Transcriptional response of mouse primary microglia to lysosomal alkalinization [HEX000413]
RNA-seq (gene expression) · mouse · 24 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
- 24 samples: 24 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 GSE272288_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 PRJNA1136029 and SRA study SRP520002. 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 24 sample titles: 24 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.
- GSM8397816 DMSO, 1 hour, replicate 1 [HSA-000022243]
- GSM8397817 DMSO, 1 hour, replicate 2 [HSA-000022244]
- GSM8397818 DMSO, 1 hour, replicate 3 [HSA-000022245]
- GSM8397819 BafA1, 1 hour, replicate 1 [HSA-000022246]
- GSM8397820 BafA1, 1 hour, replicate 2 [HSA-000022247]
- GSM8397821 BafA1, 1 hour, replicate 3 [HSA-000022248]
- GSM8397822 DMSO, 7 hours, replicate 1 [HSA-000022249]
- GSM8397823 DMSO, 7 hours, replicate 2 [HSA-000022250]
- GSM8397824 DMSO, 7 hours, replicate 3 [HSA-000022251]
- GSM8397825 BafA1, 7 hours, replicate 1 [HSA-000022252]
- GSM8397826 BafA1, 7 hours, replicate 2 [HSA-000022253]
- GSM8397827 BafA1, 7 hours, replicate 3 [HSA-000022254]
- GSM8397828 DMSO, 14 hours, replicate 1 [HSA-000022255]
- GSM8397829 DMSO, 14 hours, replicate 2 [HSA-000022256]
- GSM8397830 DMSO, 14 hours, replicate 3 [HSA-000022257]
- GSM8397831 BafA1, 14 hours, replicate 1 [HSA-000022258]
- GSM8397832 BafA1, 14 hours, replicate 2 [HSA-000022259]
- GSM8397833 BafA1, 14 hours, replicate 3 [HSA-000022260]
- GSM8397834 DMSO, 22 hours, replicate 1 [HSA-000022261]
- GSM8397835 DMSO, 22 hours, replicate 2 [HSA-000022262]
- GSM8397836 DMSO, 22 hours, replicate 3 [HSA-000022263]
- GSM8397837 BafA1, 22 hours, replicate 1 [HSA-000022264]
- GSM8397838 BafA1, 22 hours, replicate 2 [HSA-000022265]
- GSM8397839 BafA1, 22 hours, replicate 3 [HSA-000022266]
- GSE272755 Transcriptional effects of lysosome stress on mouse bone marrow-derived macrophages and primary microglia 263 samples shares microglia, primary
- GSE284475 Neuropathy-associated Tecpr2 mutation knock-in mice reveal endolysosomal loss of function phenotypes in neurons and microglia 16 samples shares microglia, lysosomal
- GSE293041 Single-cell transcriptome analysis of wildtype, TREM2 knockout, GPR34 knock-out or TREM2/GPR34 double knock-out primary microglia from wildtype and APP knock-in mice (8 months) 10 samples shares microglia, primary
- GSE272357 Transcriptional response of BMDMs to CRISPR KO of key lysosomal genes [HEX000527] 69 samples shares lysosomal
- GSE300113 Heterogenous microglial reactivity contrasts with stable vascular transcriptional programs in mouse models of Alzheimer’s, CADASIL, and Traumatic Brain Injury (Main dataset) 59 samples shares microglia
- GSE252343 Hofbauer cells and fetal brain microglia share transcriptional profiles and responses to maternal diet-induced obesity 34 samples shares microglia
- GSE264105 Plate-based scRNA-seq of plasma-positive microglia and plasma-negative microglia in young mice 1111 samples shares microglia
- GSE267786 Impact of SLC15A4, TASL and TASL2(Gm6377) deficiency on endolysosomal TLR7 and TLR9 responses 95 samples shares lysosomal
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.