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Expression data from Head and neck squamous cell carcinoma cell lines cell line Cal27 after TCF19 knockout mediated by CRISPR/CAS9

ABSTRACT: The deletion of TCF19 in CAL27,oral squamous cell carcinoma cell line,was conducted by using CRISPR/Cas9 system. For WT and TCF19 KO CAL27 cell lines, samples were done in triplicates. A total of 3μg of high-quality RNA per sample was used for ribosomal RNA removal by the Epicentre Ribo-zero rRNA Removal Kit (Epicentre, USA) and the sequencing library was prepared using the rRNA-depleted RNA by the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina, San Diego, CA, USA), followed by the 150-bp paired-end sequencing on the HiSeq X Ten instrument (Illumina, San Diego, CA, USA) according to the manufacturer’s protocols.

ORGANISM(S): Homo sapiens

PROVIDER: GSE153354 | GEO | 2021/01/01

REPOSITORIES: GEO

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Project description:Purpose: To understand the biological function of citratemt accumulation, we performed RNA-seq analysis. Methods:MLE12 cells were transfected simultaneously with shIdh3α lentivirus (MOI: 50) and shSlc25a1 lentivirus (MOI: 50) and negative control (shCtrl lentivirus, MOI: 50) in the presence of 1HitransG P (Lot: REVG005, GeneChem).Empty construct was used as control for all experiments. The cells were washed with fresh complete medium 16 h later and then cultivated for an additional 80 h.Total RNA was extracted from control and Slc25a1 plus Idh3α-deficient MLE12 cells. The transcriptome library for sequencing was generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following the manufacturer’s recommendations. The index codes were added to attribute sequences to each sample. After the quality of sequencing libraries was confirmed on the Agilent 2100 system, clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia, San Diego, CA, USA) according to the manufacturer’s instructions. The library preparations were then sequenced on an Illumina Hiseq 2500 platform (Illumina, San Diego, CA, USA), and paired-end reads were generated. Transcriptome assembly was accomplished based on the left.fq and right.fq using Trinity with min_kmer_cov set to 2 by default and all other parameters set to default. Results: Using an optimized data analysis workflow,We found that 215 genes were upregulated in MLE12 cells with citratemt accumulation . To determine the functional properties of the top 30 genes upregulated by citratemt, we performed Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. KEGG pathway analysis indicated that the 30 genes were involved in regulating the TNF signaling pathway , one of the critical signaling pathways for triggering necroptosis Conclusions: These results further suggest that citratemt accumulation specifically drives necroptosis

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Expression data from Head and neck squamous cell carcinoma cell lines cell line Cal27 after TCF19 knockout mediated by CRISPR/CAS9

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