Systematic identification and characterization of Exon-intron circRNAs in the human transcriptome
RNA-seq (gene expression) · human · 34 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
- 34 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 GSE241685_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 PRJNA1009102 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 34 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,
- GSM7733694 P-In,input
- GSM7733695 P-In,high-GFP
- GSM7733696 P-In,low-GFP
- GSM7733697 E-In,input
- GSM7733698 E-In,high-GFP
- GSM7733699 E-In,low-GFP
- GSM8016807 shCtrl,nascent
- GSM8016808 shSRSF1,nascent
- GSE241679 Systematic identification and characterization of Exon-intron circRNAs (RNA-Seq) 26 samples shares exon-intron, systematic, circrnas
- GSE279285 Systematic characterization of the composition and dynamics of processing body-associated mRNAs 597 samples shares systematic
- GSE279284 Systematic characterization of the composition and dynamics of processing body-associated mRNAs [dataset 2] 131 samples shares systematic
- GSE293514 Development of a split-toxin CRISPR screening platform to systematically identify upstream regulators of human myoblast fusion 57 samples shares systematic
- GSE159749 A systematic dissection of determinants and consequences of snoRNA-guided pseudouridylation of human mRNA 44 samples shares systematic
- GSE319266 Identification of target genes and regulatory networks for bone mineral density GWAS loci through systematic targeting and inhibition [hFOB BMD STING-seq] 24 samples shares systematic
- GSE190905 Single-cell RNA and TCR sequencing reveals distinct systematic immune response induced by SABR with or without prior anti-PD-1 therapy 16 samples shares systematic
- GSE273164 Systematic evaluation of GAPs and GEFs identifies ARHGAP45 as a targetable leukemia-specific RhoGAP dependency 15 samples shares systematic
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.