Systematic characterization of brain cellular crosstalk reveals a novel role for SEMA6D in TREM2-associated microglial function in Alzheimer’s disease
RNA-seq (gene expression) · human · 12 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
- 12 samples: 3 × iMGL WT no treat vs 3 × iMGL WT SEMA6D treat vs 3 × iMGL TREM2 KO no treat vs 3 × iMGL TREM2 KO SEMA6D treatGroups 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
- Systematic analysis of cellular cross-talk reveals a role for SEMA6D-TREM2 regulating microglial function in Alzheimer's diseaseScience translational medicine · 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 GSE226507_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 PRJNA940453 and SRA study SRP425354. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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.
- GSM7078128 iMGL WT no treat rep 1 iMGL WT no treat
- GSM7078129 iMGL WT no treat rep 2 iMGL WT no treat
- GSM7078130 iMGL WT no treat rep 3 iMGL WT no treat
- GSM7078131 iMGL WT SEMA6D treat rep 1 iMGL WT SEMA6D treat
- GSM7078132 iMGL WT SEMA6D treat rep 2 iMGL WT SEMA6D treat
- GSM7078133 iMGL WT SEMA6D treat rep 3 iMGL WT SEMA6D treat
- GSM7078134 iMGL TREM2 KO no treat rep 1 iMGL TREM2 KO no treat
- GSM7078135 iMGL TREM2 KO no treat rep 2 iMGL TREM2 KO no treat
- GSM7078136 iMGL TREM2 KO no treat rep 3 iMGL TREM2 KO no treat
- GSM7078137 iMGL TREM2 KO SEMA6D treat rep 1 iMGL TREM2 KO SEMA6D tr…
- GSM7078138 iMGL TREM2 KO SEMA6D treat rep 2 iMGL TREM2 KO SEMA6D tr…
- GSM7078139 iMGL TREM2 KO SEMA6D treat rep 3 iMGL TREM2 KO SEMA6D tr…
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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.