Endogenous glucocorticoids are required for normal macrophage activation and gastric Helicobacter pylori immunity [RNA-seq]
RNA-seq (gene expression) · mouse · 16 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
- Mus musculus (mouse)
- Samples
- 16 samples: 16 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
- Endogenous glucocorticoids are required for normal macrophage activation and gastric Helicobacter pylori immunityAmerican journal of physiology. Gastrointestinal and liver physiology · 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 GSE253584_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 PRJNA1066316 and SRA study SRP484560. 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 16 sample titles: 16 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.
- GSM8023869 GD1992-Busada_LIR_01-WT
- GSM8023870 GD1993-Busada_LIR_02-WT
- GSM8023871 GD1994-Busada_LIR_03-WT
- GSM8023872 GD1995-Busada_LIR_04-WT
- GSM8023873 GD1996-Busada_LIR_05-GR
- GSM8023874 GD1997-Busada_LIR_06-GR
- GSM8023875 GD1998-Busada_LIR_07-GR
- GSM8023876 GD1999-Busada_LIR_08-GR
- GSM8023877 GD2000-Busada_LIR_KO1
- GSM8023878 GD2001-Busada_LIR_KO2
- GSM8023879 GD2002-Busada_LIR_KO3
- GSM8023880 GD2003-Busada_LIR_KO4
- GSM8023881 GD2004-Busada_LIR_WT1
- GSM8023882 GD2005-Busada_LIR_WT2
- GSM8023883 GD2006-Busada_LIR_WT3
- GSM8023884 GD2007-Busada_LIR_WT4
- GSE272424 Rejuvenating endogenous antitumor immunity via a chimeric receptor-engineered oncolytic virus targeting tumor-associated macrophages 6 samples shares endogenous, macrophage, immunity
- GSE280514 Spatially-restricted and ontogenically-distinct hepatic macrophages are required for tissue repair. 48 samples shares macrophage, required
- GSE300925 Lyn expression in macrophages promotes TLR activation and restricts proliferation in an isoform-independent manner 48 samples shares macrophage, activation
- GSE245648 The Heme-regulated transcriptional repressor, BACH1 safeguards macrophage enhancer selection, activation andtissue adaptation [RNA-seq_BMDM] 24 samples shares macrophage, activation
- GSE324935 IFN-γ and TLR9 signaling reprogram tumor-associated macrophages to promote antitumor immunity in melanoma 20 samples shares macrophage, immunity
- GSE99296 α-ketoglutarate orchestrates macrophage activation through metabolic and epigenetic reprogramming 18 samples shares macrophage, activation
- GSE286348 Macrophages foster anti-tumor immunity by ZEB1-dependent cytotoxic T cell chemoattraction 18 samples shares macrophage, immunity
- GSE281001 The C3-C3aR axis modulates trained immunity in alveolar macrophages 8 samples shares macrophage, immunity
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.