A Simplified Preparation Method for Single-Nucleus RNA-Sequencing Using Long-Term Frozen Brain Tumor Tissues
Single-nucleus RNA-seq · human · 15 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).
- Organism
- Homo sapiens (human)
- Samples
- 15 samples: 15 samples, each with a distinct title — no replicated groupsGroups 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
- A simplified preparation method for single-nucleus RNA-sequencing using long-term frozen brain tumor tissuesScientific reports · 2025
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 GSE268496_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 PRJNA1117461. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 15 sample titles: 15 distinct titles with little repetition. 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.
- GSM8292020 ICGC_GBM61_HiSeq4000
- GSM8292021 ICGC_GBM61_NextSeq500
- GSM8292022 ICGC_GBM61_NovaSeq6000
- GSM8292023 ICGC_PA56_HiSeq4000
- GSM8292024 ICGC_PA56_NextSeq500
- GSM8292025 ICGC_PA56_NovaSeq6000
- GSM8292026 B062_004_H1013_10X
- GSM8292027 B062_004_H1013_FluidigmC1
- GSM8292028 B062_004_H1013_DropSeq
- GSM8292029 ICGC_PA74_standard_library
- GSM8292030 ICGC_PA74_short_library
- GSM8292031 ICGC_PA74_combined_libraries
- GSM8292032 I007_024_standard_library
- GSM8292033 I007_024_short_library
- GSM8292034 I007_024_combined_libraries
- GSE266117 RoCK and ROI: a single-cell RNA-sequencing method with enhanced transcriptome information via targeted enrichment of transcripts and preselected, region-specific sequencing II 4 samples shares rna-sequencing, method
- GSE235167 Establishment of breast cancer PDX RNA-sequencing data library [bulk RNA-seq] 76 samples shares rna-sequencing
- GSE233208 Single-nucleus RNA-Seq and spatial transcriptomics characterization of Alzheimer’s Disease and Down Syndrome 185 samples shares single-nucleus
- GSE336954 Central amygdala single-nucleus atlas reveals chromatin and gene transcription dynamics in human alcohol use disorder 126 samples shares single-nucleus
- GSE44183 Genetic Programs in Human and Mouse Early Embryos Revealed by Single-Cell RNA-Sequencing 47 samples shares rna-sequencing
- GSE325427 Integrative single-nucleus multiomic, CUT&Tag, and bulk RNA-seq profiling of human and mouse prefrontal cortex reveals gene regulatory mechanisms of cortical development and Meis2 function 34 samples shares single-nucleus
- GSE306575 Spatial and single-nucleus transcriptomic profiling of CHB liver biopsies 13 samples shares single-nucleus
- GSE277747 Pooled CRISPR screens with joint single-nucleus chromatin accessibility and transcriptome profiling 1 samples shares single-nucleus
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.