Large field of view and spatial region of interest transcriptomics in frozen and FFPE tissue
RNA-seq (gene expression) · human · 26 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
- 26 samples: 7 conditions, mostly with about 4 replicates eachGroups 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
- Large field of view and spatial region of interest transcriptomics in fixed tissueCommunications 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 GSE268148_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 PRJNA1114766 and SRA study SRP509264. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 26 samples.
How we read this: 7 replicated groups read from 26 sample titles; they account for 26 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.
- GSM8286373 Brain 4ROIs replicate 1 Brain 4ROIs
- GSM8286374 Brain 4ROIs replicate 2 Brain 4ROIs
- GSM8286375 Brain 4ROIs replicate 3 Brain 4ROIs
- GSM8286376 Brain 4ROIs replicate 4 Brain 4ROIs
- GSM8286377 Mouse embryo replicate 1 Mouse embryo
- GSM8286378 Mouse embryo replicate 2 Mouse embryo
- GSM8286379 Mouse embryo replicate 3 Mouse embryo
- GSM8286380 FFPE mouse embryo replicate 1 FFPE mouse embryo
- GSM8286381 FFPE mouse embryo replicate 2 FFPE mouse embryo
- GSM8286382 FFPE mouse embryo replicate 3 FFPE mouse embryo
- GSM8286383 Rare cell replicate 1 Rare cell
- GSM8286384 Rare cell replicate 2 Rare cell
- GSM8286385 Rare cell replicate 3 Rare cell
- GSM8286386 Rare cell replicate 4 Rare cell
- GSM8286387 Sub cell replicate 1 Sub cell
- GSM8286388 Sub cell replicate 2 Sub cell
- GSM8286389 Sub cell replicate 3 Sub cell
- GSM8286390 Sub cell replicate 4 Sub cell
- GSM8286391 Sta Cytoplasm replicate 1 Sta Cytoplasm
- GSM8286392 Sta Cytoplasm replicate 2 Sta Cytoplasm
- GSM8286393 Sta Cytoplasm replicate 3 Sta Cytoplasm
- GSM8286394 Sta Cytoplasm replicate 4 Sta Cytoplasm
- GSM8286395 Sta Nucleus replicate 1 Sta Nucleus
- GSM8286396 Sta Nucleus replicate 2 Sta Nucleus
- GSM8286397 Sta Nucleus replicate 3 Sta Nucleus
- GSM8286398 Sta Nucleus replicate 4 Sta Nucleus
- GSE261351 Direct measurement of RNA Polymerase II hypertranscription in cancer FFPE samples 278 samples shares ffpe
- GSE291155 Unlocking single cell chromatin accessibility in formalin-fixed paraffin-embedded tissues by scFFPE-ATAC 8 samples shares ffpe
- GSE246613 Single-cell and spatial profiling identify three response trajectories to pembrolizumab and radiation therapy in triple negative breast cancer 266 samples shares spatial
- GSE285764 Single Alkyl Phosphonate Modification of the siRNA Backbone in the Seed Region Enhances Specificity and Therapeutic Profile 110 samples shares region
- GSE313756 Tuning siRNA Specificity through Seed Region Incorporation of Deoxyribonucleotide Stereoisomers 104 samples shares region
- GSE292893 A cost-effective and flexible workflow for high-resolution spatial transcriptomics in fixed tissue 52 samples shares spatial
- 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 region
- GSE233208 Single-nucleus RNA-Seq and spatial transcriptomics characterization of Alzheimer’s Disease and Down Syndrome 185 samples shares spatial
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.