Pathogenic variants in the splicing factor SF1 lead to a new neurodevelopmental disorder.
RNA-seq (gene expression) · human · 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
- Homo sapiens (human)
- Samples
- 12 samples: 6 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
- Heterozygous pathogenic variants in the splicing factor SF1 lead to a large spectrum of neurodevelopmental disordersAmerican journal of human genetics · 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 GSE288121_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 PRJNA1216233 and SRA study SRP560144. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 6 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.
- GSM8759298 siCTRL-1, NPC line 1 siCTRL-1, NPC line
- GSM8759299 siCTRL-2, NPC line 1 siCTRL-2, NPC line
- GSM8759300 siCTRL-3, NPC line 1 siCTRL-3, NPC line
- GSM8759301 siSF1-1, NPC line 1 siSF1-1, NPC line
- GSM8759302 siSF1-2, NPC line 1 siSF1-2, NPC line
- GSM8759303 siSF1-3, NPC line 1 siSF1-3, NPC line
- GSM8759304 siCTRL-1, NPC line 2 siCTRL-1, NPC line
- GSM8759305 siCTRL-2, NPC line 2 siCTRL-2, NPC line
- GSM8759306 siCTRL-3, NPC line 2 siCTRL-3, NPC line
- GSM8759307 siSF1-1, NPC line 2 siSF1-1, NPC line
- GSM8759308 siSF1-2, NPC line 2 siSF1-2, NPC line
- GSM8759309 siSF1-3, NPC line 2 siSF1-3, NPC line
- GSE301239 SETBP1 variants outside the degron disrupt DNA-binding, transcription and neuronal differentiation capacity to cause a heterogeneous neurodevelopmental disorder [induced neurons] 51 samples shares neurodevelopmental, variants, disorder
- GSE301142 Multiple mechanisms lead to differential loss-of-function effects of pathogenic SARS2 variants: implications for genotype-phenotype analyses 18 samples shares pathogenic, variants, lead
- GSE329548 Multiple mechanisms lead to differential loss-of-function effects of pathogenic SARS2 variants: implications for genotype-phenotype analyses II 9 samples shares pathogenic, variants, lead
- GSE293189 Histologic variants in bladder cancer share aggressive molecular features including a CA125+ cell state and targetable TM4SF1 expression 67 samples shares sf1, variants
- GSE176189 Integrative single-cell and spatial transcriptomic analyses identify a pathogenic cholangiocyte niche and TNFRSF12A as therapeutic target for biliary atresia 36 samples shares sf1, pathogenic
- GSE302052 IRF2 is an Essential Transcription Factor with Pathogenic and Prognostic Impact in Multiple Myeloma 257 samples shares pathogenic, factor
- GSE247367 Pathogenic TSC2 variants alter developmental trajectories of human cortical organoids and perturb cell-cell communication networks [bulk RNA-seq] 80 samples shares pathogenic, variants
- GSE119316 Impaired oxysterol-liver X receptor signaling underlies aberrant cortical neurogenesis in a stem cell model of neurodevelopmental disorder 71 samples shares neurodevelopmental, disorder
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.