Deciphering the cis-regulatory code of alternative splicing in human cell lines
RNA-seq (gene expression) · human · 11 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
- 11 samples: 5 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
- Massively parallel assay of human splice variants reveals cis-regulatory drivers of disease-associated and cell type-specific splicing regulationbioRxiv : the preprint server for biology · 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 GSE307247_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 PRJNA1314833 and SRA study SRP617140. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 10 samples.
How we read this: 5 replicated groups read from 11 sample titles; they account for 10 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.
- GSM9219919 HEK293 MPRA replicate 1 HEK293 MPRA
- GSM9219920 HEK293 MPRA replicate 2 HEK293 MPRA
- GSM9219921 HeLa MPRA replicate 1 HeLa MPRA
- GSM9219922 HeLa MPRA replicate 2 HeLa MPRA
- GSM9219923 HMC3 MPRA replicate 1 HMC3 MPRA
- GSM9219924 HMC3 MPRA replicate 2 HMC3 MPRA
- GSM9219925 K562 MPRA replicate 1 K562 MPRA
- GSM9219926 K562 MPRA replicate 2 K562 MPRA
- GSM9219927 MCF7 MPRA replicate 1 MCF7 MPRA
- GSM9219928 MCF7 MPRA replicate 2 MCF7 MPRA
- GSM9219929 ESL DNA-seq
- GSE250435 High-density resolution of the Kaposi’s Sarcoma associated Herpesvirus transcriptome identifies novel transcript isoforms generated by long-range transcription and alternative splicing 23 samples shares alternative, splicing
- GSE334651 Alternative splicing- and gene fusion-derived neoepitopes in MASLD-associated hepatocellular carcinoma 120 samples shares alternative, splicing
- GSE270408 OBSCN undergoes extensive alternative splicing throughout human cardiac and skeletal muscle development 71 samples shares alternative, splicing
- GSE231555 Splicing and gene expression changes in cell lines treated with splicing switching oligonucleotide targeting TRA2B 46 samples shares splicing, lines
- GSE100638 Large-scale tethering of RNA binding proteins discovers alternative splicing regulators 220 samples shares alternative, splicing
- GSE297994 Native long-read RNA sequencing of human monocytes reveals activation-induced alternative splicing toward functional isoforms 22 samples shares alternative, splicing
- GSE262667 SRSF7-mediated Alternative Splicing of USO1 Promotes Hepatocellular Carcinoma by Activating the MAPK/ERK1-ELK1 Pathway 19 samples shares alternative, splicing
- GSE279274 Alternative splicing is an FXRα loss-of-function mechanism and impacts energy metabolism in hepatocarcinoma cells. 16 samples shares alternative, 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.