DOI: 10.57760/sciencedb.26123
title: Ribosome Profiling (KYSE450SOX2KO vs KYSE450WT)
title: Ribosome Profiling (KYSE450SOX2KO vs KYSE450WT)

description: The data uploaded herein consists of ribosome profiling sequencing results comparing KYSE450 human esophageal squamous cell carcinoma cells with SOX2 gene knockout (KYSE450SOX2KO) against wild-type controls (KYSE450WT). Ribosome profiling is a technique used for global analysis of the translation state. At the initiation of the experiment, KYSE450SOX2KO and KYSE450WT cells were cultured to a specific growth phase. Subsequently, the cells were treated with specific chemical reagents (such as cycloheximide) to stabilize and fix the positions of cellular ribosomes on the mRNA. Following this, through steps including cell lysis, removal of ribosome-free RNA, and separation of ribosomal subunits, mRNA fragments bound to ribosomes were enriched. Standard library preparation procedures were then performed on these fragments, including end repair, adapter ligation, and PCR amplification, followed by high-throughput sequencing. The resulting sequencing reads primarily cover the coding regions (CDS) of the mRNA, with their start and end positions reflecting the dynamics of ribosomes during translation. Through bioinformatics analysis of these reads, such as alignment against a reference genome or transcriptome, the translation levels of each gene can be quantified, and the efficiency of translation initiation, elongation, and termination can be assessed. The final expression matrix records the ribosome binding read counts for each gene in each sample and is saved in a standard .xls spreadsheet format. This data file contains translational profiling information for two samples (KYSE450SOX2KO and KYSE450WT), providing a valuable resource for studying the impact of SOX2 gene knockout on the translational level in KYSE450 cells. It facilitates subsequent research, such as differential expression analysis at the translational level and exploration of translational regulatory mechanisms.
description: The data uploaded herein consists of ribosome profiling sequencing results comparing KYSE450 human esophageal squamous cell carcinoma cells with SOX2 gene knockout (KYSE450SOX2KO) against wild-type controls (KYSE450WT). Ribosome profiling is a technique used for global analysis of the translation state. At the initiation of the experiment, KYSE450SOX2KO and KYSE450WT cells were cultured to a specific growth phase. Subsequently, the cells were treated with specific chemical reagents (such as cycloheximide) to stabilize and fix the positions of cellular ribosomes on the mRNA. Following this, through steps including cell lysis, removal of ribosome-free RNA, and separation of ribosomal subunits, mRNA fragments bound to ribosomes were enriched. Standard library preparation procedures were then performed on these fragments, including end repair, adapter ligation, and PCR amplification, followed by high-throughput sequencing. The resulting sequencing reads primarily cover the coding regions (CDS) of the mRNA, with their start and end positions reflecting the dynamics of ribosomes during translation. Through bioinformatics analysis of these reads, such as alignment against a reference genome or transcriptome, the translation levels of each gene can be quantified, and the efficiency of translation initiation, elongation, and termination can be assessed. The final expression matrix records the ribosome binding read counts for each gene in each sample and is saved in a standard .xls spreadsheet format. This data file contains translational profiling information for two samples (KYSE450SOX2KO and KYSE450WT), providing a valuable resource for studying the impact of SOX2 gene knockout on the translational level in KYSE450 cells. It facilitates subsequent research, such as differential expression analysis at the translational level and exploration of translational regulatory mechanisms.