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

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

PROVIDER: PRJNA1061110 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR27431435_1.fastq.gz	Fastqsanger.gz
	SRR27431435_2.fastq.gz	Fastqsanger.gz
	SRR27431436_1.fastq.gz	Fastqsanger.gz
	SRR27431436_2.fastq.gz	Fastqsanger.gz
	SRR27431437_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:RNA-sequencing assay to Identify changed gene expression in stomach adenocarcinoma (STAD) cells with ACAT2 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 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

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.

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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

human gastric cancer cell AGS shTOPK LC-MSMS

Project description:Knockdown of TOPK expression in human gastric cancer cells AGS, Phosphoproteomic assay for control and shTOPK groups

2023-05-10 | PXD036814 | Pride

Genes regulated by SET7/9 knockdown in gastric cancer cells

2015-07-24 | GSE59834 | GEO

Genes regulated by SET7/9 knockdown in gastric cancer cells

Project description:Expression of SET7/9, a histone methyltransferase, was frequently reduced in cultured and primary gastric cancers. To identify the SET7/9 target genes in gastric cancer, we performed siRNA-based knockdown of SET7/9 in MKN74 and MKN45 cells and then examined significant expression changes of genes by microarray. Transfection of SET7/9 siRNA into MKN74 and MKN45 cells were performed by electroporation. After 48hrs, cells were harvested. Total RNA was used for cDNA microarray.

2015-07-24 | E-GEOD-59834 | biostudies-arrayexpress

Twist1 knockdown in two gastric cancer-associated fibroblast lines

Project description:Primary human gastric cancer-associated fibroblast (CAF) cultures (CAF14 and CAF32) were establised from 2 gastrectomy specimens. Silencing the expression (loss-of-function effect) of Twist1 in CAFs showed candidate target genes regulated by Twist1 and abrogated their tumor-promoting properties. Experiment design: two gastric CAFs (CAF14 adn CAF32, respectively) were establised from two gastric cancer patients and Twist1 knockdown studies were performed using shRNA.

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