GEO DataSets

(Submitter supplied) With more than 130 clinical trials and eight approved gene therapy products, AAVs stand as one of the most popular vehicles to deliver therapeutic DNA in vivo. One critical quality attribute analyzed in AAV batches is the presence of residual DNA, as it could pose genotoxic risks or induce immune responses. Surprisingly, the presence of small cell‑derived RNAs, such as micro‑RNAs, has not been previously investigated. more...

Organism:

unclassified Adeno-associated dependoparvovirus A; Homo sapiens

Type:

Expression profiling by RT-PCR

Platform:

GPL34639

3 Samples

Download data: TXT

(Submitter supplied) To address the role of miRNAs in Hirschsprund disease (HSCR), we carried out microRNA (miRNA) array analysis by using human intestinal samples obtained from HSCR patients and controls, and identified dysregulated miRNAs involved in the pathogenesis of HSCR.

Organism:

Herpesvirus saimiri (strain 11); JC polyomavirus; Human gammaherpesvirus 8; Merkel cell polyomavirus; Homo sapiens; Human alphaherpesvirus 1; Human betaherpesvirus 5; Human immunodeficiency virus 1; Human betaherpesvirus 6B

Type:

Non-coding RNA profiling by array

Platform:

GPL32145

10 Samples

Download data: GPR, TXT

(Submitter supplied) The mechanism by which aging induces aortic aneurysm and dissection (AAD) remains unclear. A total of 430 subjects were recruited for screening of differentially expressed plasma microRNAs. We found that miR-1204 was significantly increased in both plasma and aorta of elder patients with AAD, and was positively correlated with age. Cell senescence induced the expression of miR-1204 through p53 interaction with plasmacytoma variant translocation 1, and miR-1204 induced vascular smooth muscle cell (VSMC) senescence to form a positive feedback loop. more...

Organism:

Herpesvirus saimiri (strain 11); JC polyomavirus; Human gammaherpesvirus 8; Betapolyomavirus hominis; Human alphaherpesvirus 2; human gammaherpesvirus 4; Human betaherpesvirus 6B; Betapolyomavirus macacae; Homo sapiens; Human alphaherpesvirus 1; Macacine alphaherpesvirus 1; Human betaherpesvirus 5; Human immunodeficiency virus 1; Merkel cell polyomavirus

Type:

Non-coding RNA profiling by array

Platform:

GPL21439

12 Samples

Download data: GPR, XLSX

(Submitter supplied) Excessive alcohol consumption adversely affects the immune system and triggers the activation of peripheral blood (PB) monocytes and tissue macrophages, contributing to alcohol- related organ damage. This study aimed to analyze the M1/M2 and inflammatory phenotypes of circulating monocytes and macrophage-derived monocytes (MDMs). This single-center cross- sectional study included 20 excessive alcohol drinkers (EADs) and 22 healthy controls. more...

Organism:

human gammaherpesvirus 4; JC polyomavirus; Human gammaherpesvirus 8; Betapolyomavirus macacae; Rattus norvegicus; Human alphaherpesvirus 2; Merkel cell polyomavirus; Mus musculus cytomegalovirus 2; Murid gammaherpesvirus 4; Betapolyomavirus hominis; Homo sapiens; Mus musculus; Human alphaherpesvirus 1; Human betaherpesvirus 5; Murid betaherpesvirus 1; Human immunodeficiency virus 1

Type:

Non-coding RNA profiling by array

Platform:

GPL11434

22 Samples

Download data: GPR, TXT

(Submitter supplied) Genome-wide association studies (GWAS) have successfully identified 145 genomic regions that contribute to schizophrenia risk, but linkage disequilibrium (LD) makes it challenging to discern causal variants. Computational finemapping prioritized thousands of credible variants, ~98% of which lie within poorly characterized non-coding regions. To functionally validate their regulatory effects, we performed a massively parallel reporter assay (MPRA) on 5,173 finemapped schizophrenia GWAS variants in primary human neural progenitors (HNPs). more...

Organism:

Adeno-associated virus; Homo sapiens

Type:

Other

Platforms:

GPL32565 GPL24676

18 Samples

Download data: TSV, TXT

(Submitter supplied) 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. more...

Organism:

Adeno-associated virus

Type:

Other

Platform:

GPL27708

10 Samples

Download data: CSV

(Submitter supplied) Here, we selected >1000 variants from over 30 depression-associated loci using brain epigenomic data, and functionally assayed them using in vivo functional assays in the mouse brain to examine sex-by-genotype interactions. We identify extensive sex-by-allele effects in mature hippocampus, suggesting genetic risk and thus disease mechanisms may be distinct between the sexes. Unbiased informatics approaches indicated a role for nuclear hormone receptors, which was supported by . more...

Organism:

Adeno-associated virus 9; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24247 GPL30885

38 Samples

Download data: TXT

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

Organism:

Adeno-associated virus 9; Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL24247 GPL30885

69 Samples

Download data

(Submitter supplied) Here, we selected >1000 variants from over 30 depression-associated loci using brain epigenomic data, and functionally assayed them using in vivo functional assays in the mouse brain to examine sex-by-genotype interactions. We identify extensive sex-by-allele effects in mature hippocampus, suggesting genetic risk and thus disease mechanisms may be distinct between the sexes. Unbiased informatics approaches indicated a role for nuclear hormone receptors, which was supported by . more...

Organism:

Adeno-associated virus 9; Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL24247 GPL30885

44 Samples

Download data: TXT

(Submitter supplied) Here, we selected >1000 variants from over 30 depression-associated loci using brain epigenomic data, and functionally assayed them using in vivo functional assays in the mouse brain to examine sex-by-genotype interactions. We identify extensive sex-by-allele effects in mature hippocampus, suggesting genetic risk and thus disease mechanisms may be distinct between the sexes. Unbiased informatics approaches indicated a role for nuclear hormone receptors, which was supported by . more...

Organism:

Adeno-associated virus 9; Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL24247 GPL30885

25 Samples

Download data: TXT

(Submitter supplied) Tomato curly stunt virus (ToCSV) is a monopartite begomovirus infecting tomatoes in South Africa, with sequence similarity to tomato yellow leaf curl virus (TYLCV). While there are numerous reports on the mechanism of TYLCV resistance in tomato, the underlying mechanisms in the tomato-ToCSV pathosystem is still relatively unknown. The main aim of this study was to investigate and compare the global methylation profile of ToCSV in two near-isogenic tomato lines, one with a tolerant phenotype (T, NIL396) and one with a susceptible phenotype (S, NIL395). more...

Organism:

Tomato curly stunt virus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL33059

6 Samples

Download data: PDF, TXT

(Submitter supplied) The activity of enhancers with dynamic P300 binding or mutagenized nuclear receptor motifs was assessed by massively parallel reporter assay during CM maturation.

Organism:

Adeno-associated virus 9; Mus musculus

Type:

Other

Platforms:

GPL31917 GPL19057

88 Samples

Download data: CSV

(Submitter supplied) Evolved an AAV6 capsid library on Murine T-cells.

Organism:

Dependoparvovirus

Type:

Other

Platforms:

GPL32774 GPL32772 GPL32773

4 Samples

Download data: CSV

(Submitter supplied) Silencing of the adaptor SH3BP2 impairs Gastrointestinal stromal tumors growth through miRNAs We dissected SH3BP2 pathway in Gastrointestinal Stromal Tumor cells (GIST) performing a miRNA array in SH3BP2-silenced GIST cells

Organism:

Homo sapiens; Macacine alphaherpesvirus 1; Merkel cell polyomavirus; Herpesvirus saimiri (strain 11); JC polyomavirus; Human immunodeficiency virus 1; Human gammaherpesvirus 8; Human alphaherpesvirus 1; Human betaherpesvirus 5; human gammaherpesvirus 4; Human betaherpesvirus 6B; Betapolyomavirus macacae; Human alphaherpesvirus 2; Betapolyomavirus hominis

Type:

Non-coding RNA profiling by array

Platform:

GPL21599

12 Samples

Download data: TXT, XLSX

(Submitter supplied) Characterization of pluripotent states, in which cells can both self-renew or differentiate, with the irreversible loss of pluripotency, are important research areas in developmental biology. Although microRNAs (miRNAs) have been shown to be crucial for embryonic stem (ES) self-renewal maintenance and cellular differentiation, the role of miRNAs integrated into gene regulatory networks and its dynamic changes during these state transitions remain elusive. more...

Organism:

Human alphaherpesvirus 2; Murid gammaherpesvirus 4; Mus musculus; Rattus norvegicus; Murid betaherpesvirus 1; JC polyomavirus; Human immunodeficiency virus 1; Merkel cell polyomavirus; Homo sapiens; Human alphaherpesvirus 1; Human betaherpesvirus 5; Betapolyomavirus hominis; human gammaherpesvirus 4; Human gammaherpesvirus 8; Betapolyomavirus macacae

Type:

Non-coding RNA profiling by array

Platform:

GPL18658

12 Samples

Download data: TXT

(Submitter supplied) MicroRNAs profile of circulating CD4+ T Cells in Aged Patients with Atherosclerosis Obliterans comparing healthy persons without symptoms or lesion associated with atherosclerosis.

Organism:

Homo sapiens; Rhadinovirus; Human immunodeficiency virus 1; Merkel cell polyomavirus; Human alphaherpesvirus 2; Lymphocryptovirus; JC polyomavirus

Type:

Non-coding RNA profiling by array

Platform:

GPL26002

14 Samples

Download data: GPR, XLSX

(Submitter supplied) To extend the applicability of our approach, we tested a more extensively multiplexed pool of phages which contained ~50 clones with each phage equally distributed across the pool. Most of the factors tested are associated with cancer progression.

Organism:

Escherichia phage M13

Type:

Other

Platform:

GPL30822

11 Samples

Download data: XLSX

(Submitter supplied) In order to better understand the nature of the changes in chromatin structure which occur during encapsidation, we have analyzed SV40 virions and minichromosomes for the organization of nucleosomes carrying specific histone tail modifications and RNA Polymerase II (RNAPII) and report here evidence that encapsidation leads to a reorganization of chromatin structure within the regulatory region of the virus and relief of the repression of early transcription.

Organism:

Betapolyomavirus macacae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL25757

139 Samples

Download data: BEDGRAPH

(Submitter supplied) Two tree-man syndrome lesions immersed in RNA later were snap-frozen in liquid nitrogen and crushed with a tissue pulverizer kit (Cell crusher) according to the manufacturer’s instructions. Total RNA was extracted with the RNeasy Fibrous Tissue Mini Kit (QIAGEN), according to the manufacturer’s instructions. The procedure included a DNAse digestion step or an additional column to remove contaminating DNA. more...

Organism:

Homo sapiens; Human papillomavirus type 2

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27648

2 Samples

Download data: TXT

(Submitter supplied) Ribonucleotides incorporated in the genome are a source of endogenous DNA damage, and also serve as signals for repair. Although recent advances of ribonucleotide detection by sequencing, the balance between incorporation and repair of ribonucleotides has not been elucidated. Here, we describe a competitive sequencing method, Ribonucleotide Scanning Quantification sequencing (RiSQ-seq), which enables absolute quantification of misincorporated ribonucleotides throughout the genome by background normalization and standard adjustment within a single sample. more...

Organism:

Saccharomyces cerevisiae BY4741; Sinsheimervirus phiX174

Type:

Other

Platforms:

GPL21372 GPL22273

58 Samples

Download data: BED, BEDGRAPH, FA, GTF, TSV