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Next Generation Sequencing identifies differentially expressed genes regulated by overexpression of tRF AS-tDR-007333 in A549 cells

ABSTRACT: Next Generation Sequencing identifies differentially expressed genes regulated by overexpression of tRF AS-tDR-007333 in A549 cells

PROVIDER: PRJNA765668 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR16027435_1.fastq.gz	Fastqsanger.gz
	SRR16027435_2.fastq.gz	Fastqsanger.gz
	SRR16027436_1.fastq.gz	Fastqsanger.gz
	SRR16027436_2.fastq.gz	Fastqsanger.gz
	SRR16027437_1.fastq.gz	Fastqsanger.gz

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Next Generation Sequencing identifies differentially expressed genes regulated by overexpression of tRF AS-tDR-007333 in A549 cells

Project description:Our previous study identified that a novel tRNA-derived fragment (tRF) termed AS-tDR-007333 was up-regulated in non-small cell lung cancer (NSCLC), but the molecular mechanisms of AS-tDR-007333 in NSCLC were unclear. Here, we used RNA-seq for high-throughput profiling of transcriptomes in A549 cells transfected with AS-tDR-007333, in order to find differentially expressed genes regulated by AS-tDR-007333.

2022-05-25 | GSE184690 | GEO

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3'-tRF-CysGCA overexpression alters the expression profile of HEK-293 cells and modulates cellular processes and pathways

Project description:tRNA fragments (tRFs) are small non-coding RNA molecules that are generated through the cleavage of tRNAs and have been implicated in various biological processes. Among the different types of tRFs, the 3′-tRFs have attracted considerable scientific interest due to their regulatory role in gene expression. In this study, we investigated the role of 3′-tRF-CysGCA, a tRF derived from cleavage in the T-loop of tRNACysGCA, in the regulation of gene expression in HEK-293 cells. Previous studies have shown that 3′-tRF-CysGCA is incorporated into the RISC complex and interacts with Argonaute proteins, suggesting its involvement in the regulation of gene expression. However, the general role and effect of the deregulation of 3′-tRF-CysGCA levels in human cells have not been investigated so far. To address this gap, we stably overexpressed 3′-tRF-CysGCA in HEK-293 cells and performed transcriptomics and proteomics experiments. Moreover, we validated the interaction of this tRF with putative targets whose levels were affected after 3′-tRF-CysGCA overexpression. Last, we investigated the implication of 3′-tRF-CysGCA in various pathways using extensive bioinformatics analysis. Our results indicate that 3′-tRF-CysGCA overexpression led to changes in the cell expression profile, and we identified multiple pathways that were affected by the deregulation of this tRF. Additionally, our reporter assays demonstrated that 3′-tRF-CysGCA directly interacted with TMPO and ERGIC1, leading to changes in their expression levels. Taken together, these findings suggest that 3′-tRF-CysGCA plays a significant role in the regulation of gene expression and highlight the potential importance of this tRF in cellular processes.

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Project description:The rapid development of high-throughput sequencing is conducive to the discovery of many new theories. The purpose of this study is to explore the differentially expressed of tRF & tiRNA in cholangiocarcinoma by high-throughput sequencing technology. We collected cholangiocarcinoma and adjacent normal tissues from three patients. After RNA extraction and RNA library preparation, we determined the raw data of tRF & tiRNA in cholangiocarcinoma and adjacent normal tissues by high-throughput RNA sequencing. Raw data were generated after sequencing,image analysis,basecalling and quality filtering on lllumina sequencer.Firstly,Q30 was used to perform quality control.The adaptor sequences were trimmed and the adaptor-trimmed-reads(>=16nt) were left by cut adapt software(v1.9.3).Then,the raw counts of each tRF&tiRNA(MINTbasev2.0) was calculated for all samples,defined as the raw expression level soft.The results showed that a total of 20102 tsRNA were detected in the two groups, 9616tsRNA were upregulated and 10486 were downregulated. There were 535 differentially expressed tsRNA in cholangiocarcinoma after edger standardization, of which 241 were upregulated and 294 were downregulated (| log2 (foldchange) | = 1andpvalue < 0.05). This study shows that high-throughput sequencing technology is helpful for us to determine the expression of tRF & tiRNA in cholangiocarcinoma, and to screen out differentially expressed tRF & tiRNA, and further to explore the factors that affect the progress of cholangiocarcinoma.

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Project description:This study aimed to identify differential expressed genes before and after treatment with Sulforaphene, using the A549 lung cancer cell line as a model.

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Analysis of differentially expressed genes in A549 after treatment with Sulforaphene

Project description:This study aimed to identify differential expressed genes before and after treatment with Sulforaphene, using the A549 lung cancer cell line as a model. There were a total of 4 samples examined. Two replicates have been included (2 control samples and 2 test samples).

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