Systematic identification and characterization of Exon-intron circRNAs (RNA-Seq)
RNA-seq (gene expression) · human · 26 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)
- Samples
- 26 samples: 12 conditions, mostly in duplicateGroups 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
- Systematic identification and characterization of exon-intron circRNAsGenome research · 2024
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 GSE241679_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 PRJNA1009108 and SRA study SRP456982. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 26 samples.
How we read this: 12 replicated groups read from 26 sample titles; they account for 26 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.
- GSM7733658 HEK293,RNaseR,rep1 HEK293,RNaseR,
- GSM7733659 HEK293,RNaseR,rep2 HEK293,RNaseR,
- GSM7733660 HEK293,RNaseR,rep3 HEK293,RNaseR,
- GSM7733661 HEK293,RNaseR,rep4 HEK293,RNaseR,
- GSM7733662 HEK293,polyA,rep1 HEK293,polyA,
- GSM7733663 HEK293,polyA,rep2 HEK293,polyA,
- GSM7733664 HEK293,shCtrl,RNaseR,rep1 HEK293,shCtrl,RNaseR,
- GSM7733665 HEK293,shCtrl,RNaseR,rep2 HEK293,shCtrl,RNaseR,
- GSM7733666 HEK293,shSRSF1,RNaseR,rep1 HEK293,shSRSF1,RNaseR,
- GSM7733667 HEK293,shSRSF1,RNaseR,rep2 HEK293,shSRSF1,RNaseR,
- GSM7733668 HEK293,shCtrl,polyA,rep1 HEK293,shCtrl,polyA,
- GSM7733669 HEK293,shCtrl,polyA,rep2 HEK293,shCtrl,polyA,
- GSM7733670 HEK293,shSRSF1,polyA,rep1 HEK293,shSRSF1,polyA,
- GSM7733671 HEK293,shSRSF1,polyA,rep2 HEK293,shSRSF1,polyA,
- GSM7733672 SH-SY5Y,D0,polyA,rep1 SH-SY5Y,D0,polyA,
- GSM7733673 SH-SY5Y,D0,polyA,rep2 SH-SY5Y,D0,polyA,
- GSM7733674 SH-SY5Y,D3,polyA,rep1 SH-SY5Y,D3,polyA,
- GSM7733675 SH-SY5Y,D3,polyA,rep2 SH-SY5Y,D3,polyA,
- GSM7733676 SH-SY5Y,D6,polyA,rep1 SH-SY5Y,D6,polyA,
- GSM7733677 SH-SY5Y,D6,polyA,rep2 SH-SY5Y,D6,polyA,
- GSM7733678 SH-SY5Y,D0,RNaseR,rep1 SH-SY5Y,D0,RNaseR,
- GSM7733679 SH-SY5Y,D0,RNaseR,rep2 SH-SY5Y,D0,RNaseR,
- GSM7733680 SH-SY5Y,D3,RNaseR,rep1 SH-SY5Y,D3,RNaseR,
- GSM7733681 SH-SY5Y,D3,RNaseR,rep2 SH-SY5Y,D3,RNaseR,
- GSM7733682 SH-SY5Y,D6,RNaseR,rep1 SH-SY5Y,D6,RNaseR,
- GSM7733683 SH-SY5Y,D6,RNaseR,rep2 SH-SY5Y,D6,RNaseR,
- GSE348445 Identification and Characterization of Adrenergic and Mesenchymal Cancer Cell States in Neuroblastoma Using Spatial-Omics [RNA-Seq] 33 samples shares rna-seq
- GSE319641 RNA-Seq profiling of pre- and on-treatment tumor samples from breast cancer patients enrolled in the NeoTRIP trial. 401 samples shares rna-seq
- GSE205154 Bulk RNA-Seq gene expression data for 289 primary and metastatic pancreatic ductal adenocarcinoma (PDAC) tumor samples from FFPE blocks. 289 samples shares rna-seq
- GSE309595 Longitudinal Analysis of Multiple Myeloma: Therapeutic Response and Immune Microenvironment Dynamics in the Context of Tumor Heterogeneity [scRNA-seq] 270 samples shares rna-seq
- GSE297742 Bulk RNA-seq of primary tumor biopsy samples from prostate adenocarcinoma patients 234 samples shares rna-seq
- GSE293805 Single nucleus RNA-sequencing atlas of pediatric solid tumors 182 samples shares rna-seq
- GSE251778 Sex-specific and multiomic integration enhance accuracy of peripheral blood biomarkers of major depressive disorder [RNA-Seq] 169 samples shares rna-seq
- GSE327707 Sorted bulk RNA-seq profiling of human peripheral blood mononuclear cell populations across diverse in vitro immune stimuli 150 samples shares 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.