GEO DataSets

(Submitter supplied) Adeno-associated virus (AAV)-mediated gene therapies are rapidly advancing to the clinic, and AAV engineering has resulted in vectors with increased ability to deliver therapeutic genes. Although the choice of vector is critical, quantitative comparison of AAVs, especially in large animals, remains challenging. Here, we developed an efficient single-cell AAV engineering pipeline (scAAVengr) to simultaneously quantify and rank efficiency of competing AAV vectors across all cell types in the same animal. more...

Organism:

Macaca fascicularis; Mus musculus; Callithrix jacchus

Type:

Expression profiling by high throughput sequencing

5 related Platforms

147 Samples

Download data: CSV, MTX, TSV, TXT

(Submitter supplied) Gene therapy is a rapidly developing field, and adeno-associated virus (AAV) is a leading viral vector candidate for therapeutic gene delivery. Newly engineered AAVs with improved abilities are now entering the clinic. It has proven challenging, however, to predict the translational potential of gene therapies developed in animal models, due to cross-species differences. Human retinal explants are the only available model of fully developed human retinal tissue, and are thus important for the validation of candidate AAV vectors. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15520

16 Samples

Download data: CSV, MTX, TSV, TXT

(Submitter supplied) Purpose: To identifiy mRNA changes in wt cone photoreceptors with Txnip overexpression treatment, which improved retinitis pigmentosa (RP) cone survival and visual acuity. Methods: two wt mouse strains, BALB/c and C57BL/6J were injected with AAV-Txnip or AAV-H2BGFP control subretinally at P0. Retinas were dissected out at P21 for BALB/c and P35 for C57BL/6J. 1,000 H2BGFP labeled cones per retina sample were FACS sorted out, and subject for RNA-sequencing. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

18 Samples

Download data: CSV, TXT

(Submitter supplied) Purpose: To identifiy mRNA changes in retinitis pigmentosa (RP) cone photoreceptors with Txnip overexpression treatment, which improved RP cone survival and visual acuity. Methods: two RP mouse strains, rd1 and Rho-/-, were injected with AAV-Txnip or AAV-H2BGFP control subretinally at P0. Retinas were dissected out at P21 for rd1 and P90 for Rho-/-. 1,000 H2BGFP labeled cones per retina sample were FACS sorted out, and subject for RNA-sequencing. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

17 Samples

Download data: CSV, TXT

(Submitter supplied) Zhu et al. report the application of single-cell RNA-sequencing technology for profiling the cell-specific transgene expression and transcriptome dysregulation in mouse liver following intravenous administration of AAV vectors. By profiling 46,500 mouse liver cells, we have identified 3 separate clusters of hepatocytes (hep1, hep2 and hep3), endothelial cells, Kupffer cells and lymphocytes. Assessment of the AAVrh.10mCherry treated liver demonstrated transgene expression in not only hepatocytes, but in all cell types, with significant cell-type-specific expression heterogeneity. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

9 Samples

Download data: TXT

(Submitter supplied) To investigate if the truncated PE can be dilivered by dual AAV8 vectors for in vivo prime editing. We injected the dual AAV8 into 10-week-old C57BL/6J mice . Livers were isolated 4 weeks after injection and next generation sequencing showed an average of 1.4% and 5.4% precise prime editing with the low and high AAV doses, respectively (Figure 4D ). This demonstrates that PECO-Mini can be efficiently delivered by dual AAVs for in vivo prime editing.

Organism:

Mus musculus

Type:

Other

Platform:

GPL16417

9 Samples

Download data: XLSX

(Submitter supplied) Immune system responses against adeno-associated virus (AAV) vectors are potentiated after the first administration, which has prevented the clinical use of repeated administration of AAV-based gene therapies. Here, we quantify the contributions of multiple immune system components towards AAV response in mice. We identify B-cell-mediated immunity, specifically the generation of IgM antibodies, as a critical component preventing vector re-administration.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

3 Samples

Download data: H5, MTX, TSV

(Submitter supplied) Retinal structure and function have been studied in many vertebrate orders, but molecular characterization has been largely confined to mammals. Here, we used single-cell RNA sequencing (scRNA-seq) to generate a cell atlas of the chick retina. From ~40000 single cell transcriptomes, we identified ~150 cell types distributed among the six classes conserved across vertebrates – photoreceptor, horizontal, bipolar, amacrine, retinal ganglion and glial cells. more...

Organism:

Gallus gallus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19005

12 Samples

Download data: CSV

(Submitter supplied) This study reports the baseline effects of systemic (i.v.) administration of AAV8-TBG-null and AAV8-TBG-Cre on the liver of male, wild-type C57Black6/J mice. We performed polyA RNAseq of whole liver lysates from mice 2, 4 and 7 days post AAV8-TBG-null or AAV8-TBG-Cre administration and compared their transcriptome with that of male mice of similar age that didn't receive any AAV8 (day 0). We report some changes in gene expression of genes related to circadian rythm and response to infection at certain timepoints. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

28 Samples

Download data: TXT

(Submitter supplied) Large genes including several CRISPR-Cas modules, such as gene activators (CRISPRa), require dual adeno-associated viral (AAV) vectors for efficient in vivo delivery and expression. Current dual AAV vector approaches have important limitations, e.g., low reconstitution efficiency, production of alien proteins, or low flexibility in split site selection. Here, we present a dual AAV vector technology based on reconstitution via mRNA trans-splicing (REVeRT). more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

7 Samples

Download data: CSV

(Submitter supplied) Large genes including several CRISPR-Cas modules, such as gene activators (CRISPRa), require dual adeno-associated viral (AAV) vectors for efficient in vivo delivery and expression. Current dual AAV vector approaches have important limitations, e.g., low reconstitution efficiency, production of alien proteins, or low flexibility in split site selection. Here, we present a dual AAV vector technology based on reconstitution via mRNA trans-splicing (REVeRT). more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL15520

3 Samples

Download data: XLSX

(Submitter supplied) We generated adeno-associated Cre viral vectors with improved astrocyte-specific expression by including a cassette of miRNA targeting sequences (4x6T) to decrease off-target expression. We delivered these viruses in Ribotag mice using the PHP.eB serotype, either intracortically or systemically. We compared these samples with mice that received intracortical AAV2/5::GfaABC1D-Cre and transgenic Aldh1l1-CreERT2/Ribotag mice. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

32 Samples

Download data: XLSX

(Submitter supplied) Most irreversible blindness results from retinal disease. To advance our understanding of the etiology of blinding diseases, we used single-cell RNA-sequencing (scRNA-seq) to analyze the transcriptomes of ~85,000 cells from the fovea and peripheral reti-na of seven adult human donors. Utilizing computational methods, we identified 58 cell types within 6 classes: photoreceptor, horizontal, bipolar, amacrine, retinal gangli-on and non-neuronal cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

19 Samples

Download data: CSV

(Submitter supplied) Intratumour heterogeneity provides a fuel for cancer evolution enabling tumour cell populations to adapt to selective pressures imposed by the tumour microenvironment or therapeutic interventions. To uncover functionally heterogeneous subpopulations of tumour cells with different treatment sensitivity and to understand how clonal lineage-dependent transcriptomic diveristy contributes, we developed WILDseq, a hihg-complexity expressed barcode library for simultanous mapping of each cells' clonal identity and transcriptional states.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

46 Samples

Download data: MTX, RDS, TSV

(Submitter supplied) Among mammals, only primates including human possess a small central retinal region called the fovea, which mediates high acuity vision. As other mammals lack a fovea, molecular bases of its specialized function and dysfunction in retinal diseases remain poorly understood. By analyzing >165,000 single-cell transcriptomes from macaque fovea and peripheral retina, we identified and molecularly characterized >60 major cell types in each region. more...

Organism:

Macaca fascicularis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20302

17 Samples

Download data: CSV

(Submitter supplied) Among mammals, only primates including human possess a small central retinal region called the fovea, which mediates high acuity vision. As other mammals lack a fovea, molecular bases of its specialized function and dysfunction in retinal diseases remain poorly understood. By analyzing >165,000 single-cell transcriptomes from macaque fovea and peripheral retina, we identified and molecularly characterized >60 major cell types in each region. more...

Organism:

Macaca fascicularis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20302

22 Samples

Download data: CSV, RDATA

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Macaca fascicularis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20302

39 Samples

Download data

(Submitter supplied) Inherited retinal disorders (IRD) have become a primary focus of gene therapy research since the success of AAV-based therapeutics (voretigene neparvovec-rzyl) for Leber congenital amaurosis type 2 (LCA2). Dozens of monogenic IRDs could be potentially treated with a similar approach using adeno-associated virus (AAV) to transfer a functional gene into the retina. Here, we present the results of design, production and in vitro testing of the AAV serotype 9 (AAV9) vector carrying the codon-optimized (co) copy of aryl hydrocarbon receptor interacting protein like-1 (AIPL1) as a possible treatment for LCA4. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18460

12 Samples

Download data: TAB, TXT

(Submitter supplied) Recombinant adeno-associated viral vectors (rAAV) hold a natural ability to stimulate homologous recombination (AAV-HR). Moreover, they are also reported to randomly integrate into numerous locations throughout the genome. Here, we describe DNA/RNA immune precipitation sequencing (DRIP-seq) studies in HEPA1-6 cells and whole murine liver to detect genomic r-loops. Through genetic and pharmacological manipulation of r-loops formation, we showed a significant enhancement of AAV-HR. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL21103

12 Samples

Download data: BED, BW

(Submitter supplied) IS-Seq pipeline is developed,and 4 data sets are used to compare different abundance estimation methods of this pipeline

Organism:

Homo sapiens

Type:

Other

Platform:

GPL15520

3 Samples

Download data: CSV, TXT, XLSX