Genome organization around nuclear speckles drives mRNA splicing efficiency
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 × Muscle SPRITE vs 12 × Human H1 DNA SPRITEGroups 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
- Genome organization around nuclear speckles drives mRNA splicing efficiencyNature · 2024
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 GSE247833_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 PRJNA1040796 and SRA study SRP472090. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 24 samples.
How we read this: 2 replicated groups read from 26 sample titles; they account for 24 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.
- GSM7901411 pSM33 cells, 10min 5EU feed
- GSM8173708 Muscle SPRITE 1 Muscle SPRITE
- GSM8173709 Muscle SPRITE 2 Muscle SPRITE
- GSM8173710 Muscle SPRITE 3 Muscle SPRITE
- GSM8173711 Muscle SPRITE 4 Muscle SPRITE
- GSM8173712 Muscle SPRITE 5 Muscle SPRITE
- GSM8173713 Muscle SPRITE 6 Muscle SPRITE
- GSM8173714 Muscle SPRITE 7 Muscle SPRITE
- GSM8173715 Muscle SPRITE 8 Muscle SPRITE
- GSM8173716 Muscle SPRITE 9 Muscle SPRITE
- GSM8173717 Muscle SPRITE 10 Muscle SPRITE
- GSM8173718 Muscle SPRITE 11 Muscle SPRITE
- GSM8173719 Muscle SPRITE 12 Muscle SPRITE
- GSM8173720 Human H1 RD SPRITE
- GSM8173721 Human H1 DNA SPRITE 1 Human H1 DNA SPRITE
- GSM8173722 Human H1 DNA SPRITE 2 Human H1 DNA SPRITE
- GSM8173723 Human H1 DNA SPRITE 3 Human H1 DNA SPRITE
- GSM8173724 Human H1 DNA SPRITE 4 Human H1 DNA SPRITE
- GSM8173725 Human H1 DNA SPRITE 5 Human H1 DNA SPRITE
- GSM8173726 Human H1 DNA SPRITE 6 Human H1 DNA SPRITE
- GSM8173727 Human H1 DNA SPRITE 7 Human H1 DNA SPRITE
- GSM8173728 Human H1 DNA SPRITE 8 Human H1 DNA SPRITE
- GSM8173729 Human H1 DNA SPRITE 9 Human H1 DNA SPRITE
- GSM8173730 Human H1 DNA SPRITE 10 Human H1 DNA SPRITE
- GSM8173731 Human H1 DNA SPRITE 11 Human H1 DNA SPRITE
- GSM8173732 Human H1 DNA SPRITE 12 Human H1 DNA SPRITE
- GSE286557 Nitric oxide drives proteomic diversity through alternative splicing 44 samples shares splicing, drives
- GSE239745 Mis-splicing Drives Loss of Function of p53E224D Point Mutation 15 samples shares splicing, drives
- GSE324908 Alternative splicing-triggered mRNA decay informs splice-switching targets for neurodevelopmental disorders 14 samples shares splicing, mrna
- GSE80006 Single-cell Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition 246 samples shares organization
- GSE255769 Polyamine-dependent metabolic shielding regulates alternative splicing 144 samples shares splicing
- GSE294247 The PRMT5-splicing axis is a critical oncogenic vulnerability that regulates detained intron splicing 110 samples shares splicing
- GSE293172 Pioneer factors orchestrate tissue-specific cohesin-NIPBL chromatin entry and 3D genome organization [ChIP-seq] 68 samples shares organization
- GSE270445 The drug-elicitable alternative splicing module for tunable vector expression in the heart 36 samples shares splicing
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.