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

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

PROVIDER: GSE189892 | GEO | 2024/12/01

REPOSITORIES: GEO

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