A streamlined and comprehensive protocol for the generation and multi-omic analysis of human monocyte-derived macrophages [bulk RNA-Seq]
Single-nucleus RNA-seq · human · 20 samples
- What it is
- Single-nucleus RNA-seqGene activity measured in individual nuclei (used when whole cells are hard to isolate, for example from frozen tissue). Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
- Organism
- Homo sapiens (human)
- Samples
- 20 samples: 20 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 GSE300680_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.
Also filed as BioProject PRJNA1281655 and SRA study SRP594314. 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 20 sample titles: 20 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.
- GSM9066305 Female donor 1, M1 macrophage, IFNg 20 ng/mL + LPS 10 ng/mL
- GSM9066306 Female donor 1, M1 macrophage, IFNg 20 ng/mL + LPS 100 ng/mL
- GSM9066307 Female donor 1, M2 macrophage, IL-4 20ng/mL
- GSM9066308 Female donor 2, M0 macrophage, 25ng/mL M-CSF
- GSM9066309 Female donor 2, M0 macrophage, 50ng/mL M-CSF
- GSM9066310 Female donor 3, M0 macrophage, 25ng/mL M-CSF
- GSM9066311 Female donor 3, M0 macrophage, 50ng/mL M-CSF
- GSM9066312 Female donor 3, M1 macrophage, IFNg 20 ng/mL + LPS 10 ng/mL
- GSM9066313 Female donor 3, M1 macrophage, IFNg 20 ng/mL + LPS 100 ng/mL
- GSM9066314 Female donor 3, M2 macrophage, IL-4 20ng/mL
- GSM9066315 Male donor 1, M0 macrophage, 25ng/mL M-CSF
- GSM9066316 Male donor 1, M0 macrophage, 50ng/mL M-CSF
- GSM9066317 Male donor 1, M1 macrophage, IFNg 20 ng/mL + LPS 10 ng/mL
- GSM9066318 Male donor 1, M1 macrophage, IFNg 20 ng/mL + LPS 100 ng/mL
- GSM9066319 Male donor 1, M2 macrophage, IL-4 20ng/mL
- GSM9066320 Male donor 3, M0 macrophage, 25ng/mL M-CSF
- GSM9066321 Male donor 3, M0 macrophage, 50ng/mL M-CSF
- GSM9066322 Male donor 3, M1 macrophage, IFNg 20 ng/mL + LPS 10 ng/mL
- GSM9066323 Male donor 3, M1 macrophage, IFNg 20 ng/mL + LPS 100 ng/mL
- GSM9066324 Male donor 3, M2 macrophage, IL-4 20ng/mL
- GSE281471 Targeting CD206+ macrophages disrupts the establishment of a key anti-tumor immune axis [Bulk RNA-seq] 243 samples shares macrophages, rna-seq, bulk
- 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 generation, rna-seq, bulk
- GSE298244 Bulk RNA-seq of iPSC-derived macrophages exposed to disease-relevant stimuli 30 samples shares macrophages, rna-seq, bulk
- GSE269571 Generation of Stable Chambered Cardioids from human Pluripotent Stem Cells [bulk RNA-seq] 24 samples shares generation, rna-seq, bulk
- GSE269009 RNA-seq of monocyte derived macrophages and dendritic cells in a Peruvian Tuberculosis cohort 227 samples shares macrophages, rna-seq
- GSE255626 Next generation sequencing from primary glioblastoma patient tissues (Total RNA-seq) 109 samples shares generation, rna-seq
- GSE292970 Spatially organizing million callus cells identify the core-network enable tomato shoot regeneration [RNA-Seq] 54 samples shares generation, rna-seq
- GSE272978 Multi-omics Analysis of Umbilical Cord Hematopoietic Stem Cells from a Multi-ethnic Cohort of Hawaii Reveals the Intergenerational Effect of Maternal Pre-Pregnancy Obesity and Risk Prediction for Cancers 50 samples shares generation, multi-omic
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.