New strategies for the identification of intronic variants related to splicing events in pancreas cancer [RNA-Seq]
Single-nucleus RNA-seq · human · 24 samples
- What it is
- Single-nucleus RNA-seqGene activity measured in individual nuclei (used when whole cells are hard to isolate, for example from frozen tissue). Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
- Organism
- Homo sapiens (human)
- Samples
- 24 samples
- 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
- A single-cell strategy for the identification of intronic variants related to mis-splicing in pancreatic cancerNAR genomics and bioinformatics · 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 GSE228844_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.
Also filed as BioProject PRJNA951721 and SRA study SRP430707. Searching any of these in the dataset finder brings you back here.
The grouping that defines any comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Sample titles run KFO-1 … KFO-24 and carry no group information.
- GSM7140361 KFO-1
- GSM7140362 KFO-2
- GSM7140363 KFO-3
- GSM7140364 KFO-4
- GSM7140365 KFO-5
- GSM7140366 KFO-6
- GSM7140367 KFO-7
- GSM7140368 KFO-8
- GSM7140369 KFO-9
- GSM7140370 KFO-10
- GSM7140371 KFO-11
- GSM7140372 KFO-12
- GSM7140373 KFO-13
- GSM7140374 KFO-14
- GSM7140375 KFO-15
- GSM7140376 KFO-16
- GSM7140377 KFO-17
- GSM7140378 KFO-18
- GSM7140379 KFO-19
- GSM7140380 KFO-20
- GSM7140381 KFO-21
- GSM7140382 KFO-22
- GSM7140383 KFO-23
- GSM7140384 KFO-24
- GSE281106 Single-cell RNA-seq of peripheral blood links cell-type-specific regulation of splicing to autoimmune and inflammatory diseases [scRNAseq_KR_SGI] 352 samples shares splicing, rna-seq
- GSE325047 Pervasive Enhanced Transcription in Inflammatory Breast Cancer Tumors and PBMCs Impacts RNA Splicing and Intronic RNAs in Plasma 80 samples shares intronic, splicing
- GSE247367 Pathogenic TSC2 variants alter developmental trajectories of human cortical organoids and perturb cell-cell communication networks [bulk RNA-seq] 80 samples shares variants, rna-seq
- GSE285077 Chromatin-associated lncRNA-splicing factor condensates regulate hypoxia responsive RNA processing of genes pre-positioned near nuclear speckles [RNA-seq] 76 samples shares splicing, rna-seq
- GSE306690 QKI ensures splicing fidelity during cardiogenesis by engaging the U6 tri-snRNP to activate splicing at weak 5’splice sites [RNA-Seq] 30 samples shares splicing, rna-seq
- GSE277221 Role of the SAF-A SAP domain in X inactivation, transcription, splicing, and cell proliferation [RNA-seq] 28 samples shares splicing, rna-seq
- GSE284387 DNMT1 RFTS mutation alters RNA splicing and drives neurodegeneration via its RNA-binding function [RNA-Seq] 26 samples shares splicing, rna-seq
- GSE278450 Glioblastoma scRNA-seq shows treatment-induced, immune-dependent increase in mesenchymal cancer cells and structural variants in distal neural stem cells 22 samples shares variants, rna-seq
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.