Transcriptional characteristics of human primary, bone marrow-derived and iPSC-derived monocytes and macrophages [RNA-Seq]
RNA-seq (gene expression) · human · 19 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
- 19 samples: 3 × Control_A_M vs 3 × Control_B_M vs 3 × Control_C_M vs 2 × BM_mono_DGroups 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 GSE261696_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 PRJNA1088438 and SRA study SRP495436. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 11 samples.
How we read this: 4 replicated groups read from 19 sample titles; they account for 11 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.
- GSM8148874 Control_A_mono
- GSM8148875 Control_A_M0 Control_A_M
- GSM8148876 Control_A_M1 Control_A_M
- GSM8148877 Control_A_M2 Control_A_M
- GSM8148878 Control_B_mono
- GSM8148879 Control_B_M0 Control_B_M
- GSM8148880 Control_B_M1 Control_B_M
- GSM8148881 Control_B_M2 Control_B_M
- GSM8148882 Control_C_mono
- GSM8148883 Control_C_M0 Control_C_M
- GSM8148884 Control_C_M1 Control_C_M
- GSM8148885 Control_C_M2 Control_C_M
- GSM8148886 iPSC_mono_115-4H
- GSM8148887 iPSC_mono_141-31B
- GSM8148888 iPSC_mono_143-18
- GSM8148889 iPSC_mono_144-41
- GSM8148890 BM_mono_D6 BM_mono_D
- GSM8148891 BM_mono_D8 BM_mono_D
- GSM8148892 BM_mono_DB2
- GSE298244 Bulk RNA-seq of iPSC-derived macrophages exposed to disease-relevant stimuli 30 samples shares ipsc-derived, macrophages, rna-seq
- GSE237489 RNA-seq for iPSC-derived macrophages with/without Lipopolysaccharide (LPS) stimulation. 8 samples shares ipsc-derived, macrophages, rna-seq
- GSE281471 Targeting CD206+ macrophages disrupts the establishment of a key anti-tumor immune axis [Bulk RNA-seq] 243 samples shares macrophages, rna-seq
- GSE269009 RNA-seq of monocyte derived macrophages and dendritic cells in a Peruvian Tuberculosis cohort 227 samples shares macrophages, rna-seq
- GSE334500 Psychotropic-drug and neurotransmitter perturbation RNA-seq of human iPSC-derived cardiac and retinal organoids (ToxiPred) 96 samples shares ipsc-derived, rna-seq
- 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, rna-seq
- GSE307755 Direct contact between iPSC-derived macrophages and hepatocytes drives reciprocal acquisition of Kupffer cell identity and hepatocyte maturation 53 samples shares ipsc-derived, macrophages
- GSE311899 Autologous cell therapy with CD133+ bone marrow-derived stem cells for Asherman Syndrome: a phase 1/2 trial [biopsies] 35 samples shares marrow-derived, bone
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.