Hypoxia-induced gene expression profiling of esophageal cancer cell lines
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 × KYSE150 Normoxia vs 3 × KYSE150 Hypoxia vs 3 × KYSE410 Normoxia vs 3 × KYSE410 HypoxiaGroups 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.
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.
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.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE225645_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA936875 and SRA study SRP423543. Searching any of these in the dataset finder brings you back here.
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.
- GSM7053643 KYSE150 Normoxia rep1 KYSE150 Normoxia
- GSM7053644 KYSE150 Normoxia rep2 KYSE150 Normoxia
- GSM7053645 KYSE150 Normoxia rep3 KYSE150 Normoxia
- GSM7053646 KYSE150 Hypoxia rep1 KYSE150 Hypoxia
- GSM7053647 KYSE150 Hypoxia rep2 KYSE150 Hypoxia
- GSM7053648 KYSE150 Hypoxia rep3 KYSE150 Hypoxia
- GSM7053649 KYSE410 Normoxia rep1 KYSE410 Normoxia
- GSM7053650 KYSE410 Normoxia rep2 KYSE410 Normoxia
- GSM7053651 KYSE410 Normoxia rep3 KYSE410 Normoxia
- GSM7053652 KYSE410 Hypoxia rep1 KYSE410 Hypoxia
- GSM7053653 KYSE410 Hypoxia rep2 KYSE410 Hypoxia
- GSM7053654 KYSE410 Hypoxia rep3 KYSE410 Hypoxia
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- GSE173164 To investigate the effects of NRF2 inhibitors (pyrimethamine and mitoxantrone) on gene expression in a human esophageal squamous cell carcinoma cell line (KYSE70) 8 samples same disease briefing · shares esophageal
- GSE160269 Dissecting esophageal squamous-cell carcinoma ecosystem by single-cell transcriptomic analysis 128 samples same disease briefing · shares esophageal
- GSE182090 RNA-sequencing assay to Identify Genes Promoting Lung Metastasis of Esophageal Squamous Cell Carcinoma (ESCC) Cells 12 samples same disease briefing · shares esophageal
- GSE169337 Identification of differentially expressed genes in cisplatin-resistant and parental esophageal squamous cell carcinoma cells 8 samples same disease briefing · shares esophageal
- GSE232467 Single-cell Transcriptomic Analysis Reveals Landscape of Epithelial-Mesenchymal Transition Molecular Heterogeneity in Esophageal Squamous Cell Carcinoma 6 samples same disease briefing · shares esophageal
- GSE185617 Long non-coding RNA LINC00680 functions as a ceRNA to promote esophageal squamous cell carcinoma progression through the miR-423-5p/PAK6 axis 24 samples same disease briefing · shares esophageal
- GSE203067 Single-Cell Transcriptomic Analysis of Primary and Metastatic Tumor Ecosystems in Esophageal Squamous Cell Carcinoma 21 samples same disease briefing · shares esophageal
Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.