Transcriptional response of WT and Trem2 KO BMDMs to lysosomal alkalinization [HEX000434]
RNA-seq (gene expression) · mouse · 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
- Mus musculus (mouse)
- Samples
- 12 samples: 12 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.
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 GSE272356_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 PRJNA1136509 and SRA study SRP520274. 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 12 sample titles: 12 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.
- GSM8399289 WT, DMSO, replicate 1 [HSA-000022459]
- GSM8399290 WT, DMSO, replicate 2 [HSA-000022460]
- GSM8399291 WT, DMSO, replicate 3 [HSA-000022461]
- GSM8399292 WT, BafA1, replicate 1 [HSA-000022462]
- GSM8399293 WT, BafA1, replicate 2 [HSA-000022463]
- GSM8399294 WT, BafA1, replicate 3 [HSA-000022464]
- GSM8399295 Trem2 KO, DMSO, replicate 1 [HSA-000022465]
- GSM8399296 Trem2 KO, DMSO, replicate 2 [HSA-000022466]
- GSM8399297 Trem2 KO, DMSO, replicate 3 [HSA-000022467]
- GSM8399298 Trem2 KO, BafA1, replicate 1 [HSA-000022468]
- GSM8399299 Trem2 KO, BafA1, replicate 2 [HSA-000022469]
- GSM8399300 Trem2 KO, BafA1, replicate 3 [HSA-000022470]
- GSE272298 Transcriptional response of mouse BMDMs to diverse lysosomal stressors [HEX000414] 90 samples shares lysosomal, bmdms
- GSE272357 Transcriptional response of BMDMs to CRISPR KO of key lysosomal genes [HEX000527] 69 samples shares lysosomal, bmdms
- GSE272288 Transcriptional response of mouse primary microglia to lysosomal alkalinization [HEX000413] 24 samples shares alkalinization, lysosomal
- GSE102564 The TREM2-APOE pathway drives the transcriptional phenotype of dysfunctional microglia in neurodegenerative diseases VI 39 samples shares trem2
- GSE291648 PLCG2 modulates TREM2 expression and signaling in response to Alzheimer’s disease pathology 24 samples shares trem2
- GSE102562 The TREM2-APOE pathway drives the transcriptional phenotype of dysfunctional microglia in neurodegenerative diseases IV 20 samples shares trem2
- GSE102563 The TREM2-APOE pathway drives the transcriptional phenotype of dysfunctional microglia in neurodegenerative diseases V 18 samples shares trem2
- GSE279164 Transcriptome and proteome profiling reveals TREM2-dependent and -independent glial response and metabolic perturbation in an Alzheimer’s mouse model 12 samples shares trem2
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.