GPR34 loss-of-function rescues TREM2 metabolic dysfunction and promotes responsive microglial states
RNA-seq (gene expression) · mouse · 56 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
- Mus musculus (mouse)
- Samples
- 56 samples: 14 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.
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 GSE293117_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 PRJNA1242834 and SRA study SRP573366. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 44 samples.
How we read this: 14 replicated groups read from 56 sample titles; they account for 44 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.
- GSM8874380 WT, PBS, rep 1 WT, PBS,
- GSM8874381 WT, Myelin, rep 1 WT, Myelin,
- GSM8874382 GPR34KO, PBS, rep 1 GPR34KO, PBS,
- GSM8874383 GPR34KO, Myelin, rep 1 GPR34KO, Myelin,
- GSM8874384 TREM2KO, PBS, rep 1 TREM2KO, PBS,
- GSM8874385 TREM2KO, Myelin, rep 1 TREM2KO, Myelin,
- GSM8874386 GPR34, TREM2KO, PBS, rep 1 GPR34, TREM2KO, PBS,
- GSM8874387 GPR34, TREM2KO, Myelin, rep 1 GPR34, TREM2KO, Myelin,
- GSM8874388 WT, PBS, rep 2 WT, PBS,
- GSM8874389 WT, Myelin, rep 2 WT, Myelin,
- GSM8874390 GPR34KO, PBS, rep 2 GPR34KO, PBS,
- GSM8874391 GPR34KO, Myelin, rep 2 GPR34KO, Myelin,
- GSM8874392 TREM2KO, PBS, rep 2 TREM2KO, PBS,
- GSM8874393 TREM2KO, Myelin, rep 2 TREM2KO, Myelin,
- GSM8874394 GPR34, TREM2KO, PBS, rep 2 GPR34, TREM2KO, PBS,
- GSM8874395 GPR34, TREM2KO, Myelin, rep 2 GPR34, TREM2KO, Myelin,
- GSM8874396 WT, PBS, rep 3 WT, PBS,
- GSM8874397 WT, Myelin, rep 3 WT, Myelin,
- GSM8874398 GPR34KO, PBS, rep 3 GPR34KO, PBS,
- GSM8874399 GPR34KO, Myelin, rep 3 GPR34KO, Myelin,
- GSM8874400 TREM2KO, PBS, rep 3 TREM2KO, PBS,
- GSM8874401 TREM2KO, Myelin, rep 3 TREM2KO, Myelin,
- GSM8874402 GPR34, TREM2KO, PBS, rep 3 GPR34, TREM2KO, PBS,
- GSM8874403 GPR34, TREM2KO, Myelin, rep 3 GPR34, TREM2KO, Myelin,
- GSM8874404 WT, PBS, rep 4 WT, PBS,
- GSM8874405 WT, Myelin, rep 4 WT, Myelin,
- GSM8874406 GPR34KO, PBS, rep 4 GPR34KO, PBS,
- GSM8874407 GPR34KO, Myelin, rep 4 GPR34KO, Myelin,
- GSM8874408 TREM2KO, PBS, rep 4 TREM2KO, PBS,
- GSM8874409 TREM2KO, Myelin, rep 4 TREM2KO, Myelin,
- GSM8874410 GPR34, TREM2KO, PBS, rep 4 GPR34, TREM2KO, PBS,
- GSM8874411 GPR34, TREM2KO, Myelin, rep 4 GPR34, TREM2KO, Myelin,
- GSM8874458 Pool 3, GEX
- GSM8874459 Pool 5, GEX
- GSM8874460 Pool 7, GEX
- GSM8874461 Pool 3, CMO
- GSM8874462 Pool 5, CMO
- GSM8874463 Pool 7, CMO
- GSM8874464 Pool 1A, GEX Pool 1A, GEX
- GSM8874465 Pool 1B, GEX Pool 1B, GEX
+ 16 more — browse all 56 samples with per-sample file links →
- GSE295918 TREM2+ Macrophage Infiltration Underlies Breast Cancer Lung Metastasis due to Paclitaxel Treatment [ATAC-seq] 8 samples shares trem2
- GSE246221 A Mouse Model for Metabolic Dysfunction-associated Steatotic Liver Disease and Hepatocellular Carcinoma [RNA-seq] 148 samples shares dysfunction
- GSE328222 Acute rapamycin treatment reveals novel mechanisms of dysfunction in a maternal inflammation mouse model 32 samples shares dysfunction
- GSE246223 A Mouse Model for Metabolic Dysfunction-associated Steatotic Liver Disease and Hepatocellular Carcinoma 160 samples shares dysfunction
- GSE291636 RBBP6 orchestrates diabetic endothelial dysfunction viadisrupting JUNB-centric chromatin topology 73 samples shares dysfunction
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.