NF-κB- and TET2-mediated macrophage reprogramming overrides the anti-inflammatory effects of hypoxia and improves responses in human cancer ChIP-Seq).
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 24 samples
- What it is
- ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
- Organism
- Homo sapiens (human)
- Samples
- 24 samples: 24 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 GSE261321_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.
Also filed as BioProject PRJNA1086491 and SRA study SRP494556. 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 24 sample titles: 24 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.
- GSM8140499 iMAC21_p65_A
- GSM8140500 mMAC21_p65_A
- GSM8140501 iMAC21_p65_B
- GSM8140502 mMAC21_p65_B
- GSM8140503 iMAC1_p65_A
- GSM8140504 mMAC1_p65_A
- GSM8140505 iMAC1_p65_B
- GSM8140506 mMAC1_p65_B
- GSM8140507 iMAC21_HIF1A_A
- GSM8140508 mMAC21_HIF1A_A
- GSM8140509 iMAC21_HIF1A_B
- GSM8140510 mMAC21_HIF1A_B
- GSM8140511 iMAC1_HIF1A_A
- GSM8140512 mMAC1_HIF1A_A
- GSM8140513 iMAC1_HIF1A_B
- GSM8140514 mMAC1_HIF1A_B
- GSM8140515 input_iMAC21A
- GSM8140516 input_iMAC21B
- GSM8140517 input_mMAC21A
- GSM8140518 input_mMAC21B
- GSM8140519 input_iMAC1A
- GSM8140520 input_iMAC1B
- GSM8140521 input_mMAC1A
- GSM8140522 input_mMAC1B
- GSE296831 Epigenetic Context Defines the Transcriptional Activity of Canonical and Noncanonical NF-kappaB Signaling in Pancreatic Cancer [ChIP-Seq] 48 samples shares nf, chip-seq
- GSE323311 Human Macrophages Encode Stimulus-Specific Information of Prior Exposures Through Trained Immunity 48 samples shares nf, macrophage
- GSE292059 Inflammatory Epithelial and Macrophage Pathways Underlie Residual Asthma Exacerbations in Urban Children Treated with Mepolizumab 965 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
- GSE342301 SIRT2 deacylase modulators control B cell metabolic reprogramming in EBV infection and mitogenic activation 8 samples shares nf, reprogramming
- GSE308983 Reprogramming lineage features promotes epithelial behavior in carcinoma cells [ChIP-Seq] 23 samples shares reprogramming, chip-seq
- GSE307326 Continuous NRTI-based antiretroviral therapy induces progressive senescence-like reprogramming of alveolar macrophages [snMultiomics] 32 samples shares reprogramming, macrophage
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.