Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Effects of Different Doses of rAAV 5-mCherry on Transcriptome of Hippocampal Pyramidal Neurons in Male Mouse

ABSTRACT: Effects of Different Doses of rAAV 5-mCherry on Transcriptome of Hippocampal Pyramidal Neurons in Male Mouse

PROVIDER: PRJNA587942 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR10407277_1.fastq.gz	Fastqsanger.gz
	SRR10407277_2.fastq.gz	Fastqsanger.gz
	SRR10407278_1.fastq.gz	Fastqsanger.gz
	SRR10407278_2.fastq.gz	Fastqsanger.gz
	SRR10407279_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 18

Similar Datasets

Effects of Different Doses of rAAV 5-mCherry on Transcriptome of Hippocampal Pyramidal Neurons in Male Mouse

Project description:Purpose: Here, we evaluated the effects of three different doses of rAAV5 vectors, which are widely used for functional studies in the brain, on hippocampal pyramidal neurons transcription in male mice. Results: There was a strong correlation between rAAV dose and toxicity. As dose increased, rAAV5-DIO-mCherry upregulated genes related to the immune and inflammation response and neuron death and downregulated genes associated with the synapse and axon compartments, mitochondrial potein complex suggesting that higher dose rAAV 5-DIO-mCherry may induce pyramidal neuronal fragility and impair synaptic transmission and structure. Conclusions:the dose should be taken into consideration when rAAV vectors are used for gene transduction studies.

2022-10-04 | GSE139997 | GEO

Transcriptional changes induced by rAAV-mediated Npas4 overexpression in hippocampal primary cell culture compared to GFP-control

Project description:Hippocampal neuron cultures were prepared from neonatal C57BL/6N mice as previously described (Bading and Greenberg, Science, 1991). Cells were plated in dishes coated with Poly-D-Lysine (2mg/ml) and Laminin (10 µg/ml). Two days prior to harvesting, the medium was changed from NBA to transfection medium. Infection with rAAV-Npas4-flag of rAAV-GFP-myc was performed on day 5 in culture and cells were harvested on day 11. Total RNA was isolated using the RNeasy kit (Qiagen GmbH, Germany) according to the manufacturer’s instructions, including on-column DNase I digestion. Microarray analysis was performed with Illumina MouseWG-6 v2.0 Expression BeadChips®. The Genomics and Proteomics Core Facility at the DKFZ (Heidelberg, Germany) processed the RNA samples. RNA quality assessment was performed with the Nanodrop ND-1000 (Agilent 2100 Bioanalyzer). 4 μg of RNA was used for each microarray replicate. Raw microarray data was analyzed using Chipster (Kallio et al., 2011) by using R and Bioconductor packages. Statistical testing was performed using t-tests over all beads (e.g., one probeID over all beads of all samples of a group) in original scale. Benjamini-Hochberg correction was applied over all p-values of the differential expression analysis. We used a false discovery rate (FDR) of 5 % as a cut-off for determination of significance.

2021-10-18 | E-MTAB-10706 | biostudies-arrayexpress

Sex-biased effects on hippocampal circuit development by perinatal SERT expression in CA3 pyramidal neurons

Project description:We demonstrate in mice that perinatal SERT expression in glutamatergic pyramidal neurons in the hippocampus and mPFC modulates sexually dimorphic gene expression during hippocampal circuit assembly and is a source for sex-biased susceptibilities to cognitive and behavioral impairments.

2022-10-01 | GSE214392 | GEO

Doublecortin mutation leads to persistent defects in the Golgi apparatus and mitochondria in adult hippocampal pyramidal cells

Project description:Human doublecortin (DCX) mutations are associated with severe brain malformations leading to aberrant neuron positioning (heterotopia), intellectual disability and epilepsy. DCX is a microtubule-associated protein which plays a key role during neurodevelopment in neuronal migration and differentiation. Dcx knockout (KO) mice show disorganized hippocampal pyramidal neurons. The CA2/CA3 pyramidal cell layer is present as two abnormal layers and disorganized CA3 KO pyramidal neurons are also more excitable than wild-type (WT) cells. To further identify abnormalities, we characterized Dcx KO hippocampal neurons at subcellular, molecular and ultrastructural levels. Severe defects were observed in mitochondria, affecting number and distribution. Also, the Golgi apparatus was visibly abnormal, increased in volume and abnormally organized. Transcriptome analyses from laser microdissected hippocampal tissue at postnatal day 60 (P60) highlighted organelle abnormalities. Ultrastructural studies of CA3 cells performed in P60 (young adult) and > 9 months (mature) tissue showed that organelle defects are persistent throughout life. Locomotor activity and fear conditioning behavior of young and mature adults was also abnormal: KO mice consistently performed less well than WT littermates, with defects becoming more severe with age. Thus, we show that disruption of a neurodevelopmentally-regulated gene can lead to permanent organelle anomalies contributing to abnormal adult behavior

2022-03-29 | GSE185031 | GEO

Zbtb20-mediated repression of genes in developing CA1 pyramidal neurons

Project description:The transcriptional repressor Zbtb20 is essential for specification of hippocampal CA1 pyramidal neurons. Moreover, ectopic expression of Zbtb20 is sufficient to transform subicular and retrosplenial areas of D6/Zbtb20S mice to CA1. We used microarrays to identify genes that are repressed by Zbtb20 in developing CA1 pyramidal neurons in the CA1-transformed cortex of D6/Zbtb20S mice. For RNA extraction and hybridization on Affymetrix microarrays, we isolated the CA1-transformed subiculum and retrosplenial cortex from postnatal day 1 D6/Zbtb20S mice, as well as corresponding areas from their wildtype littermates. Total RNA was extracted using the RNeasy Lipid Tissue Mini Kit (Qiagen). Each RNA sample represents a pool of RNA obtained from dissected tissues of seven animals.

2014-04-11 | E-GEOD-38837 | biostudies-arrayexpress

Zbtb20-mediated repression of genes in developing CA1 pyramidal neurons

2014-04-11 | GSE38837 | GEO

Spatial gene expression gradients underlie prominent heterogeneity of CA1 pyramidal neurons

Project description:Tissue and organ function has been conventionally understood in terms of the interactions among discrete and homogeneous cell types. This approach has proven difficult in neuroscience due to the marked diversity across different neuron classes, but may also be further hampered by prominent within-class variability. Here, we considered a well-defined, canonical neuronal population â hippocampal CA1 pyramidal cells â and systematically examined the extent and spatial rules of transcriptional heterogeneity. Using next-generation RNA sequencing, we identified striking variability in CA1 PCs, such that the differences along the dorsal-ventral axis rivaled differences across distinct pyramidal neuron classes. This variability emerged from a spectrum of continuous expression gradients, producing a profile consistent with a multifarious continuum of cells. This work reveals an unexpected amount of variability within a canonical and narrowly defined neuronal population and suggests that continuous, within-class heterogeneity may be an important feature of neural circuits. Hippocampal RNA profiles were generated by deep sequencing on Illumina HiSeq 2500, with three biological replicates per population

2016-01-05 | E-GEOD-67403 | biostudies-arrayexpress

The organoid generated from murine small intestine: mCherry-positive vs. mCherry-negative

Project description:The organoids heterogenously expressed mCherry by the lentivirus transduction were dissociated into single cells. A single mCherry- positive and -negative cell were collected and grown up to the organoids, respectivery. The difference of the gene expression profile between mCherry- positive and -negative organoids was assessd by maicroarray.

2014-07-16 | GSE59425 | GEO

Hippocampal CA1 Pyramidal Neurons Display Sublayer and Circuitry Dependent Degenerative Expression Profiles in Aged Female Down Syndrome Mice

Project description:People with Down syndrome (DS) have intellectual disability (ID) and develop hallmark Alzheimer’s disease (AD) pathology during midlife. There are several circuits underlying memory and executive function in the DS and AD brain that are particularly vulnerable and degenerate early in disease, most notably the septohippocampal circuit and the trisynaptic loop in the hippocampus. A fundamental lack of knowledge exists as to the etiology and mechanisms of disease progression within these critical circuits vulnerable to degeneration in DS, AD, and relevant models. This is compounded by new evidence that suggests spatial localization of neurons has profound effects on activity and innervation within the hippocampal CA1 region. We postulated gene expression changes in a DS mouse model, at a time that these circuits of input to the CA1 are degraded, would have a significant effect on gene expression in CA1 pyramidal neurons. Further, this dysfunction may be specific to spatial localization and innervation. Laser capture microscopy on pyramidal neurons from CA1 was performed, isolating the entire CA1 pyramidal neuron layer, which was compared to select populations of deep and superficial pyramidal neurons from CA1a (distal CA1, adjacent to the subiculum). RNA-seq and bioinformatic analysis was performed where profound differences in dysregulation in the DS mouse model based on their spatial location and postulated circuitry were examined.

2024-08-26 | GSE264258 | GEO

Sex-biased effects on hippocampal circuit development by perinatal SERT expression in CA3 pyramidal neurons

Project description:Sex-biased effects on hippocampal circuit development by perinatal SERT expression in CA3 pyramidal neurons

| PRJNA885115 | ENA