Predicting relevant microglia-associated cell-cell communication pathways in Alzheimer’s disease: a role for SPP1
Single-nucleus RNA-seq · human · 10 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
- 10 samples: 10 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.
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 GSE335667_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 PRJNA1479072 and SRA study SRP710159. 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 10 sample titles: 10 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.
- GSM9817297 Sample1_IB5328
- GSM9817298 Sample2_IB5431
- GSM9817299 Sample3_IB5508
- GSM9817300 Sample4_IB5816
- GSM9817301 Sample5_IB5869
- GSM9817302 Sample6_IB5875
- GSM9817303 Sample7_IB6001
- GSM9817304 Sample8_IB6125
- GSM9817305 Sample9_IB6237
- GSM9817306 Sample10_IB6239
- GSE281280 Microglia-RPE Cell Communication via the SPP1-ITGAV Axis Drives EMT and Retinal Degeneration in Dry AMD 6 samples shares spp1, communication
- GSE247369 Pathogenic TSC2 variants alter developmental trajectories of human cortical organoids and perturb cell-cell communication networks 92 samples shares communication, cell-cell
- GSE247367 Pathogenic TSC2 variants alter developmental trajectories of human cortical organoids and perturb cell-cell communication networks [bulk RNA-seq] 80 samples shares communication, cell-cell
- GSE242346 Human stem cells with in vivo high plasticity generated by cell-cell communication 22 samples shares communication, cell-cell
- GSE247368 Pathogenic TSC2 variants alter developmental trajectories of human cortical organoids and perturb cell-cell communication networks [scRNA-seq] 12 samples shares communication, cell-cell
- GSE269390 A single-cell RNA sequencing atlas of the COPD distal lung to predict cell-cell communication 6 samples shares communication, cell-cell
- GSE243002 Comprehensive Profiling of Peripheral Blood Mononuclear Cells Reveals Monocyte-CD8+ T cell-B cell Communication as Central Cell-cell Interaction and pathogenesis in IgA Vasculitis 21 samples shares communication, cell-cell
- GSE262245 NEST: Spatially-mapped cell-cell communication patterns using a deep learning-based attention mechanism 2 samples shares communication, cell-cell
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.