Trans-Seq for mammalian retinotectal circuit mapping
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA835142 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR19088048.fastq.gz | Fastqsanger.gz | |||
| SRR19088049.fastq.gz | Fastqsanger.gz | |||
| SRR19088050.fastq.gz | Fastqsanger.gz | |||
| SRR19088051.fastq.gz | Fastqsanger.gz | |||
| SRR19088052.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 16 |
Similar Datasets
Project description:The mouse visual system serves as an accessible model to understand mammalian circuit wiring. Despite rich knowledge in retinal circuits, the long-range connectivity map from distinct retinal ganglion cell (RGC) types to diverse brain neuron types remains unknown. Here we developed an integrated approach, named Trans-Seq, to map RGC to superior collicular (SC) circuits. Trans-Seq combines a fluorescent anterograde transsynaptic tracer, consisting of codon-optimized wheat germ agglutinin fused to mCherry, with single-cell RNA Sequencing. We used Trans-Seq to classify SC neuron types innervated by genetically-defined RGC types and predicted a neuronal pair from αRGCs to Nephronectin-positive wide-field neurons (NPWFs). We validated this connection using genetic labeling, electrophysiology, and retrograde tracing. We then utilized transcriptomic data from Trans-Seq to identify Nephronectin as a determinant for selective synaptic choice from αRGC to NPWFs via binding to Integrin-α8β1. The Trans-Seq approach can be broadly applied for postsynaptic circuit discovery from genetically-defined presynaptic neurons.
2022-05-07 | GSE202257 | GEO
Project description:MYC oncogenes are activated in broad spectrum of human malignancies and transcriptionally reprogram the genome to drive cancer cell growth. Given this it is unclear if targeting a single effector will have a therapeutic benefit. MYC activates the polyaminehypusine circuit, which post-translationally modifies the translation factor eIF5A. The hypusine axis has been proposed to suppress tumorigenesis. Here we report essential roles for hypusinated eIF5A in the development and maintenance of Myc-driven lymphoma, where loss of eIF5A hypusination abolishes malignant transformation. Mechanistically, integrating RNA-seq, Ribo-seq and proteomic analyses revealed that efficient translation of select targets is dependent upon eIF5A hypusination, including key regulators of G1 to S phase cell cycle progression. Notably, this circuit controls Myc’s proliferative response at several levels, and it is activated across multiple tumor types. These findings suggest the hypusine circuit as a therapeutic target for a broad spectrum of malignancies.
2024-01-26 | PXD031361 | Pride
Project description:Nanobody is one special type of single-domain antibody fragment with multiple advantages over traditional antibody. Our previous work established linear-double-stranded DNA (ldsDNA, or PCR amplicon) as novel biological parts for building AND gate genetic circuits in mammalian cells. During this AND-gate circuit formation process, the co-transfected up- and down-stream ldsDNAs could be linked together to form intact gene expression cassette. Here, we employed this ldsDNA-based AND-gate (LBAG) strategy to construct nanobody library in mammalian cells. The sequence complexity of complementary determining regions (CDRs) was introduced into ldsDNA by PCR amplification. After being co-transfected into mammalian cells, the up- and down- stream ldsDNAs undergo AND gate linkage and form full nanobody coding regions, containing CDR1-3. High throughput sequencing identified 22,173 unique oligonucleotide sequences in total generated by this strategy. Thus, we developed a novel method to construct nanobody library, which is a start point for building high content nanobody library in mammalian cells.
2021-07-24 | GSE155159 | GEO
Project description:We report the characterization of a synthetic genetic circuit using RNA-Seq data. Data is collected for all input inducer combinations and cells harboring the circuit are grown in two conditions (14 ml culture tubes and 250 ml Erlenmeyer flasks).
2017-09-29 | GSE88835 | GEO
Project description:Transcriptome Mapping of Internal N7-methylguanosine Methylome in Mammalian mRNA
| PRJNA445453 | ENA
Project description:Deep Sequencing of mRNA from Drosophila melanogaster, Drosophila Sechellia, and their F1 hybrid. These data were generated in a study to analyze the extent and specificity of trans-splicing in Drosophila. mRNA-seq libraies were prepared from poly(A)+ RNA prepared from whole F1 hybrids of D. melanogaster and D. sechellia (female 0-3d post eclosion). Separate control libraries were prepared from D. melanogaster and D. sechellia total RNA (mixed before library preparation). The results of this study identified 80 novel trans-splicing events between homologous alleles of the same gene. Keywords: RNA-Seq Keywords: Expression profiling by high throughput sequencing There were 2 total samples in this study. Paired-end mRNA-seq was used to survey trans-splicing in F1 hybrids of D. melanogaster and D. sechellia. A mixed "control" library was used to assess the frequency of false-positive trans-splicing signal resulting from errors in reference genomes, high-throughput sequencing, and RT-PCR amplification based strand-switching.
2010-07-19 | E-GEOD-22588 | biostudies-arrayexpress
Project description:Cell communication within tissues is mediated by multiple paracrine signals including growth factors, which control cell survival and proliferation. Cells and the growth factors they produce and receive constitute a circuit, yet the design features of cell circuits involved in tissue homeostasis are unknown. Here we used computational and experimental approaches to characterize the features of cell circuits based on growth factor exchange between macrophages and fibroblasts, two cell types found in most mammalian tissues. We found that the macrophage-fibroblast cell circuit is stable and robust to perturbations. We employed analytical screening of all possible two-cell circuit topologies and defined the circuit features sufficient for stability, including environmental constraint and negative feedback regulation. Moreover, we discovered that cell-cell contact was essential for the stability of the macrophage-fibroblast circuit. These findings highlight general principles of cell circuit design, and provide a new perspective on quantitative understanding of tissue homeostasis.
2018-02-08 | GSE104511 | GEO
Project description:DNA modification has been characterized as a critical epigenetic regulator in gene expression. N6-deoxyadenosine methylation (6mA) is the most widespread type in prokaryotes and some unicellular eukaryotes. Nevertheless, the lack of a precise and comprehensive mapping method greatly hinders studying the presence and biological significance of 6mA in mammals. Here, we develop a new method MM-seq (Modification-induced Mismatch Sequencing) for genome-wide 6mA mapping in single-base resolution. This method balances accuracy and sensitivity based on a novel detection principle. We find modified DNA bases are likely to flip out of the DNA duplex, forming a mismatch-like structure that an antibody can capture. The mismatch-like structure can be recognized by endonuclease or exonuclease, which marks the exact modified site for readout via sequencing. Using this method, we examine the genomic positions of 6mA in bacteria, green algae, and mammalian cells. We find that human and mouse genomes contain rare and randomly distributed 6mA sites, with almost no overlap between different cell types. After knock-out of the RNA m6A methyltransferase Mettl3, limited 6mA sites in gDNA are diminished. Our results support the perspective that rare 6mA in the mammalian genome is caused by the misincorporation of N6-methyladenine via the nucleotide-salvage pathway.
2023-01-11 | GSE171698 | GEO