RNA transcripts regulate G-quadruplex landscapes through G-loop formation (RNA-Seq)
RNA-seq (gene expression) · mouse · 12 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
- Mus musculus (mouse)
- Samples
- 12 samples: 3 × RNA-seq WT mESC vs 3 × RNA-seq DHX36 knockout mESC vs 3 × RNA-seq FANCJ knockout mESC vs 3 × RNA-seq DHX36/FANCJ double knockout mESCGroups 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
- RNA transcripts regulate G-quadruplex landscapes through G-loop formationScience (New York, N.Y.) · 2025
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 GSE269081_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 PRJNA1120076 and SRA study SRP511760. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 9 samples read as cases, 3 as controls.
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.
- GSM8305977 RNA-seq WT mESC 1 RNA-seq WT mESC
- GSM8305978 RNA-seq WT mESC 2 RNA-seq WT mESC
- GSM8305979 RNA-seq WT mESC 3 RNA-seq WT mESC
- GSM8305980 RNA-seq DHX36 knockout mESC 1 RNA-seq DHX36 knockout …
- GSM8305981 RNA-seq DHX36 knockout mESC 2 RNA-seq DHX36 knockout …
- GSM8305982 RNA-seq DHX36 knockout mESC 3 RNA-seq DHX36 knockout …
- GSM8305983 RNA-seq FANCJ knockout mESC 1 RNA-seq FANCJ knockout …
- GSM8305984 RNA-seq FANCJ knockout mESC 2 RNA-seq FANCJ knockout …
- GSM8305985 RNA-seq FANCJ knockout mESC 3 RNA-seq FANCJ knockout …
- GSM8305986 RNA-seq DHX36/FANCJ double knockout mESC 1 RNA-seq DHX36/FANCJ dou…
- GSM8305987 RNA-seq DHX36/FANCJ double knockout mESC 2 RNA-seq DHX36/FANCJ dou…
- GSM8305988 RNA-seq DHX36/FANCJ double knockout mESC 3 RNA-seq DHX36/FANCJ dou…
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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.