Single Nucleus RNAseq dissection of choroid plexus tumor cell heterogeneity
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). 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
- 15 samples: 5 × choroid plexus tumor, CPC, sample vs 4 × choroid plexus, normal, sample vs 4 × choroid plexus tumor, CPP, sample vs 2 × choroid plexus tumor, aCPP, sampleGroups 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
- Single-nucleus RNA-seq dissection of choroid plexus tumor cell heterogeneityThe EMBO journal · 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 GSE264154_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 PRJNA1101064 and SRA study SRP502101. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 11 samples read as cases, 4 as controls.
How we read this: 4 replicated groups read from 15 sample titles; they account for 15 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.
- GSM8213045 choroid plexus, normal, sample 1 choroid plexus, normal,…
- GSM8213046 choroid plexus, normal, sample 2 choroid plexus, normal,…
- GSM8213047 choroid plexus, normal, sample 3 choroid plexus, normal,…
- GSM8213048 choroid plexus, normal, sample 4 choroid plexus, normal,…
- GSM8213049 choroid plexus tumor, aCPP, sample 1 choroid plexus tumor, a…
- GSM8213050 choroid plexus tumor, aCPP, sample 2 choroid plexus tumor, a…
- GSM8213051 choroid plexus tumor, CPP, sample 1 choroid plexus tumor, C…
- GSM8213052 choroid plexus tumor, CPP, sample 2 choroid plexus tumor, C…
- GSM8213053 choroid plexus tumor, CPP, sample 3 choroid plexus tumor, C…
- GSM8213054 choroid plexus tumor, CPP, sample 4 choroid plexus tumor, C…
- GSM8213055 choroid plexus tumor, CPC, sample 1 choroid plexus tumor, C…
- GSM8213056 choroid plexus tumor, CPC, sample 2 choroid plexus tumor, C…
- GSM8213057 choroid plexus tumor, CPC, sample 3 choroid plexus tumor, C…
- GSM8213058 choroid plexus tumor, CPC, sample 4 choroid plexus tumor, C…
- GSM8213059 choroid plexus tumor, CPC, sample 5 choroid plexus tumor, C…
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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.