CRP-seq: a reliable and fast method for sequencing RNA G-quadruplexes transcriptome-wide
RNA-seq (gene expression) · human · 18 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
- 18 samples: 7 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
- Ultra-Specific G-Quadruplex-Colistin Interaction for Efficient Transcriptome-Wide G4 MappingJournal of the American Chemical Society · 2025
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 GSE260479_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 PRJNA1081860 and SRA study SRP492359. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 14 samples.
How we read this: 7 replicated groups read from 18 sample titles; they account for 14 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.
- GSM8118113 BG4,10ug,Flag, R1 BG4,10ug,Flag,
- GSM8118114 BG4,10ug,Flag, R2 BG4,10ug,Flag,
- GSM8118115 BG4,10ug, IP, R1 BG4,10ug, IP,
- GSM8118116 BG4,10ug, IP, R2 BG4,10ug, IP,
- GSM8118117 BG4,1ug,IP, R1 BG4,1ug,IP,
- GSM8118118 BG4,1ug,IP, R2 BG4,1ug,IP,
- GSM8118119 BG4,Input, R1 BG4,Input,
- GSM8118120 BG4,Input, R2 BG4,Input,
- GSM8118121 CRPseq,CMScontrol, R1 CRPseq,CMScontrol,
- GSM8118122 CRPseq,CMScontrol, R2 CRPseq,CMScontrol,
- GSM8118123 CRPseq,Input, R1 CRPseq,Input,
- GSM8118124 CRPseq,Input, R2 CRPseq,Input,
- GSM8118125 CRPseq,IP, R1 CRPseq,IP,
- GSM8118126 CRPseq,IP, R2 CRPseq,IP,
- GSM8118127 CRPseq.Li, R1
- GSM8118128 CRPseq,Li, R2
- GSM8118129 CRPseq,Input,500ng
- GSM8118130 CRPseq,IP,500ng
- GSE248461 An in situ method for identification of transcriptome-wide protein-RNA interactions in cells [in_situ_STAMP II] 14 samples shares transcriptome-wide, method
- GSE255775 Transcriptomic Profiling of Plasma Extracellular Vesicles Enables Reliable Annotation of the Cancer-specific Transcriptome and Molecular Subtype 319 samples shares reliable
- GSE264667 Transcriptome-wide characterization of genetic perturbations 224 samples shares transcriptome-wide
- GSE259422 Transcriptomic Profiling of Plasma Extracellular Vesicles Enables Reliable Annotation of the Cancer-specific Transcriptome and Molecular Subtype (plasma_cancer) 156 samples shares reliable
- GSE254194 Transcriptome-wide identification of 5-methylcytosine by deaminase and reader protein-assisted sequencing 20 samples shares transcriptome-wide
- GSE21918 Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP: sequencing data 15 samples shares transcriptome-wide
- GSE301521 FOCAS: Transcriptome-wide screening of individual m6A sites functionally dissects epitranscriptomic control of gene expression in cancer [FOCAS_4cellline_RNAseq] 72 samples shares transcriptome-wide
- GSE260560 Transcriptomic Profiling of Plasma Extracellular Vesicles Enables Reliable Annotation of the Cancer-specific Transcriptome and Molecular Subtype (plasma_healthy) 70 samples shares reliable
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.