Transcriptome profiles of wild-type, IRF8KO microglia
RNA-seq (gene expression) · mouse · 16 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
- 16 samples: 3 × WT_P9 vs 3 × IRF8KO_P9 vs 3 × WT_P14 vs 3 × IRF8KO_P14Groups 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
- IRF8 defines the epigenetic landscape in postnatal microglia, thereby directing their transcriptome programsNature immunology · 2024
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 GSE266422_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 PRJNA1107154 and SRA study SRP505336. 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 16 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.
- GSM8246727 WT_P9_rep1 WT_P9
- GSM8246728 WT_P9_rep2 WT_P9
- GSM8246729 WT_P9_rep3 WT_P9
- GSM8246730 IRF8KO_P9_rep1 IRF8KO_P9
- GSM8246731 IRF8KO_P9_rep2 IRF8KO_P9
- GSM8246732 IRF8KO_P9_rep3 IRF8KO_P9
- GSM8246733 WT_P14_rep1 WT_P14
- GSM8246734 WT_P14_rep2 WT_P14
- GSM8246735 WT_P14_rep3 WT_P14
- GSM8246736 IRF8KO_P14_rep1 IRF8KO_P14
- GSM8246737 IRF8KO_P14_rep2 IRF8KO_P14
- GSM8246738 IRF8KO_P14_rep3 IRF8KO_P14
- GSM8246739 WT_adult_rep1_batch#2
- GSM8246740 WT_adult_rep2_batch#2
- GSM8246741 IRF8KO_adult_rep1_batch#2
- GSM8246742 IRF8KO_adult_rep2_batch#2
- GSE252343 Hofbauer cells and fetal brain microglia share transcriptional profiles and responses to maternal diet-induced obesity 34 samples shares microglia, profiles
- GSE327960 Transcription profiles of mouse microglia isolated by FACS from WT and Grn KO animals, separated by lipofuscin levels [hex001110] 24 samples shares microglia, profiles
- GSE302019 Bulk RNA sequencing to investigate transcriptional profiles of lung macrophage subpopulations isolated from wild-type C57BL/6J and Spp1-EGFP knock-in reporter mice subjected to intratracheal administration of bleomycin or PBS. 24 samples shares wild-type, profiles
- GSE303725 Effects of attenuating astrocytic Ca2+ activity in the medial prefrontal cortex with iβARK on transcriptional profiles in wild-type mice. 17 samples shares wild-type, profiles
- GSE241165 Characterizing the gene expression profiles of 4T1 and 4T1.2 cells at different stages of bone metastsis using SMART-Seq2 technology 1248 samples shares profiles
- GSE264105 Plate-based scRNA-seq of plasma-positive microglia and plasma-negative microglia in young mice 1111 samples shares microglia
- GSE201417 Gene expression profiles of cardiac neural crest cells during heart development 294 samples shares profiles
- GSE272755 Transcriptional effects of lysosome stress on mouse bone marrow-derived macrophages and primary microglia 263 samples shares microglia
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.