ApoE-dependent reprogramming of glioma-associated microglia into a tumor-promoting phenotype
RNA-seq (gene expression) · mouse · 21 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
- 21 samples: 7 × WT vs 5 × Apoe vs 5 × PBS vs 4 × FGroups 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 GSE174328_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 PRJNA729462 and SRA study SRP319471. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 21 samples.
How we read this: 4 replicated groups read from 21 sample titles; they account for 21 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.
- GSM5291837 Apoe1 Apoe
- GSM5291838 Apoe2 Apoe
- GSM5291839 Apoe3 Apoe
- GSM5291840 Apoe4 Apoe
- GSM5291841 Apoe5 Apoe
- GSM5291842 F1 F
- GSM5291843 F2 F
- GSM5291844 F3 F
- GSM5291845 F4 F
- GSM5291846 PBS1 PBS
- GSM5291847 PBS2 PBS
- GSM5291848 PBS3 PBS
- GSM5291849 PBS4 PBS
- GSM5291850 PBS5 PBS
- GSM5291851 WT1 WT
- GSM5291852 WT2 WT
- GSM5291853 WT3 WT
- GSM5291854 WT4 WT
- GSM5291855 WT6 WT
- GSM5291856 WT7 WT
- GSM5291857 WT8 WT
- GSE302857 Multi-tier signaling and epigenomic reprogramming drive microglial inflammatory states and functions associated with demyelination [RNA-seq] 81 samples shares reprogramming, microglia
- GSE319246 ApoE4 Drives Microglial Lipid Dysregulation in Alzheimer’s Disease via Epigenetic Reprogramming of the AsxL1/LXRα–H3K4me3 Axis 24 samples shares reprogramming, microglia
- GSE263625 Microglial reprogramming enhances antitumor immunity and immunotherapy response in melanoma brain metastases 19 samples shares reprogramming, microglia
- GSE296768 Plaque-induced transcriptional reprogramming of microglia towards lymphoid receptor expression protects against Alzheimer's disease [scRNA-seq] 12 samples shares reprogramming, microglia
- GSE302858 Multi-tier signaling and epigenomic reprogramming drive microglial inflammatory states and functions associated with demyelination [ATAC-seq] 42 samples shares reprogramming, microglia
- GSE302859 Multi-tier signaling and epigenomic reprogramming drive microglial inflammatory states and functions associated with demyelination [ChIP-seq] 28 samples shares reprogramming, microglia
- GSE268822 Transcriptional landscapes underlying Notch-induced lineage conversion and reprogramming of mammary cells 840 samples shares reprogramming
- GSE222745 Enhanced activities of OCT4 and SOX2 facilitates epigenetic reprogramming by modulating cell cycle [scRNA-Seq] 422 samples shares reprogramming
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.