Differentially expressed genes in human monocyte-derived macrophages overexpressing TRIM21, NFATc3, or ASK1
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: 3 × Control vs 3 × TRIM21 vs 3 × NFATc3 vs 3 × ASK1Groups 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 GSE315074_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 PRJNA1394957 and SRA study SRP658537. 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 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.
- GSM9420911 Control_1 Control
- GSM9420912 Control_2 Control
- GSM9420913 Control_3 Control
- GSM9420914 TRIM21_1 TRIM21
- GSM9420915 TRIM21_2 TRIM21
- GSM9420916 TRIM21_3 TRIM21
- GSM9420917 NFATc3_1 NFATc3
- GSM9420918 NFATc3_2 NFATc3
- GSM9420919 NFATc3_3 NFATc3
- GSM9420920 ASK1_1 ASK1
- GSM9420921 ASK1_2 ASK1
- GSM9420922 ASK1_3 ASK1
- GSE254956 RNA-seq analysis of differentially expressed genes between WT and shTRIM21 RKO cells. 6 samples shares trim21, differentially, expressed
- GSE236156 Mycobacterium tuberculosis induced interferon pathways distinguish responses of Human Alveolar Macrophages from Monocyte-Derived Macrophages 55 samples shares monocyte-derived, macrophages
- GSE232628 Expansion of profibrotic monocyte-derived alveolar macrophages in patients with persistent respiratory symptoms and radiographic abnormalities after COVID-19 46 samples shares monocyte-derived, macrophages
- GSE335752 Characterization of human M2-like (TGFbeta/IL10) vs M0 monocyte-derived macrophages 36 samples shares monocyte-derived, macrophages
- GSE316027 β-hydroxybutyrate-driven histone lysine β-hydroxybutyrylation promotes the immunostimulatory activity of monocyte-derived macrophages in rectal cancer 32 samples shares monocyte-derived, macrophages
- GSE240075 Gene expression in human monocyte-derived macrophages: effect of loss of MYC or USF1 30 samples shares monocyte-derived, macrophages
- GSE232627 Expansion of profibrotic monocyte-derived alveolar macrophages in patients with persistent respiratory symptoms and radiographic abnormalities after COVID-19 [PASC] 30 samples shares monocyte-derived, macrophages
- GSE228088 RNA-seq of Monocyte-derived Macrophages and Hepatic Stellate Cell Activation after 72hr 28 samples shares monocyte-derived, macrophages
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.