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ScRNA-seq analysis (drop-seq) of pharmacological HCN channel block with ZD7288 on rat primary cortical neuronal stem cells

ABSTRACT: scRNA-seq analysis (drop-seq) of pharmacological HCN channel block with ZD7288 on rat primary cortical neuronal stem cells

PROVIDER: PRJNA754128 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR15425692_1.fastq.gz	Fastqsanger.gz
	SRR15425692_2.fastq.gz	Fastqsanger.gz
	SRR15425693_1.fastq.gz	Fastqsanger.gz
	SRR15425693_2.fastq.gz	Fastqsanger.gz
	SRR15425694_1.fastq.gz	Fastqsanger.gz

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scRNA-seq analysis (drop-seq) of pharmacological HCN channel block with ZD7288 on rat primary cortical neuronal stem cells

Project description:We analysed transcriptomic changes of single cell transcriptomes from primary rat cortical neuronal stem cells (NSC) after pharmacologically blocking HCN channels with ZD7288 compared to untreated NSC. This drop-seq scRNA-seq aproach showed accumulation of ZD7288 treated cells in G1 phase and confirmed our previous findings from a well-based scRNA-seq approach with cell cycle arrest in G1 after HCN channel block.

2021-08-13 | GSE181979 | GEO

scRNA-seq analysis of pharmacological HCN channel block with ZD7288 on rat primary cortical neuronal stem cells

Project description:scRNA-seq analysis of pharmacological HCN channel block with ZD7288 on rat primary cortical neuronal stem cells

| PRJNA754124 | ENA

scRNA-seq analysis (well-based) of pharmacological HCN channel block with ZD7288 on rat primary cortical neuronal stem cells

Project description:scRNA-seq analysis (well-based) of pharmacological HCN channel block with ZD7288 on rat primary cortical neuronal stem cells

| PRJNA754129 | ENA

scRNA-seq analysis (well-based) of pharmacological HCN channel block with ZD7288 on rat primary cortical neuronal stem cells

Project description:We analysed transcriptomic changes of single cell transcriptomes from primary rat cortical neuronal stem cells (NSC) after pharmacologically blocking HCN channels with ZD7288 compared to untreated NSC. This well-based scRNA-seq aproach revealed a pronounced cell cycle arrest in G1 phase of ZD7288 treated (HCN blocked) NSC.

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Expression data from Pseudomonas aeruginosa PAO1 and an isogenic HCN negative mutant (PAO6344), grown under cyanogenic conditions.

Project description:Pseudomonas aeruginosa produces the toxic secondary metabolite hydrogen cyanide (HCN) at high cell population densities and low aeration. We have used Affimetrix microarrays to investigate the impact of HCN as a signal in cell-cell communication by comparing the transcriptome of the wild-type strain PAO1 to that of an HCN-negative mutant (PAO6344) under cyanogenic conditions. Total RNA was extracted from cultures of the wild-type strain PAO1 as well as from the isogenic HCN negative mutant (PAO6344), when HCN production was maximal (i.e. end of exponential growth phase). Each RNA pool derived from 3 technical replicates. 1 biological replicate per strain was performed on a different day.

2013-09-16 | E-GEOD-48587 | biostudies-arrayexpress

scRNA-seq analysis of pharmacological HCN channel block with ZD7288 on rat primary cortical neuronal stem cells

Project description:This SuperSeries is composed of the SubSeries listed below.

2021-08-13 | GSE181980 | GEO

Expression data from Pseudomonas aeruginosa PAO1 and an isogenic HCN negative mutant (PAO6344), grown under cyanogenic conditions.

2013-09-16 | GSE48587 | GEO

Genome-wide sequencing of REST binding (ChIP-seq) in adult hippocampal neural stem cells in vitro a.k.a. HCN cells in quiescent (iQNP) and proliferative (TAP) conditions

Project description:We report the high-throughput profiling of REST binding in mammalian adult hippocampal stem cells in culture (HCN cells). By obtaining 33 to 38 million single-end reads of sequence from chromatin immunoprecipitated DNA, we generated genome-wide REST binding state of HCN cells in induced quiescent (iQNP) and proliferating (TAP) conditions. Thereafter, we annotated the peaks to genomic regions and associated genes. We find that with +/-10kb of transcription start site of genes, REST efficiently binds neuronal genes and represses them in HCN cells in both iQNP and TAP conditions. Moreover, only in the iQNP REST also binds non-neuronal genes like DNA replication genes. This study reveals that in addition to its well known function as a neuronal repressor in non-neuronal tissue, REST can also play other diverse roles in non-neuronal tissues.

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Genome wide transcriptome analysis (RNA-seq) of adult hippocampal neural stem cells in vitro a.k.a. HCN cells in quiescent and proliferative conditions in non-electroporated or electroporated with control empty vector or REST knock-down shRNA vector

Project description:We report the high-throughput transcriptome profiling of induced quiescent (iQNP) and proliferative (TAP) conditions in mammalian adult hippocampal stem cells in culture (HCN cells). By obtaining 145 to 78 million pair-end reads of sequence from isolated RNA from HCN cells in iQNP and TAP conditions. Thereafter, we intersected this gene expression data with REST bound ChIP-seq peaks within +/-10kb of transcription start site of genes also from HCN cells in iQNP and TAP conditions. We find that with +/-10kb of transcription start site of genes, REST efficiently binds neuronal genes and represses them in HCN cells in both iQNP and TAP conditions. Moreover, only in the iQNP REST also binds non-neuronal genes like DNA replication genes. We also report the high-throughput transcriptome profiling of iQNP and TAP condition HCN cells electroporated with a control empty vector or REST knock-down shRNA vector. By obtaining 145 to 78 million pair-end reads of sequence from isolated RNA from HCN cells in electroporated control empty vector or REST knock-down vector in iQNP and TAP conditions. In REST knockdown in iQNP and TAP conditions we found that predominantly non-neuronal genes and neuronal genes were derepressed. This study reveals that in addition to its well known function as a neuronal repressor in non-neuronal tissue, REST can also play other diverse roles in non-neuronal tissues.

2016-11-09 | GSE70696 | GEO

Expression data of the mouse heart of a nose-only HCN inhalation model and a subcutaneous KCN injection model

Project description:Smoke inhalation from a structure fire is a common route of cyanide poisoning in the U.S. Cyanide inhibits cellular respiration, often leading to death. Its rapid distribution throughout the body can result in injuries to multiple organs, and cyanide victims were reported to experience myocardial infarction and other cardiac complications. We performed oligonucleotide microarrays to establish cardiac transcriptomes of an animal model of nose-only inhalation exposure to hydrogen cyanide (HCN), which is relevant to smoke inhalation. We also profiled cardiac transcriptomes after subcutaneous injection of potassium cyanide (KCN). Although the KCN injection model has been often used to evaluate medical countermeasures, this study demonstrated that cardiac transcriptomes are largely different from that of the HCN inhalation model at multiple time points within 24 hours after exposure.

2021-11-02 | GSE158994 | GEO

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