RNA-Seq profiling of circular RNAs in human colorectal cancer 5-fluorouracil resistance and the potential biomarkers
Non-coding RNA profiling · human · 12 samples
- What it is
- Non-coding RNA profilingLevels of RNAs that do not code for proteins, such as miRNA or lncRNA.
- Organism
- Homo sapiens (human)
- Topic
- Colorectal cancerThis series is part of our curated briefing on it.
- Samples
- 12 samples: 3 × HCT116WT vs 3 × HCT116-5Fu vs 3 × Lovo-WT vs 3 × Lovo-5FuGroups 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 GSE181537_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.
Also filed as BioProject PRJNA752379 and SRA study SRP331246. 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.
- GSM5504745 HCT116WT1 HCT116WT
- GSM5504746 HCT116WT2 HCT116WT
- GSM5504747 HCT116WT3 HCT116WT
- GSM5504748 HCT116-5FuR1 HCT116-5Fu
- GSM5504749 HCT116-5FuR2 HCT116-5Fu
- GSM5504750 HCT116-5FuR3 HCT116-5Fu
- GSM5504751 Lovo-WT1 Lovo-WT
- GSM5504752 Lovo-WT2 Lovo-WT
- GSM5504753 Lovo-WT3 Lovo-WT
- GSM5504754 Lovo-5FuR1 Lovo-5Fu
- GSM5504755 Lovo-5FuR2 Lovo-5Fu
- GSM5504756 Lovo-5FuR3 Lovo-5Fu
- 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
- GSE110009 Single cell transcriptome landscape of primary and metastatic tumor in colon cancer 76 samples same disease briefing
- GSE289499 Uncovering Stage-Specific Biomarkers in Colorectal Cancer: RNA-Seq Analysis of Adenoma and Carcinoma Progression 29 samples shares colorectal, biomarkers, rna-seq
- GSE312983 A single-nucleus RNA-seq atlas of colorectal cancer across the age continuum reveals distinct features of early-onset colorectal cancer 189 samples shares colorectal, 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
- GSE287540 Transcriptomic and proteomic characterization of cell and protein biomarkers of checkpoint inhibitor-induced liver injury [bulk RNA-seq] 128 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.