Uncovering Stage-Specific Biomarkers in Colorectal Cancer: RNA-Seq Analysis of Adenoma and Carcinoma Progression
RNA-seq (gene expression) · human · 29 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
- Colorectal cancerThis series is part of our curated briefing on it.
- Samples
- 29 samples: 11 × Adenocarcinoma vs 10 × Tubular_Adenoma vs 8 × Carcinoma_In_SituGroups 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.
Read the full summary ↓
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 GSE289499_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 PRJNA1223315 and SRA study SRP563675. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 29 samples.
How we read this: 3 replicated groups read from 29 sample titles; they account for 29 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.
- GSM8792791 Tubular_Adenoma_1 Tubular_Adenoma
- GSM8792792 Tubular_Adenoma_2 Tubular_Adenoma
- GSM8792793 Tubular_Adenoma_3 Tubular_Adenoma
- GSM8792794 Tubular_Adenoma_4 Tubular_Adenoma
- GSM8792795 Tubular_Adenoma_5 Tubular_Adenoma
- GSM8792796 Tubular_Adenoma_6 Tubular_Adenoma
- GSM8792797 Tubular_Adenoma_7 Tubular_Adenoma
- GSM8792798 Tubular_Adenoma_8 Tubular_Adenoma
- GSM8792799 Tubular_Adenoma_9 Tubular_Adenoma
- GSM8792800 Tubular_Adenoma_10 Tubular_Adenoma
- GSM8792801 Adenocarcinoma_1 Adenocarcinoma
- GSM8792802 Adenocarcinoma_2 Adenocarcinoma
- GSM8792803 Adenocarcinoma_3 Adenocarcinoma
- GSM8792804 Adenocarcinoma_4 Adenocarcinoma
- GSM8792805 Adenocarcinoma_5 Adenocarcinoma
- GSM8792806 Adenocarcinoma_6 Adenocarcinoma
- GSM8792807 Adenocarcinoma_7 Adenocarcinoma
- GSM8792808 Adenocarcinoma_8 Adenocarcinoma
- GSM8792809 Adenocarcinoma_9 Adenocarcinoma
- GSM8792810 Adenocarcinoma_10 Adenocarcinoma
- GSM8792811 Adenocarcinoma_11 Adenocarcinoma
- GSM8792812 Carcinoma_In_Situ_1 Carcinoma_In_Situ
- GSM8792813 Carcinoma_In_Situ_2 Carcinoma_In_Situ
- GSM8792814 Carcinoma_In_Situ_3 Carcinoma_In_Situ
- GSM8792815 Carcinoma_In_Situ_4 Carcinoma_In_Situ
- GSM8792816 Carcinoma_In_Situ_5 Carcinoma_In_Situ
- GSM8792817 Carcinoma_In_Situ_6 Carcinoma_In_Situ
- GSM8792818 Carcinoma_In_Situ_7 Carcinoma_In_Situ
- GSM8792819 Carcinoma_In_Situ_8 Carcinoma_In_Situ
- GSE250000 Bulk RNA-sequencing of transduced colorectal cancer cell line HCT-116 and breast cancer cell line MCF-7 overexpressing full-lenght p53β or p53β-stop-lost. 4 samples same disease briefing · shares colorectal, rna-seq
- GSE12032 Inherent gene signature of stage II and III colorectal cancer leads in individual recurrence 198 samples same disease briefing · shares colorectal
- GSE109308 Single-cell transcriptomic survey of adenomatous polyposis patients with germline APC mutations 97 samples same disease briefing · shares adenoma
- GSE110009 Single cell transcriptome landscape of primary and metastatic tumor in colon cancer 76 samples same disease briefing
- GSE319969 Spatial and Bulk Transcriptomic Profiling Defines the Molecular Evolution of Cutaneous Squamous Cell Carcinoma and Reveals Stage-Specific Biomarkers of Clinical Relevance [RNA-Seq] 24 samples shares stage-specific, biomarkers, rna-seq
- GSE181537 RNA-Seq profiling of circular RNAs in human colorectal cancer 5-fluorouracil resistance and the potential biomarkers 12 samples shares biomarkers, colorectal, rna-seq
- GSE325054 Time-Resolved Multi-Omics Identify Biomarkers of Immediate Reactions to mRNA Vaccination [RNA-Seq] 187 samples shares biomarkers, rna-seq
- GSE251778 Sex-specific and multiomic integration enhance accuracy of peripheral blood biomarkers of major depressive disorder [RNA-Seq] 169 samples shares biomarkers, rna-seq
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.