snPATHO-seq: unlocking the FFPE archives for single nucleus RNA profiling [snRNA-seq]
Single-nucleus RNA-seq · human · 37 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
- 37 samples: 37 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
- snPATHO-seq, a versatile FFPE single-nucleus RNA sequencing method to unlock pathology archivesCommunications biology · 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 GSE268426_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 PRJNA1117352 and SRA study SRP510236. 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 37 sample titles: 37 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.
- GSM8291032 4066, FFPE, single-nucleus, snPATHO-seq workflow
- GSM8291033 4066, FFPE, single-cell, scFFPE workflow
- GSM8291034 4066, snap frozen, single-nucleus, FLEX workflow
- GSM8291035 4066, snap frozen, single-nucleus, 3' workflow
- GSM8291036 4399, FFPE, single-nucleus, snPATHO-seq workflow
- GSM8291037 4399, FFPE, single-cell, scFFPE workflow
- GSM8291038 4399, snap frozen, single-nucleus, FLEX workflow
- GSM8291039 4399, snap frozen, single-nucleus, 3' workflow
- GSM8291040 4411, FFPE, single-nucleus, snPATHO-seq workflow
- GSM8291041 4411, FFPE, single-cell, scFFPE workflow
- GSM8291042 4411, snap frozen, single-nucleus, FLEX workflow
- GSM8291043 4411, snap frozen, single-nucleus, 3' workflow
- GSM8291044 PBMC, replicate 1, viably frozen, single-cell, FLEX workflow
- GSM8291045 PBMC, replicate 1, viably frozen, single-cell, 3' workflow
- GSM8291046 PBMC, replicate 2, viably frozen, single-cell, FLEX workflow
- GSM8291047 PBMC, replicate 2, viably frozen, single-cell, 3' workflow
- GSM8291048 Kidney_k48, FFPE, single-nucleus, snPATHO-seq workflow
- GSM8291049 Kidney_k48, FFPE, single-cell, scFFPE workflow
- GSM8291050 Colon_1328A, FFPE, single-nucleus, snPATHO-seq workflow
- GSM8291051 Colon_1328A, FFPE, single-cell, scFFPE workflow
- GSM8291052 Endocervical_Adenocarcinoma_6707, FFPE, single-nucleus, snPATHO-seq workflow
- GSM8291053 Endocervical_Adenocarcinoma_6707, FFPE, single-cell, scFFPE workflow
- GSM8291054 Glioblastoma_1773A, FFPE, single-nucleus, snPATHO-seq workflow
- GSM8291055 Glioblastoma_1773A, FFPE, single-cell, scFFPE workflow
- GSM8291056 Kidney_1305272B, FFPE, single-nucleus, snPATHO-seq workflow
- GSM8291057 Kidney_1305272B, FFPE, single-cell, scFFPE workflow
- GSM8291058 liver_8754A, FFPE, single-nucleus, snPATHO-seq workflow
- GSM8291059 liver_8754A, FFPE, single-cell, scFFPE workflow
- GSM8291060 lung_20011329NL, FFPE, single-nucleus, snPATHO-seq workflow
- GSM8291061 lung_20011329NL, FFPE, single-cell, scFFPE workflow
- GSM8291062 lung_cancer_20011329LC, FFPE, single-nucleus, snPATHO-seq workflow
- GSM8291063 lung_cancer_20011329LC, FFPE, single-cell, scFFPE workflow
- GSM8291064 melanoma_7167A, FFPE, single-nucleus, snPATHO-seq workflow
- GSM8291065 melanoma_7167A, FFPE, single-cell, scFFPE workflow
- GSM8291066 Colon_213641, FFPE, single-nucleus, snPATHO-seq workflow
- GSM8291067 Endometrium_220952, FFPE, single-nucleus, snPATHO-seq workflow
- GSM8291068 Ovary_230303, FFPE, single-nucleus, snPATHO-seq workflow
- GSE274141 Single-Cell RNA Sequencing Identifies Molecular Biomarkers Predicting Late Progression to CDK4/6 Inhibition in Patients with HR+/HER2- Metastatic Breast Cancer [FFPE] 54 samples shares ffpe
- GSE205154 Bulk RNA-Seq gene expression data for 289 primary and metastatic pancreatic ductal adenocarcinoma (PDAC) tumor samples from FFPE blocks. 289 samples shares ffpe
- GSE228375 A gene expression profiling study to identify distinct molecular markers in formalin-fixed, paraffin-embedded samples of Pseudomyxoma Peritonei [FFPE] 34 samples shares ffpe
- GSE272042 Transcriptomics of FFPE-derived primary brain tumours 153 samples shares ffpe
- GSE253548 The whole transcriptome analysis using FFPE and fresh tissue samples identifies the molecular fingerprint of osteosarcoma 90 samples shares ffpe
- GSE289743 Cancer-induced nerve injury promotes resistance to anti-PD-1 therapy [RNA-Seq FFPE] 83 samples shares ffpe
- GSE336901 RNA-seq profiling of FFPE samples from treatment-sensitive and treatment-resistant breast cancer cases 10 samples shares ffpe
- GSE278793 Single-cell RNA sequencing of breast cancer cells from fresh fixed (FF) and formalin-fixed paraffin-embedded (FFPE) tissue identified multi-ciliary cells 4 samples shares ffpe
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.