MRNA transcriptome analysis of hypoxia with shSETDB1 in hela cells
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PROVIDER: PRJNA743288 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Purpose: The goals of this study are to compare NGS-derived Hela with shSETDB1 and shcontrol in hypoxia transcriptome profiling (RNA-seq) to quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods
2023-11-15 | GSE179327 | GEO
Project description:Analysis of hypoxia with sgSETDB1 in hela cells
| PRJNA743284 | ENA
Project description:Hypoxia is associated with several diseases, including cancer. Circular RNAs (circRNAs) are a novel class of non-coding RNAs that have been implicated in multiple cancers and attract increasing attention as potential biomarkers. In this study, the transcriptome-wide response of human HeLa cervical cancer cells to hypoxia was investigated. The circRNA signatures as well as differential gene expression and alternative splicing were analyzed by integrating available tools with custom approaches for quantification and statistical analysis.
2019-12-04 | GSE131379 | GEO
Project description:Purpose: The goals of this study are to compare NGS-derived Hela with sgSETDB1 and shcontrol in hypoxia transcriptome profiling (RNA-seq) to quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods
2023-11-15 | GSE179329 | GEO
Project description:Total RNA transcriptome analysis of hypoxia with sgSETDB1 in hela cells
| PRJNA743293 | ENA
Project description:Oxygen is vital for the development and survival of mammals. In response to hypoxia, the brain initiates numerous adaptive responses at the organ level as well as at the molecular and cellular level, including the alteration of gene expression. Astrocytes play critical roles in the proper functioning of the brain, thus the manner in which astrocytes respond to hypoxia is likely important in determining the outcome of brain hypoxia. We used microarray gene expression profiling and data analysis algorithms to identify and analyze hypoxia-responsive genes in primary human astrocytes. We also compared the gene expression patterns in astrocytes with those in human HeLa cells and pulmonary artery endothelial cells (ECs). Remarkably, in astrocytes, 5 times as many genes were up-regulated as down-regulated, whereas in HeLa and pulmonary ECs, as many or more genes were down-regulated as up-regulated. More genes encoding hypoxia-inducible functions, such as glycolytic enzymes and angiogenic growth factors, were strongly induced in astrocytes compared to HeLa cells. The extent of induction was also greater than in HeLa cells. Further, gene ontology and computational algorithms revealed that many target genes of the EGF and insulin signaling pathways and the transcriptional regulators Myc, Jun and p53 were selectively altered by hypoxia in astrocytes and HeLa cells to a varying degree. These results provide a global view of the signaling and regulatory network mediating oxygen regulation in astrocytes, in comparison with that in HeLa cells. Keywords: response to hypoxia
2006-03-16 | GSE3051 | GEO
Project description:Hypoxia effects on the transcriptome of HeLa cells
| PRJNA543429 | ENA
Project description:The purpose of experiment is to compare the mRNA expression differences between HeLa cells conditioned with normoxia 21% oxygen and hypoxia 1% oxygen at 6h and 20h.
2016-03-11 | GSE79069 | GEO
Project description:Purpose: The goal of this study is to identify the mRNA clusters that are regulated by EGFR under normoxia or hypoxia. Method: Total RNAs were extracted from HeLa cells expressing scrambled control or EGFR shRNA-E1 that cultured under normoxia or hypoxia (1% O2) for 24h. Customized Next-Generation RNA Deep Sequencing, including both small RNA application and whole transcriptome analysis, was performed according to the standard procedure instructed by Applied Biosystems. For whole transcriptome analysis, SOLiD fragment colorspace transcriptome reads (50nt) were mapped to the human genome (hg19) and assigned to ensemble transcripts using Bioscope 1.3.1 (Life Technologies). The values of reads per kilobase per million reads (RPKM) were determined by Bioscope 1.3.1 CountTags tool using default parameters. Primary alignments with a minimum mapping quality of 10 and minimum alignment score of 10 were counted. Results: Deep sequencing analysis identified subclasses of mRNAs that were affected by EGFR either under normoxia or hypoxia. EGFR-regulated mRNAs (with Log2 fold-change affected by EGFR M-bM-^IM-% 0.4 or M-bM-^IM-$ -0.4) were sorted and over-lapped with mRNAs that were targeted (based on published data and TargetScan prediction with total context score M-bM-^IM-$ -0.20) by the top miRNA candidates affected by EGFR under hypoxia, resulting in 439 mRNAs that regulated by EGFR and likely targeted by the miRNA candidates in response to hypoxia. Conclusion: Whole transcriptome analysis revealed a novel cluster of mRNAs that are likely regulated by EGFR through miRNAs in response to hypoxic stress. RNA profiles of HeLa cells expressing scrambled control (S) or EGFR shRNA-E1 (A1) that cultured under normoxia or hypoxia (1% O2) for 24h were generated by AB SOLiD curstomarized next-generation sequencing, including both small RNA application and whole transcriptome analysis. S: HeLa expressing scrambled control cultured under normoxia; A1: HeLa expressing EGFR shRNA-E1 cultured under normoxia; HS: HeLa expressing scrambled control cultured under hypoxia for 24h; HA1: HeLa expressing EGFR shRNA-E1 cultured under hypoxia for 24h. In total, 4 biological samples with no replicates resulted in 4 whole transcriptome RNA profiles.
2013-10-01 | E-GEOD-44801 | biostudies-arrayexpress
Project description:It has been well-known that cancer cells acquire approximately three-fold radioresistance under hypoxia than under normoxia due to both radiation chemical and radiation biological mechanisms, causing a negative impact on the outcome of radiation therapy. In the present study, to identify genes responsive to hypoxia in human cervical epithelial adenocarcinoma HeLa cells, global-scale gene expression analysis was carried out using a GeneChip® system.
2020-11-13 | GSE161393 | GEO