NF-κB- and TET2-mediated macrophage reprogramming overrides the anti-inflammatory effects of hypoxia and improves responses in human cancer (RNA-Seq I).
RNA-seq (gene expression) · human · 20 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
- 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.
- Paper
- NF-κB and TET2 promote macrophage reprogramming in hypoxia that overrides the immunosuppressive effects of the tumor microenvironmentScience advances · 2024
Read the full summary ↓
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 GSE261322_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 PRJNA1086490 and SRA study SRP494558. 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.
- GSM8140523 MO A
- GSM8140524 MO B
- GSM8140525 MO C
- GSM8140526 MO D
- GSM8140527 iMAC21 A
- GSM8140528 iMAC21 B
- GSM8140529 iMAC21 C
- GSM8140530 iMAC21 D
- GSM8140531 mMAC21 A
- GSM8140532 mMAC21 B
- GSM8140533 mMAC21 C
- GSM8140534 mMAC21 D
- GSM8140535 iMAC1 A
- GSM8140536 iMAC1 B
- GSM8140537 iMAC1 C
- GSM8140538 iMAC1 D
- GSM8140539 mMAC1 A
- GSM8140540 mMAC1 B
- GSM8140541 mMAC1 C
- GSM8140542 mMAC1 D
- GSE292059 Inflammatory Epithelial and Macrophage Pathways Underlie Residual Asthma Exacerbations in Urban Children Treated with Mepolizumab 965 samples shares nf, macrophage
- GSE342301 SIRT2 deacylase modulators control B cell metabolic reprogramming in EBV infection and mitogenic activation 8 samples shares nf, reprogramming
- GSE323311 Human Macrophages Encode Stimulus-Specific Information of Prior Exposures Through Trained Immunity 48 samples shares nf, macrophage
- GSE312129 Single-nuclei multiome and spatial analyses of early, untreated SSc skin identify a proinflammatory vascular niche of macrophage-fibroblast signaling 38 samples shares nf, macrophage
- GSE317257 Mapping Endothelial-Macrophage Interactions in Diabetic Vasculature: Role of TREM2 in Vascular Inflammation and Ischemic Respons 35 samples shares nf, macrophage
- GSE307326 Continuous NRTI-based antiretroviral therapy induces progressive senescence-like reprogramming of alveolar macrophages [snMultiomics] 32 samples shares reprogramming, macrophage
- GSE282464 Molecular landscape of respiratory infection: A large-scale, multi-centre blood transcriptome dataset 377 samples shares nf
- GSE154200 Skin transcriptome of non-communicable inflammatory skin diseases 376 samples shares nf
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.