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RNA-sequencing assay to Identify changed gene expression in stomach adenocarcinoma (STAD) cells with ACAT2 knockdown

ABSTRACT: RNA-sequencing assay to Identify changed gene expression in stomach adenocarcinoma (STAD) cells with ACAT2 knockdown

PROVIDER: PRJNA1033647 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR26589175_1.fastq.gz	Fastqsanger.gz
	SRR26589175_2.fastq.gz	Fastqsanger.gz
	SRR26589176_1.fastq.gz	Fastqsanger.gz
	SRR26589176_2.fastq.gz	Fastqsanger.gz
	SRR26589177_1.fastq.gz	Fastqsanger.gz

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RNA-sequencing assay to Identify changed gene expression in stomach adenocarcinoma (STAD) cells with ACAT2 knockdown

Project description:Purpose: To elucidate how ACAT2 influenced the expression profile in STAD cells, ACAT2 expression was reduced using one shRNA in STAD HGC-27 cells. Then, transcriptional profiling of cells with ACAT2 knockdown (shACAT2) and the control cells (shNC) was performed to characterize differentially expressed genes (DEG).Methods: When shNC and shACAT2 cells grew to approximately 80% confluence, these cells were washed twice using pre-chilled PBS. Total RNAs were harvested using Trizol reagents (Thermo Fisher Scientific). Poly(A) mRNA was isolated and enriched using NEBNext Poly(A) mRNA Magnetic Isolation Module. The mRNA was then recovered for library generation with NEBNext ® Ultra™ Directional RNA Library Prep Kit for Illumina (NEB, E7420S) following the manufacturer’s instructions. The cDNA libraries were sequenced at WuXiNextCODE (China). FastQC was used to examine the quality of raw reads. Read alignment was conducted using STAR (v2.5.1b), and R package edgeR (v3.8.5) was used to determine relative transcript abundances and differentially expressed genes (DEGs) between sample pairs. Results: Generally, 241 genes were increased and 117 genes decreased in HGC-27 shACAT2 cells, compared with shNC cells (FDR<0.05, Fold Change>2). GO analysis showed that these changed genes were significantly enriched in signal pathways related to cancer. Conclusions: Reduced ACAT2 expression alters multiple cancer-related signal pathways.

2023-11-04 | GSE246567 | GEO

RNA-sequencing assay to identify changed gene expression in lung adenocarcinoma (LUAD) cells before and after osimertinib resistance

Project description:RNA-sequencing assay to identify changed gene expression in lung adenocarcinoma (LUAD) cells before and after osimertinib resistance

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RNA-sequencing assay to Identify changed gene expression in gastric cancer cells with SCAMP1 knockdown

Project description:RNA-sequencing assay to Identify changed gene expression in gastric cancer cells with SCAMP1 knockdown

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RNA-sequencing assay to Identify changed gene expression in esophageal squamous cell carcinoma (ESCC) cells with RAB23 knockdown

Project description:RNA-sequencing assay to Identify changed gene expression in esophageal squamous cell carcinoma (ESCC) cells with RAB23 knockdown

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RNA-sequencing assay to Identify changed gene expression in esophageal squamous cell carcinoma (ESCC) cells with RAB23 knockdown

Project description:Purpose: To elucidate how RAB23 influenced the expression profile in ESCC cells, RAB23 expression was reduced using two siRNAs in ESCC KYSE30 cells. Then, transcriptional profiling of two populations of cells with RAB23 knockdown (si-RAB23-1 and si-RAB23-9) and the control cells (si-NC) was performed to characterize differentially expressed genes (DEG). Methods: When si-NC, si-RAB23-1 and si-RAB23-9 cells grew to approximately 80% confluence, these cells were washed twice using pre-chilled PBS. Total RNAs were harvested using Trizol reagents (Thermo Fisher Scientific). Poly(A) mRNA was isolated and enriched using NEBNext Poly(A) mRNA Magnetic Isolation Module. The mRNA was then recovered for library generation with NEBNext ® Ultra™ Directional RNA Library Prep Kit for Illumina (NEB, E7420S) following the manufacturer’s instructions. The cDNA libraries were sequenced at WuXiNextCODE (China). FastQC was used to examine the quality of raw reads. Read alignment was conducted using STAR (v2.5.1b), and R package edgeR (v3.8.5) was used to determine relative transcript abundances and differentially expressed genes (DEGs) between sample pairs. Results: Generally, 1041 genes were increased and 1013 genes decreased in si-RAB23-1 cells, compared with si-NC cells (FDR<0.05, Fold Change>2). Additionally, 1154 genes (FDR<0.05, Fold Change>2) were increased and 958 genes decreased in si-RAB23-9 cells, relative to si-NC cells. GO analysis showed that these changed genes were significantly enriched in signal pathways related to cancer. Conclusions: Reduced RAB23 expression alters multiple cancer-related signal pathways.

2022-08-31 | GSE212200 | GEO

Comprehensive analysis of the immune implication of NOTCH1 gene in stomach adenocarcinoma

Project description:Comprehensive analysis of the immune implication of NOTCH1 gene in stomach adenocarcinoma

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RNA-sequencing assay to Identify changed gene expression in gastric cancer cells with SCAMP1 knockdown

Project description:Purpose: To understand how SCAMP1 drives the proliferation of GC cells, endogenous SCAMP1 expression was reduced using shRNA in gastric cancer cell line NCI-N87. RNA sequencing was performed to characterize differentially expressed genes (DEGs) betwenn the control (shCtrl) and the SCAMP1-depleted (shS1#1) NCI-N87 cells. Methods: When shCtrl and shS1#1 NCI-N87 cells grew to approximately 80% confluence, these cells were washed twice using pre-chilled PBS. Total RNAs were extracted using Trizol reagents (Thermo Fisher Scientific). Poly(A) mRNAs were isolated and enriched using NEBNext Poly(A) mRNA Magnetic Isolation Module. Library was generated with NEBNext ® Ultra™ Directional RNA Library Prep Kit for Illumina (NEB, E7420S) following the manufacturer’s instruction, and library was then sequenced by Novogene (Beijing, China). FastQC was used to examine the quality of raw reads. Read alignment was conducted using STAR (v2.5.1b), and R package edgeR (v3.8.5) was used to determine relative transcript abundance and differentially expressed genes (DEGs) between shCtrl and shS1#1 sample. Results: Generally, the expressions of 495 genes increased whereas the expressions of 204 genes decreased in shS1#1 cells, compared with shCtrl cells (|log2FC| > 1 and P < 0.05). Gene Ontology (GO) analysis indicated that significant portion of these differentially expressed genes were enriched in ligand-receptor interactions, such as fibroblast growth factor receptor binding, and the downstream signaling pathways, such as PI3K-Akt pathway. Conclusions: Reduced SCAMP1 expression attenuates the proliferation in GC cells via deactivating multiple pro-tumoral signaling pathways.

2024-09-25 | GSE252526 | GEO

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