Discovery of novel circular RNAs through integration of short- and long-read RNA sequencing
RNA-seq (gene expression) · human · 13 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
- 13 samples: 13 samples, each with a distinct title — no replicated groupsGroups 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.
- Paper
- Integration of Short- and Long-Read RNA Sequencing Enables the Discovery of Circular RNAsCancer research · 2026
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 GSE250483_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 PRJNA1054143 and SRA study SRP478730. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 2 samples read as cases, 1 as controls.
How we read this: Read from 13 sample titles: 13 distinct titles with little repetition. 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.
- GSM7979681 HCT116 cell line, short-read
- GSM7979682 HT29 cell line, short-read
- GSM7979683 LoVo cell line, short-read
- GSM7979684 SW480 cell line, short-read
- GSM7979685 SW620 cell line, short-read
- GSM7979686 HCT116 cell line, long-read, Nanopore pilot
- GSM7979687 HCT116 cell line, long-read, Nanopore
- GSM7979688 HCT116 cell line, long-read, PacBio
- GSM7979689 HT29 cell line, long-read, PacBio
- GSM7979690 LoVo cell line, long-read, PacBio
- GSM7979691 Normal colon mucosa, subject 722, sample ID 30, long-read, PacBio
- GSM7979692 Primary colon cancer, subject 722, sample ID 29, long-read, PacBio
- GSM7979693 Liver metastasis, subject 722, sample ID 37, long-read, PacBio
- 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
- GSE12032 Inherent gene signature of stage II and III colorectal cancer leads in individual recurrence 198 samples same disease briefing
- 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
- GSE282552 Long-read RNA sequencing reveals synaptic genes with differential isoform usage in schizophrenia [short-read RNAseq ] 18 samples shares long-read, short, rnas
- GSE282551 Long-read RNA sequencing reveals synaptic genes with differential isoform usage in schizophrenia [long-read RNAseq ] 30 samples shares long-read, rnas
- GSE271530 Accurate isoform quantification by joint short- and long-read RNA-sequencing 12 samples shares long-read, short
- GSE245986 Profiling circular RNAs across human embryonic stem cell differentiation identifies the role of circACVR2A(4-6) in neuroectoderm lineage differentiation. 54 samples shares circular, rnas
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.