Cell-free transcriptome of Barrett’s Esophagus and Esophageal Cancer [Nanopore - long read]
RNA-seq (gene expression) · human · 47 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
- 47 samples: 12 × A vs 12 × B vs 12 × D vs 11 × CGroups 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 GSE271389_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 PRJNA1131298 and SRA study SRP517728. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 47 samples.
How we read this: 4 replicated groups read from 47 sample titles; they account for 47 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.
- GSM8375942 A01 A
- GSM8375943 A02 A
- GSM8375944 A03 A
- GSM8375945 A04 A
- GSM8375946 A05 A
- GSM8375947 A06 A
- GSM8375948 A07 A
- GSM8375949 A08 A
- GSM8375950 A09 A
- GSM8375951 A10 A
- GSM8375952 A11 A
- GSM8375953 A12 A
- GSM8375954 B01 B
- GSM8375955 B02 B
- GSM8375956 B03 B
- GSM8375957 B04 B
- GSM8375958 B05 B
- GSM8375959 B06 B
- GSM8375960 B07 B
- GSM8375961 B08 B
- GSM8375962 B09 B
- GSM8375963 B10 B
- GSM8375964 B11 B
- GSM8375965 B12 B
- GSM8375966 C01 C
- GSM8375967 C02 C
- GSM8375968 C03 C
- GSM8375969 C04 C
- GSM8375970 C06 C
- GSM8375971 C07 C
- GSM8375972 C08 C
- GSM8375973 C09 C
- GSM8375974 C10 C
- GSM8375975 C11 C
- GSM8375976 C12 C
- GSM8375977 D01 D
- GSM8375978 D02 D
- GSM8375979 D03 D
- GSM8375980 D04 D
- GSM8375981 D05 D
+ 7 more — browse all 47 samples with per-sample file links →
- GSE1420 Barrett's esophagus, Barrett's-associated adenocarcinomas and normal esophageal epithelium 24 samples same disease briefing · shares esophageal, esophagus, barrett
- 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, long
- GSE13083 Barrett's vs Normal esophagus vs small intestine comparison 19 samples same disease briefing · shares esophagus, barrett
- GSE180791 Proteogenomic characterization reveals that lipid droplet formation promotes esophageal squamous cell cancer progression 102 samples same disease briefing · shares esophageal
- GSE225645 Hypoxia-induced gene expression profiling of esophageal cancer cell lines 12 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
- GSE203067 Single-Cell Transcriptomic Analysis of Primary and Metastatic Tumor Ecosystems in Esophageal Squamous Cell Carcinoma 21 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
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.