Gene expression profiles of human iPSC-derived microglia in monoculture and in co-culture with isogenic iPSC-derived neural cells
RNA-seq (gene expression) · human · 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
- Homo sapiens (human)
- Samples
- 12 samples: 6 × 10 DIV iMG co-culture vs 6 × 10 DIV iMGGroups 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
- Rapid phagosome isolation enables unbiased multiomic analysis of human microglial phagosomesImmunity · 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 GSE243370_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 PRJNA1017898 and SRA study SRP460830. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 2 replicated groups read from 12 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.
- GSM7784367 10 DIV iMG co-culture rep 1 10 DIV iMG co-culture
- GSM7784368 10 DIV iMG co-culture rep 2 10 DIV iMG co-culture
- GSM7784369 10 DIV iMG co-culture rep 3 10 DIV iMG co-culture
- GSM7784370 10 DIV iMG co-culture rep 4 10 DIV iMG co-culture
- GSM7784371 10 DIV iMG co-culture rep 5 10 DIV iMG co-culture
- GSM7784372 10 DIV iMG co-culture rep 6 10 DIV iMG co-culture
- GSM7784373 10 DIV iMG rep 1 10 DIV iMG
- GSM7784374 10 DIV iMG rep 2 10 DIV iMG
- GSM7784375 10 DIV iMG rep 3 10 DIV iMG
- GSM7784376 10 DIV iMG rep 4 10 DIV iMG
- GSM7784377 10 DIV iMG rep 5 10 DIV iMG
- GSM7784378 10 DIV iMG rep 6 10 DIV iMG
- GSE339602 Single-cell RNA sequencing of human iPSC-derived forebrain organoids following amyloid-β42 treatment, microglia co-culture, and maraviroc treatment 16 samples shares ipsc-derived, co-culture, microglia
- GSE293037 Bulk transcriptome analysis of wildtype, TREM2 knockout, GPR34 knock-out or TREM2/GPR34 double knock-out iPSC-derived human microglia treated either with PBS or myelin. 32 samples shares ipsc-derived, microglia
- GSE274283 Bulk RNA sequencing analysis of a iPSC-derived neurons, microglia and astrocytes models of mitochondrial unfolded protein response (UPRmt) activation. 18 samples shares ipsc-derived, microglia
- GSE263804 Chromatin accessibility mapping for functional GWAS risk variants of neuropsychiatric and neurodegenerative disorders in hiPSC-derived neural cells 141 samples shares ipsc-derived, neural
- GSE305145 Single-Cell Multiomic Atlas of Human Cortical Development in Down Syndrome - iPSC-derived Neural Xenografts Multiome Dataset 8 samples shares ipsc-derived, neural
- GSE279590 BMP, MEK and WNT modulation with NGN2 expression for rapid generation of hiPSC-derived neurons amenable to regional patterning [bulk RNA-seq] 61 samples shares ipsc-derived
- GSE249315 The human microglia response a resource to better understand microglia states in health and disease 398 samples shares microglia
- GSE217649 Bulk RNA sequencing for gene expression profileing of primary liver sinusoidal endothelial cells and iPSC-derived hepatic endoderm, septum mesenchymal cells, endothelial cells, and liver bud organoids 26 samples shares ipsc-derived
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.