RNAseq for peritoneal macrophages phagocytosing E.coli in the absence or presence of retinoic acid
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: 8 conditions, mostly in duplicateGroups 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.
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 GSE284043_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 PRJNA1196896 and SRA study SRP550797. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 16 samples.
How we read this: 8 replicated groups read from 16 sample titles; they account for 16 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.
- GSM8676596 Ecoli_LPM_BAC+1 Ecoli_LPM_BAC+
- GSM8676597 Ecoli_LPM_BAC-1 Ecoli_LPM_BAC
- GSM8676598 Ecoli_SPM_BAC-1 Ecoli_SPM_BAC
- GSM8676599 Ecoli_LPM_BAC+2 Ecoli_LPM_BAC+
- GSM8676600 Ecoli_SPM_BAC+1 Ecoli_SPM_BAC+
- GSM8676601 Ecoli_LPM_BAC-2 Ecoli_LPM_BAC
- GSM8676602 Ecoli_SPM_BAC-2 Ecoli_SPM_BAC
- GSM8676603 Ecoli_SPM_BAC+2 Ecoli_SPM_BAC+
- GSM8676604 RE_LPM_BAC+1 RE_LPM_BAC+
- GSM8676605 RE_SPM_BAC+1 RE_SPM_BAC+
- GSM8676606 RE_LPM_BAC-1 RE_LPM_BAC
- GSM8676607 RE_SPM_BAC-1 RE_SPM_BAC
- GSM8676608 RE_LPM_BAC+2 RE_LPM_BAC+
- GSM8676609 RE_SPM_BAC+2 RE_SPM_BAC+
- GSM8676610 RE_LPM_BAC-2 RE_LPM_BAC
- GSM8676611 RE_SPM_BAC-2 RE_SPM_BAC
- GSE263892 Single-cell analysis reveals Mycobacterium tuberculosis ESX-1-mediated accumulation of permissive macrophages in infected mouse lungs 6078 samples shares macrophages
- GSE272755 Transcriptional effects of lysosome stress on mouse bone marrow-derived macrophages and primary microglia 263 samples shares macrophages
- GSE319684 Timecourse of FACS sorted Ly6C+ monocytes, tissue resident alveolar macrophages (trAMs), monocyte derived alveolar macrophages (bmAMs) and epithelial cells from SARS-CoV-2 (maVie16) vs. IAV (PR8) infected mouse lungs 176 samples shares macrophages
- GSE300757 Efferocytosis induces proangiogenic function and chromatin remodeling in tumor-associated macrophages 127 samples shares macrophages
- GSE319035 P21+TREM2+-Senescent Macrophages Fuel Inflammaging and Metabolic Dysfunction-Associated Steatotic Liver Disease [NAFLD_time_course] 77 samples shares macrophages
- GSE268828 Transcriptomic profile of monocytes/ macrophages from injured bone, muscle, skin or heart tissues of Treg-depleted mice 56 samples shares macrophages
- GSE280514 Spatially-restricted and ontogenically-distinct hepatic macrophages are required for tissue repair. 48 samples shares macrophages
- GSE268774 Lymph node macrophages drive immune tolerance and resistance to cancer therapy by expression of the immune-regulatory cytokine IL-33 [RNA-seq] 48 samples shares 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.