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Next Generation Sequencing Facilitates Quantitative Analysis of SW480 cells and HPSE-knockdown SW480 cells Transcriptomes

ABSTRACT: Next Generation Sequencing Facilitates Quantitative Analysis of SW480 cells and HPSE-knockdown SW480 cells Transcriptomes

PROVIDER: PRJNA522246 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8570630_1.fastq.gz	Fastqsanger.gz
	SRR8570630_2.fastq.gz	Fastqsanger.gz
	SRR8570631_1.fastq.gz	Fastqsanger.gz
	SRR8570631_2.fastq.gz	Fastqsanger.gz
	SRR8570632_1.fastq.gz	Fastqsanger.gz

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Next Generation Sequencing Facilitates Quantitative Analysis of SW480 cells and HPSE-knockdown SW480 cells Transcriptomes

Project description:Heparanase (HPSE), the only known mammalian endoglycosidase responsible for heparan sulfate cleavage, is a multi-faceted protein affecting multiple malignant behaviors in cancer cells. The goals of this study are to compare the mRNA transcriptome differences between SW480 cells and HPSE-knockdown SW480 cells. Methods: mRNA profiles of SW480 cells and HPSE-knockdown SW480 cells were generated by deep sequencing, in triplicate, using Illumina.

2019-02-14 | GSE126504 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and hnRNPA2B1-KO sw480 cell line Transcriptomes

Project description:HNRNPA2B1, an RNA-binding protein, plays a key role in primary microRNA processing, alternative splicing, mRNA metabolism and transport. Interestingly, hnRNPA2B1 also works as an N6-methyladenosine(m6A) reader and is critical during tumorigenesis of various tissue types. However, its role in colon cancer is still unclear. In this study, we aimed to elucidate the biological functions of hnRNPA2B1 and to explore its underlying mechanisms in colon cancer. Methods We examined the expression of hnRNPA2B1 in Oncomine and TCGA databases. Then verified the findings in colon cancer cells and clinical samples with western blotting and immunohistochemistry (IHC). We used CRISPR/Cas9 directed gene editing to knockout hnRNPA2B1 expression in human colon cancer cell line SW480 and carried out both in vivo and in vitro experiments. The results were further confirmed by RNA-seq analysis. We found that hnRNPA2B1 significantly promoted colon cancer cell proliferation both in vitro and in vivo, while knockout of hnRNPA2B1 induced apoptosis and cell cycle arrest in SW480. RNA-seq analysis revealed that the ERK/MAPK pathway was activated by hnRNPA2B1 upregulation. In addition, both hnRNPA2B1 and MAPK pathway were activated in clinical colon cancer specimens and positively correlated. Mechanistically, hnRNPA2B1 appeared to be an upstream regulator of the ERK/MAPK pathway and inhibition of MAPK signaling blocked the effects of hnRNPA2B1. Taken together, our data demonstrated that the RNA-binding protein hnRNPA2B1 promotes cell proliferation and regulates cell cycle and apoptosis of human colon cancer by activating the ERK/MAPK signaling, which may provide a new insight into the development of hnRNPA2B1 as a potential therapeutic target for treatment of colon cancer.

2021-06-09 | GSE169211 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and hnRNPA2B1-KO sw480 cell line Transcriptomes

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and hnRNPA2B1-KO sw480 cell line Transcriptomes

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Next Generation Sequencing Facilitates Quantitative Analysis of colorectal cancer cell lines including SW480 and SW620

Project description:Purpose: The goals of this study are to compare the differentially expressed miRNAs between SW480 and SW620. Methods:Total RNA of two samples was used to prepare the miRNA sequencing library.The libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as clusters and finally sequenced for 50 cycles on Illumina NextSeq. Results:We found 72 miRNAs were downregulated on the basis of fold-change less than 0.5. However,total 160 miRNAs were upregulated on the basis of fold-change greater than 2. Conclusions: Our study represents the detailed analysis of SW480 and SW620, generated by RNA-seq technology. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of miRNA content. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

2020-01-22 | GSE144002 | GEO

Ezrin knockdown in SW480

Project description:Analysis of SW480 cells following knockdown of Ezrin using RNAi. Ezrin is a protein that regulate the organization of cytoskeleton. Ezrin KD SW480 was used to study the role of ezrin in colon cancer. Keywords: ezrin, colon cancer, migration

2008-04-29 | GSE11279 | GEO

mRNA-seq of SW480 USP22 knockdown cells

Project description:mRNA-seq of SW480 USP22 knockdown cells

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Next Generation Sequencing Facilitates Quantitative Analysis of RBM39 knockdown Transcriptomes in T47D cells

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of RBM39 knockdown Transcriptomes in T47D cells

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Next Generation Sequencing Facilitates Quantitative Analysis of Ter cells Transcriptomes

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of Ter cells Transcriptomes

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Expression data from SW480 cells with Gankyrin knockdown

Project description:We performed genome-wide screening using SW480 cells with Gankyrin knockdown on an Affymetrix gene expression array to identify the transcriptional targets of Gankyrin. Transcriptional profiling with samples from SW480 cells that were infected with control or gankyrin shRNA. Two condition experiment: control shRNA (three replicates) and NFIL3 shRNA (three replicates)

2013-02-04 | E-GEOD-44029 | biostudies-arrayexpress

Next Generation Sequencing Facilitates Quantitative Analysis of colorectal cancer cell lines including SW480 and SW620

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of colorectal cancer cell lines including SW480 and SW620

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