Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNAseq after cortical spreading depolarization (SD)

ABSTRACT: The present study aimed to perform an extensive, unbiased RNA sequencing (RNA-seq) analysis to identify biological pathways, as well as related diseases and functions, modified by SD in healthy brains. SDs were induced repetitively (2 hours, 30 min intervals) in healthy, female mice and monitored with intrinsic optical signal (IOS) imaging. SD induction was with either focal application of KCl in C57Bl/6 mice or with optogenetic stimulation in Thy1-ChR2-YFP mice. Two hours after onset of SD, total cortical RNA was extracted and subjected to Illumina paired-end RNA sequencing to identify differentially expressed genes (DEGs; fold change >1.25, p-value <0.05). We identified 101 significantly upregulated genes after KCl-induced SDs and 136 after optogenetic induction; of these 57 (31.7%) genes were in common.

ORGANISM(S): Mus musculus

PROVIDER: GSE214623 | GEO | 2022/10/05

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Decoupling the Biochemical and Mechanical Effects of Muscle Exercise on Motor Neurons with 2.5D Actuating Matrices [240614Ram_RNA-seq]

Project description:We wanted to query the differences and similarities between our wild-type C2C12 cell line and our optogenetic ChR2 C2C12 myoblasts on the same day of differentiation. After 6 days on muscle differentiation medium, we extracted the RNA and sequenced it for 6 wells each.

2024-11-06 | GSE281241 | GEO

Transcription profiling of rat depolarization induced gene from primary cortical neuron

Project description:Activation of neurons is one of the fundamental events for the functioning of nervous system. Neuronal activation relays information to next neurons. On the other hand, the activated neurons themselves are also influenced by neuronal activation. Depending on the type and condition of neuronal activation, these activated neurons change their gene expressions, thereby being able to process information more or less efficiently. We applied the microarray technology to identify hither-to-uncharacterized as activity-dependent genes. Especially, we screened the transcription factors, because early changes in the transcription factors should result in alterations of gene expression profiles and subsequent neuronal properties. Experiment Overall Design: Rat primary cortical neurons with or without KCl treatment were selected for RNA extraction and hybridization on Affymetrix microarrays. To identify the genes whose expression was induced by depolarization, we first compared gene expression profiles in control vs. 4 hr after KCl (25 mM) treated cortical neurons using Affymetrix Genechips specified for neurobiology. All four hybridizations were analyzed for correlation accuracy between the replicates of the same treatments .Control replicates (control 1, 2) KCl-treated replicates (KCl 1, 2)

2008-06-13 | E-GEOD-4472 | biostudies-arrayexpress

Whole worm proteomics after optogenetically induced mechanical muscle stress (OptIMMuS)

Project description:This project includes 16 samples of transgenic C. elegans whole worm lysate after mechanical stress in 4 replicates of 4 conditions. Transgenic C. elegans strains expressing the optogenetic channelrhodopsin mutant ChR2(C128S;H134R)-FLAG in body wall muscle cells (PP3189 hhIs251[myo-3p::ChR2(C128S,H134R)-FLAG::unc-54 3'UTR, Cbrunc-119(+)]) were used to contract the worms’ muscles by blue light illumination to induce mechanical muscle stress. The optogenetic channel is activated by adding the cofactor all-trans retinal (ATR) to it’s food source E. coli OP50. In this experiment, we compared the treatment condition (1) worms after 8 h of illumination on plates with ATR (light plus ATR) to three control conditions: (2) illumination on plates without ATR (light minus ATR), (3) worms kept in the dark on plates with ATR (dark plus ATR), and (4) worms kept in the dark on plates without ATR (dark minus ATR).

2024-07-16 | PXD045078 | Pride

Transcriptome analysis by RNA sequencing of the cortical brain in a mouse model of early life pain

Project description:Preterm children are frequently exposed to various painful stimuli in the early days of life. Early-life-pain (ELP) may affect cortical development and reduce the fitness and resilience in during youth and adult life. We developed an optogenetic Cre/loxP mouse model of "early-life-pain" (ELP) using mice with transgenic expression of an improved channelrhodopsin-2 (ChR2)/Td-Tomato fusion protein under control of the advillin promoter, that drives expression of ChR2/td-Tomato specifically in primary somatosensory neurons of the dorsal root ganglia (Avil-ChR2 mice). Floxed ChR2/td-Tomato littermates (ChR2-flfl) were used as controls. Mice were exposed to blue light in a chamber once daily from postnatal day P1-P5. Cortical gene expression was analyzed at P7 via RNA-sequencing in eight biological replicates per group. Cortices were rapidly excised and snap froze in liquid nitrogen. Total RNA was extracted from with Qiagen RNeays spin columns and quantified on a Nanodrop. Sequencing libraries were prepared using Illumina TruSeq stranded mRNA library preparation kit, and sequencing was performed on an Illumina NGS platform. The alignment was performed with SeqMan NGen 17 (Lasergene) using the reference genome mm10 provided from UCSC (GRCm38) as template, a minimum read length of 35 bp and automatic adapter trimming. Sequence reads were normalized with EdgeR and analyzed in ArrayStar 17 (Lasergene). Differential gene expression was assessed with general linear models and adjusted according to Benjamini Hochberg.

2023-09-06 | GSE200140 | GEO

Transcription profiling of mouse KCl depolarization-regulated genes in cortical neurons

Project description:we used DNA microarray analysis to identify genes that are induced by neuronal activity in excitatory neurons at the time when inhibitory synapses are forming and maturing on them. Experiment Overall Design: We cultured cortical neurons for 7 DIV until the process of inhibitory synapse development was underway, and then depolarized the neurons with 50 mM of KCl to activate L-type voltage-sensitive calcium channels (L-VSCCs) for 0, 1 or 6 hours, the cells were lysed, mRNA isolated and hybridized to Affymetrix arrays. Data were collected from 3 independent experiments.

2008-10-26 | E-GEOD-11256 | biostudies-arrayexpress

RNAseq after cortical spreading depolarization (SD)

Project description:RNAseq after cortical spreading depolarization (SD)

| PRJNA886413 | ENA

Optogenetic neural stem cells microarray

Project description:We elucidate the transcriptome effects of optogenetics on developing neural stem cells population. The application of optogenetics in neural stem cell (NSC), allow photo-modulation of NSC in an activity-dependent manner. This provided spatio-temporal tool for studying activity dependent neurogenesis, including the potential of regulating the differentiation and maturation process of transplanted NSC. Currently, this is mainly driven by virally transfected of Channelrhodopsin-2 (ChR2) gene, which also requires high irradiance and complex in vitro stimulation systems. Additionally, despite the extensive application of optogenetics in neuroscience, the question of what transcriptome changes does optogenetic stimulation induced in developing NSCs have not been elucidated yet. To address these questions, we established a NSC line, expressing high light-sensitivity step-function opsin (SFO) variant of the chimeric channelrhodopsin, ChRFR(C167A) (~40x higher than ChR2), via the non-viral piggyBac transposon system. We set up a simple low-irradiance optogenetics stimulation-incubation system, which sufficiently induced depolarization in differentiating NSCs. We significantly enhance neurogenesis with low power optogenetic stimulation by 3 folds. Through microarray analysis, we have identified the genes and signaling pathways in axonal remodeling, synaptic plasticity and microenvironment modulation from optogenetic stimulation. Our results elucidate the transcriptome effects of optogenetics and the ability to drive neurogenesis with low irradiance optogenetics.

2017-11-04 | GSE106515 | GEO

Distribution of segmental duplications in the context of higher order chromatin organisation of human chromosome 7

Project description:Background Segmental duplications (SDs) are not evenly distributed along chromosomes. The reasons for this biased susceptibility to SD insertion are poorly understood. Accumulation of SDs is associated with increased genomic instability, which can lead to structural variants and genomic disorders such as the Williams-Beuren syndrome. Despite these adverse effects, SDs have become fixed in the human genome. Focusing on chromosome 7, which is particularly rich in interstitial SDs, we have investigated the distribution of SDs in the context of evolution and the three dimensional organisation of the chromosome in order to gain insights into the mutual relationship of SDs and chromatin topology. Results Intrachromosomal SDs preferentially accumulate in those segments of chromosome 7 that are homologous to marmoset chromosome 2. Although this formerly compact segment has been re-distributed to three different sites during primate evolution, we can show by means of public data on long distance chromatin interactions that these three intervals, and consequently the paralogous SDs mapping to them, have retained their spatial proximity in the nucleus. Focusing on SD clusters implicated in the aetiology of the Williams-Beuren syndrome locus we demonstrate by cross-species comparison that these SDs have inserted at the borders of a topological domain and that they flank regions with distinct DNA conformation. Conclusions Our study suggests a link of nuclear architecture and the propagation of SDs across chromosome 7, either by promoting regional SD insertion or by contributing to the establishment of higher order chromatin organisation themselves. The latter could compensate for the high risk of structural rearrangements and thus may have contributed to their evolutionary fixation in the human genome.

2014-07-01 | GSE41356 | GEO

Identification of preoptic sleep-promoting neurons based on projection target

Project description:The preoptic area (POA) of the hypothalamus is known to be crucial for sleep generation, but the spatial intermingling of sleep- and wake-promoting neurons makes it difficult to dissect the sleep control circuit. Here we identified a population of POA sleep-promoting neurons based on their projection target. Using a lentivirus for retrograde labeling with channelrhodopsin-2 (ChR2) followed by optogenetic manipulation and recording, we found that the POA GABAergic neurons projecting to the tuberomammillary nucleus (TMN) are both sleep active and sleep promoting. Cell type- and projection-specific rabies tracing revealed the presynaptic inputs to these neurons, including an amygdala GABAergic input that promotes wakefulness. Using single-cell RNA-seq, we identified several molecular markers for these neurons, and optogenetic activation of the POA neurons labeled by these markers confirmed their sleep-promoting effects. Together, these findings define a group of sleep-promoting neurons functionally, anatomically, and genetically.

2017-05-23 | GSE79108 | GEO

RNA-seq of human and mouse stem-cell derived neurons and mouse primary cortical neurons after KCl-induced membrane depolarization against controls.

Project description:This experiment comprises RNA-seq data used to study evolutionary differences between humans and mice in neuronal activity-dependent transcriptional responses. Activity-dependent transcriptional responses in developing human stem cell-derived cortical neurons were compared with those induced in developing primary- or stem cell-derived mouse cortical neurons 4 hours after KCl-induced membrane depolarisation. Activity-dependent transcriptional responses were also measured in aneuploid mouse neurons carrying human chromosome 21, allowing study of the regulation of Hsa21 genes, plus their mouse orthologs, side-by-side in the same cellular environment of a mouse primary neuron.

2017-02-16 | E-MTAB-5489 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data