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RNA-sequencing assay to Identify Genes Promoting Lung Metastasis of Esophageal Squamous Cell Carcinoma (ESCC) Cells

GSE182090 Homo sapiens (human) RNA-seq (gene expression) 12 samples Submitted 2024/08/10 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 12 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Homo sapiens (human)
Topic
Esophageal cancerThis series is part of our curated briefing on it.
Samples
12 samples: 3 × K30 vs 3 × K30LM3 vs 3 × K450 vs 3 × K450LM2Groups are read from the sample names, not from the paper. Check the list below.
Data you can get
A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Summary (written by the submitters)
Purpose: To elucidate the molecular basis governing lung metastasis in ESCC cells, we established two subpopulations of ESCC cells with enhanced pulmonary metastatic potential, namely K30LM3 and K450LM2 respectively. Then, transcriptional profiling of highly metastatic cells (K30LM3 and K450LM2) and their parental cells (K30 and K450) were performed to characterize differentially expressed genes (DEG).
Read the full summary ↓
Methods: When parental and highly metastatic 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, 1502 genes (FDR<0.05, Fold Change>2) between K30 and K30LM3 cells and 650 genes (FDR<0.05, Fold Change>2) between K450 and K450LM2 cells were detected. Among thses DEGs, 52 genes were co-upregulated while 32 genes were co-downregulated in K30LM3/K450LM2 cells. GSEA showed that these commonly-changed genes were significantly enriched in epithelial-mesenchymal transition (EMT), cell adhesion, and anoikis process. Conclusions: In vivo selection approach enriched highly metastatic subpopulations with acquired essential molecular traits.
This dataset
Open GSE182090 in finder → Find more human RNA-seq datasets → Esophageal cancer landscape →
Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE182090_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA754435 and SRA study SRP332487. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
3 × K30 vs 3 × K30LM3 vs 3 × K450 vs 3 × K450LM2

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 12 sample titles; they account for 12 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study
More Esophageal cancer datasets

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