with the literature to provide a comprehensive list of known dendritically localized RNAs as a resource. This catalog of transcripts, including differentially localized isoforms and computationally hypothesized localization motifs, will help investigators further dissect the genome-scale mechanism of RNA localization.
| S-EPMC6344992 | biostudies-literature
Project description:Surgery still remains the mainstay of treatment for localized colorectal cancer. However, nearly 30% of patients with localized colorectal cancer (stage II and stage III) will present with recurrence. Tumor progression is mediated by both intrinsic genetic changes and by extrinsic epigenetic and host environmental factors, including interactions with the immune system. Several studies demonstrated that tumor infiltrating memory T-cells and type, density and location of infiltrating T cells are better predictors of disease-free survival in patients with CRC compared to the standard TNM staging. These data suggest that tumor invasion and progression are more accurately predicted by immune response in the primary tumor. In addition, mismatch repair (MMR)-deficient tumors are characterized a priori by a higher frequency of tumor infiltrating lymphocytes and are associated with significantly improved prognosis. Recently, Stotz et al showed that the preoperative lymphocyte to monocyte ratio in peripheral blood samples predicts clinical outcome in patients with stage III colon cancer. So far there is no comprehensive analysis of the immune-landscape in CRC.
The aim of the current project is to identify a comprehensive panel of immunomarkers in localized colorectal cancer (stage II and stage III) applicable for the detection of patients at high risk of recurrence. For the first time, specific tumor-infiltrating immune cells, mismatch repair protein expression in tumor tissue and preoperative blood based inflammatory markers from routine blood counts in corresponding peripheral blood samples and known clinicopathological features will be correlated with outcome in 300 localized CRC patients.
| 2166592 | ecrin-mdr-crc
Project description:To identify aberrant splicing isoforms and potential neoantigens, we performed full-length cDNA sequencing of lung adenocarcinoma cell lines using a long-read sequencer MinION. We constructed a comprehensive catalog of aberrant splicing isoforms and detected isoform-specific peptides using proteome analysis.
2020-12-09 | PXD019915 | JPOST Repository
Project description:Subtyping sub-Saharan esophageal squamous cell carcinoma by comprehensive molecular analysis
| PRJNA401208 | ENA
Project description:Recent studies hint that endogenous dsRNA plays an unexpected role in cellular signaling. However, a complete understanding of the mechanisms underlying endogenous dsRNA signaling is hindered by an incomplete annotation of dsRNA-producing genes. In order to identify all dsRNAs expressed in C. elegans, we developed a bioinformatics pipeline that identifies dsRNA by detecting clustered RNA editing sites, which are strictly limited to long dsRNA substrates of Adenosine Deaminases that act on RNA (ADAR). Using a combination of alignment algorithms to map both unique and repetitive reads, we detected as many as 664 editing-enriched regions (EERs). Most EERs were associated with protein-coding genes, with ~1.7% of all C. elegans mRNAs containing an EER, located primarily in introns and 3’UTRs. Introns having an embedded EER were up to 9-fold longer than the average C. elegans intron. A significant fraction of EERs were located less than 1000 base pairs downstream of protein-coding genes and likely represent a previously undetected population of edited 3’UTRs. Many EERs are predicted to possess strong internal secondary structures as well as sequence complementarity with other EERs, indicative of both intramolecular and intermolecular dsRNAs. In addition to numerous EERs associated with coding genes, we identified a population of prospective noncoding EERs, distant from protein coding genes with no overlapping genome annotation and little to no coding potential. By combining next-generation RNA sequencing with freely available bioinformatics tools, our workflow provides an easily accessible approach for the identification of dsRNAs, and more importantly, a comprehensive catalogue of the C. elegans dsRNAome.
2015-04-09 | GSE61564 | GEO
Project description:The Plasmodium falciparum human malaria parasite genome is incompletely annotated and does not accurately represent the transcriptomic diversity of this species. To address this need, we performed long-read transcriptomic sequencing. To increase representation of mRNA isoforms expressed during intraerythrocytic stages, RNA was extracted from samples taken at time-points from synchronized cultures. 5 capped mRNA was enriched and converted to cDNA library. The cDNA libraries were sequenced on Nanopore and PacBio long-read platforms. Candidate non-redundant isoforms were annotated from each library dataset for creating a new transcript annotation catalog. Isoforms with alternative 5 ends represented the largest class of novel isoforms, although the majority of these do not seem to represent the products of alternative transcription initiation events. We suggest that most isoforms do not encode protein isoforms and instead represent RNA decay products.
2022-10-26 | GSE186109 | GEO
Project description:Modern techniques in molecular biology, genomics, and mass spectrometry-based proteomics have identified a large number of novel histone posttranslational modifications (PTMs), many of whose functions are still under intense investigation. Here, we catalog histone PTMs under two classes: first, those whose functions have been fairly well studied and, second, those PTMs that have been more recently identified but whose functions remain unclear. We hope that this will be a useful resource for researchers from all biological or technical backgrounds, aiding in their chromatin and epigenetic pursuits.
| S-EPMC4563710 | biostudies-other
Project description:The retina, a complex neural tissue, encompasses a vast diversity of over 100 distinct cell types, each characterized by unique features such as morphology, function, location, and transcriptomic profiles. However, the extent of mRNA alternative splicing within individual cell types in the retina remains largely uncharted territory. To bridge this knowledge gap, we employed single-cell RNA sequencing, utilizing both short-read and long-read high-throughput technologies. Our comprehensive analysis profiled the transcriptomes of 29,191 mouse retina cells, resulting in a dataset comprising 1.54 billion Illumina short reads and 1.40 billion Oxford Nanopore long reads. Remarkably, this exploration unveiled a staggering 44,325 transcript isoforms, with 38% of them representing entirely novel discoveries and 17% exhibiting cell-class-specific expression patterns. Intriguingly, while many isoforms were expressed across various cell types, their distribution often displayed variability among them. This research substantially enriches the catalog of transcript isoforms, laying the groundwork for further investigations into the role of alternative splicing in retinal biology and its implications for related diseases. It represents a crucial step toward unraveling the intricacies of retinal function and offers promising insights into the molecular mechanisms underlying retinal disorders.
2024-11-04 | GSE255520 | GEO
Project description:Genes encoding cell-surface proteins are crucial for nervous system development and are implicated in neurological disorders. These genes produce alternative mRNA isoforms which remain poorly characterized, impeding our understanding of how disease-associated mutations cause pathology. Here we introduce a new strategy to reveal complete full-length isoform portfolios encoded by individual genes. Using our strategy to catalog diversity of neural cell surface molecules, we identified thousands of unannotated isoforms expressed in retina and brain. Mass spectrometry revealed that many newly-discovered proteins are expressed on the cell surface in vivo. Remarkably, we discover that the major isoform of the retinal degeneration gene CRB1 was previously overlooked. This isoform is the only one expressed by photoreceptors, the affected cells in CRB1 disease. By generating mouse mutants, we reveal a function for this isoform at the cell-cell junctions of the retinal outer limiting membrane, and we provide a causal link between loss of this Crb1 isoform and photoreceptor death. Therefore, our isoform identification strategy accelerates discovery of new gene functions relevant to disease.
2020-08-11 | PXD017290 | Pride