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RNA-seq for HCT116 cells with TTC22-OE or kockdown

ABSTRACT: RNA-seq for HCT116 cells with TTC22-OE or kockdown

PROVIDER: PRJNA784958 | ENA |

REPOSITORIES: ENA

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RNA-seq for HCT116 cells with TTC22-OE or kockdown

Project description:object:compare the genes influenced by TTC22 overexpression or knockdown Methods: For whole-genome transcriptome profiling, four libraries were generated from total RNA samples extracted from Flag-TTC22-OE, empty vector control, scramble RNA control, and TTC22-KD (siTTC#1&2&3) HCT116 cells using TruSeq® RNA Sample Preparation Kit (Illumina Inc.) according to the manufacturer’s protocol, and sequenced on the Illumina HiSeq PE150 platform (Genminix, Shanghai, China) using the 150–base pair single-end sequencing module. Hisat2 (version:2.0.4) was used to map the cleaned reads to the human hg38 reference genome. Results: The mRNA data obtained from transcriptome sequencing, subjected to T-test statistics and corrected by the RVM model. Significant differential mRNA (TwoClassDif) between TTC22-OE and vector control cells or between TTC22-KD and scramble RNA control cells was yielded. Up-regulated and down-regulated genes (fold change>1.5, calculated through Ballgown algorithm) were performed to find significant functions and significant signaling pathways based on the Gene Ontology database (GO-Analysis) or KEGG database.(Pathway-Analysis). Conclusion:The results suggested that TTC22 could affect the RNA metabolism pathway that controls the progression and metastasis of CC.

2024-12-01 | GSE189892 | GEO

RNA-sequencing data of HCT116-wild type (WT), HCT116-A20 knockout (KO) and HCT116-A20-KO-rescue (OE) cells

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Next Generation Sequencing Facilitates Quantitative Analysis of HCT116 Wild Type and TTC7B-KO/OE Transcriptomes

Project description:To explore the function of TTC7B on colon cancer，we established HCT116 TTC7B-KO/OE cell lines. The purpose of this study is to utilize next-generation sequencing techniques to investigate the effects of TTC7B knockout or overexpression on the biological behavior of tumor cells.

2024-10-10 | GSE247502 | GEO

RNA-seq of depletion Mina53 in HCT116 p53+/+ cells and HCT116 p53-/- cells

Project description:RNA-seq of depletion Mina53 in HCT116 p53+/+ cells and HCT116 p53-/- cells

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RNA-seq of depletion Mina53 in HCT116 p53+/+ cells and HCT116 p53-/- cells

Project description:We report the signaling pathway of Mina53 by depleting Mina53 in HCT116 p53+/+ cells and HCT116 p53-/- cells based on RNA-sequencing.

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RNA-seq in HCT116 cell lines

Project description:RNA-seq in HCT116 cell lines

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RNA-seq in HCT116 cells with LINC01534 knockdown

Project description:RNA-seq in HCT116 cells with LINC01534 knockdown

| PRJNA744400 | ENA

RNA-seq for HCT116 and KO-CREB1 cells

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RNA-seq following miR-130a overexpression (OE) in human CD34+cord blood cells

Project description:We performed RNA-seq on CD34+ human cord blood (CB) cells transduced with Control or miR-130a OE lentiviruses to identify differentially expressed genes. Sorted CD34+ cells from 3 independent cord blood pools were transduced with lentiviruses containing mOrange (mO) reporter gene. mO+ cells were sorted 3 days post-transduction and RNA was harvested for library preparation and sequencing.

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RNA-seq in HCT116 cells with LINC01534 knockdown

Project description:To obtain a detailed view of genes and pathways regulated by LINC01534 (Long Intergenic Non-Protein Coding RNA 1534) in the HCT116 cells, we carried out global RNA-seq in HCT116 cells with LINC01534 knocked down.

2023-08-02 | GSE179624 | GEO

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