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ABSTRACT: Reg-Seq Construct Mapping

PROVIDER: PRJNA603368 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10971993_1.fastq.gz	Fastqsanger.gz
	SRR10971993_2.fastq.gz	Fastqsanger.gz

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Project description:Reg-Seq

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Identification of regenerating island-derived protein 3E in dogs

Project description:Our aim was to identify Regenerating islet-derived (REG proteins in dogs. We annotated REG-family members in the canine genome and proteome, and identified one member of the REG3 subfamily, consequently termed REG3E by the Vertebrate Gene Nomenclature Committee. We verified REG3E gene expression using publicly available RNA-seq data (www.barkbase.org). We investigated the presence of REG3E protein in canine pancreatic tissue and plasma with Western blot and immunohistochemistry, using anti-human REG3A antibodies. Protein identity was subsequently confirmed with mass spectrometry on canine pancreas homogenates and plasma.

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Identification of the genome-wide binding sites of OCT2 in Reg-1fl/fl- and Reg-1ΔNK-NK cells. [ChIP-Seq]

Project description:The expression of OCT2 was also increased in NK cells from Reg-1fl/fl in response to IL-12/18 stimulation implying that OCT2 has an intrinsic function not only in Regnase-1-deleted NK cells but also in wild-type NK cells. To identify the genome-wide binding sites of OCT2, we performed chromatin immunoprecipitation sequencing (ChIP-seq) for OCT2 in Reg-1fl/fl- and Reg-1ΔNK-NK cells.

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Genome-wide analysis of alternative splicing in Zea mays: landscape and genetic regulation

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Transcriptomic profile at single cell level of TIL-NK cells and tumor cells from tumor-bearing Reg-1fl/fl and Reg-1ΔNK mice

Project description:The innate immune system can recognize tumor cells and coordinate with the adaptive immune system to initiate an anti-tumor response within the tumor microenvironment. To investigate the role of NK cells and their interaction with other immune cells in the anti-tumor immunity in Reg-1ΔNK. We subcutaneously injected B16F10 cells into Reg-1fl/fl and Reg-1ΔNK, followed by scRNA-seq analysis of the whole tumor cell suspension and sorted TIL-NK cells.

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Genome-wide analysis of gene expression from islets of different sizes in response to in vivo serpin B13 mAB treatment

Project description:By using oligonucleotide microarray-based technology as a tool for rapid mapping of unique differences in gene expression, we found that inhibiting serpin B13 in BALB/c mice treated with a mAb according to our protocol resulted in the upregulation of relatively few genes, including several Reg genes, which have been implicated in β-cell proliferation.

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RNA sequencing of host transcriptome of human foreskin fibroblast cells infected with either bradyzoites and tachyzoite of Toxoplasma gondii

Project description:The purpose of this data set is to determine if bradyzoites impact the host transcripton in a similar manner as tachyzoites. We found that 3853 differentially expressed genes (DEGs) are shared between tachyzoite infected cells and bradyzoite infected cells (41%; 2161 up-reg., 1692 down-reg.) when compared to uninfected host samples, leaving 3356 tachyzoite specific DEGs (1488 up-reg., 1868 down-reg.), and 1951 DEGs specific to bradyzoite infection (1075 up-reg., 876 down-reg). We conclude therefore that bradyzoites manipulate the host cell and that this is unique when compared to tachyzoites.

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Project description:Differential expression was used to access gene differences after Entamoeba histolytica infection. Entamoeba histolytica is an important diarrheal pathogen worldwide, and induces apoptosis of the intestinal epithelium as part of its disease process. Regenerating (REG) 1 protein is anti-apoptotic. We investigated the involvement of REG 1 in E. histolytica colitis. Colonic biopsy samples were obtained from 8 subjects with acute E. histolytica colitis, and again 60 day later during convalescence. Gene expression in the human colon during acute and convalescent E. histolytica disease was evaluated using microarray and confirmed by polymerase chain reaction (PCR). REG 1 protein expression was evaluated with immunohistochemistry. The mechanism of REG 1 involvement in E. histolytica disease was subsequently investigated with a mouse model. REG 1A and REG 1B were the most upregulated genes in the human intestine in acute versus convalescent E. histolytica disease (p=0.003 and p=0.006 respectively). PCR confirmed the microarray results (p=<0.001 and p=0.001 respectively). Increased REG 1A and REG 1B protein expression was similarly observed by immunohistochemistry. REG 1 -/-mice were found to be significantly more susceptible to E. histolytica infection than wild type mice.

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Project description:DeepRNA-Reg employs advances in deep learning to enable high-fidelity comparative analysis of paired datasets of high-throughput sequencing of RNA isolated by crosslinking immunoprecipitation (HITS-CLIP). In a HITS-CLIP experimental paradigm where Ago2 activity is precisely perturbed via gene knock-out of a microRNA cluster, DeepRNA-Reg offers a superior prediction set than the current best prescription for differential HITS-CLIP; furthermore, DeepRNA-Reg predictions adhere better to the ground-truth of the RNA primary and secondary structural motifs that enable miRNA-mediated targeting of RNA. DeepRNA-Reg uncovered novel mediators in the mechanism of microRNA-mediated restraint of type-2 immunity in T-Helper 2 cells. In a comparative analysis, DeepRNA-Reg predictions show greater translatability across distinct biological milieux, offering prediction sets with wide applicability for investigators.

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