Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA seq analysis of Cere-120 (AAV2-NRTN) pretreatment in irradiated SMGs compared to AAV2-GFP pretreatment and Non-IR controls.

ABSTRACT: Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular and molecular pathways. The goals of this study are to compare NGS-derived Cere-120 treated SMG transcriptome profile (RNA-seq) to the AAV2-GFP and Non-IR SMGs

ORGANISM(S): Mus musculus

PROVIDER: GSE150112 | GEO | 2023/05/07

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

RNA seq analysis of Cere-120 (AAV2-NRTN) pretreatment in irradiated SMGs compared to AAV2-GFP pretreatment and Non-IR controls.

Project description:RNA seq analysis of Cere-120 (AAV2-NRTN) pretreatment in irradiated SMGs compared to AAV2-GFP pretreatment and Non-IR controls.

| PRJNA631214 | ENA

Next Generation Sequencing Transcriptomes Analysis of Irradiated mouse submandibular glands with or without transient activation of Hedgehog signaling

Project description:Purpose: To compare transcriptomes of nontreated (NT), Irradiated (IR and IR+GFP) and Hedgehog-activated (IR+Gli1 and IR+Shh) mouse submandibular glands (SMGs) Methods: SMG mRNA profiles of male adult NT mice or mice 7 days after local IR were generated by deep sequencing, in triplicate, using Illumina HiSeq 2500. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by HTseq. qRT–PCR validation was performed using SYBR Green assays Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the mouse genome (build mm10) and identified 20,743 transcripts in the SMGs with TopHat workflow. Altered expression of 25 genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method. Conclusions: Our study represents the first detailed analysis of SMG transcriptomes after IR with or without transient activation of Hedgehog (Hh) signaling, with biologic replicates, generated by RNA-seq technology. Our results show that IR impaired macrophages and related innate immune responses in SMGs, whereas transient Hh activation recovered them.

2020-12-22 | GSE133482 | GEO

Comprehensive mutagenesis of AAV2 rep

Project description:Recombinant adeno-associated viruses (rAAVs) are the predominant gene therapy vector. Several rAAV vectored therapies have achieved regulatory approval, but production of sufficient rAAV quantities remains difficult. The AAV Rep proteins, which are essential for genome replication and packaging, represent a promising engineering target for improvement of rAAV production but remain underexplored. To gain a comprehensive understanding of the Rep proteins and their mutational landscape, we assayed the effects of all 39,297 possible single codon mutations to the AAV2 rep gene on AAV2 production. Most beneficial variants are not observed in nature, indicating that improved production may require synthetic mutations. Additionally, the effects of AAV2 rep mutations were largely consistent across capsid serotypes, suggesting that production benefits are capsid independent. Our results provide a detailed sequence-to-function map that enhances our understanding of Rep protein function and lays the groundwork for Rep engineering and enhancement of large scale gene therapy production.

2023-02-28 | GSE226265 | GEO

Instability of WT AAV2 genome and AAV promoter activities in the Baculovirus/Sf9 cells system

Project description:The human Adeno-Associated Virus serotype 2 (WT AAV2) is a common non-pathological virus and its recombinant form (rAAV) is widely used as gene therapy vector. However, it has been shown that WT AAV2 and recombinant AAV display significantly different characteristics, especially regarding infection rate, with a near perfect infectivity and better encapsidation rate of WT AAV2. Even though rAAVs are routinely produced in the Baculovirus/Sf9 cell system, WT AAV2 has never been produced in this context. To understand the infectivity and encapsidation rate differences between WT AAV2 and rAAV, we tried to produce WT AAV2 in baculovirus/Sf9 cells system hypothesizing that the WT AAV2 may be considered as a normal recombinant AAV transgene. Through our attempts to produce WT AAV2 in Baculovirus/Sf9, we found that WT AAV2 p5 promoter, which controls the expression of large Rep proteins in mammalian cells, was active in this system. p5 promoter activity in the baculovirus/Sf9 cell system led to the expression of Rep78 that finally excises WT AAV2 genome from the baculovirus genome during the earliest phase of baculovirus stock production. The p5 promoter expression kinetics and the specific strand RNA-Seq analysis of the WT AAV2, rAAV Rep2/Cap2 cassettes in the baculovirus context was performed. We demonstrate that the WT AAV2 native promoters, p5, p19 and p40 are all active and lead to the expression of different proteins and peptides. In addition, this study demonstrates that the baculovirus brings at least some of the helper functions needed in the AAV replication/life cycle.

2018-06-21 | GSE96855 | GEO

Comprehensive mutagenesis of AAV2 rep

Project description:Comprehensive mutagenesis of AAV2 rep

| PRJNA939270 | ENA

The Hippo pathway effector YAP is an essential regulator of submandibular gland ductal progenitor patterning

Project description:To investigate the roles of YAP in the submandibular gland (SMG) epithelium, we compared the gene expression profiles of E15.5 SMGs isolated from Yap-loxP/loxP or Yap-loxP/loxP;Shh-Cre (i.e. Cre recombinase from the Shh promoter) embryos.

2017-05-24 | GSE90480 | GEO

H3K9me3 ChIP-seq on hematopoietic stem cells sorted from mice 1 month after they were irradiated (2Gy total body irradiation = IR) or not (non irradiated = NIR)

Project description:We aim at understanding how ionizing radiations (IR) increase the risk of developing myeloid leukemia. We recently showed that IR leads to the derepression of retroelements. We demonstrated that retroelements expression in aged HSCs is regulated by the heterochromatin repressive histone mark H3K9me3. However, the mechanisms by which IR specifically triggers retroelements expression in HSCs are unknown. We hypothesized that retroelements derepression is due to IR-induced heterochromatin changes. To answer this question, we performed H3K9me3 ChIP-seq experiments in hematopoietic stem cells sorted from mice one month after they were irradiated and compared them to controls hematopoietic stem cells sorted from non-irradiated mice.

2022-06-24 | E-MTAB-11865 | biostudies-arrayexpress

Single cell RNA sequencing of mouse submandibular glands transferred with GFP or Shh gene

Project description:To determine how Hedgehog signaling regulates salivary function, we performed single cell RNA sequencing (scRNA-seq) of adult mouse submandibular glands (SMGs) harvested 7 days after intra-SMG delivery of adenoviral vectors (Ad) carrying rat Sonic Hedgehog (Shh) or control GFP gene.

2023-04-10 | GSE148541 | GEO

E-Selectin/AAV2/2 Gene Therapy Alters Angiogenesis and Inflammatory Gene Profiles in Mouse Gangrene Model [Inflammation]

Project description:For patients with chronic limb-threatening ischemia and limited revascularization options, alternate means for therapeutic angiogenesis and limb salvage are needed. E-selectin is a cell adhesion molecule that is critical for inflammation and neovascularization in areas of wound healing and ischemia. Here, we tested the efficacy of modifying ischemic limb tissue by intramuscular administration of E-selectin/AAV2/2 (adeno-associated virus serotype 2/2) to modulate angiogenic and inflammatory responses in a murine hindlimb gangrene model. Limb appearance, reperfusion, and functional recovery were assessed for 3 weeks after induction of ischemia. Mice receiving E-selectin/AAV2/2 gene therapy had reduced gangrene severity, increased limb and footpad perfusion, enhanced recruitment of endothelial progenitor cells, and improved performance on treadmill testing compared to control group. Histologically, E-selectin/AAV2/2 gene therapy was associated with increased vascularity and preserved myofiber integrity. E-selectin/AAV2/2 gene therapy also upregulated a panel of pro-angiogenic genes yet downregulated another group of genes associated with the inflammatory response. This novel gene therapy did not induce adverse effects on coagulability, or hematologic, hepatic, and renal function. Our findings highlight the potential of E-selectin/AAV2/2 gene therapy for improving limb perfusion and function in patients with chronic limb-threatening ischemia.

2022-04-29 | GSE201479 | GEO

E-Selectin/AAV2/2 Gene Therapy Alters Angiogenesis and Inflammatory Gene Profiles in Mouse Gangrene Model [Angiogenesis]

2022-04-29 | GSE201476 | GEO