RNA-seq in wild type and EGR2 knock-out mouse alveolar macrophages upon vehicle and zymosan treatment
RNA-seq (gene expression) · mouse · 22 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
- 22 samples: 22 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
- EGR2 is an epigenomic regulator of phagocytosis and antifungal immunity in alveolar macrophagesJCI insight · 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 GSE181086_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 PRJNA750657 and SRA study SRP330417. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 8 samples read as cases, 6 as controls.
How we read this: Read from 22 sample titles: 22 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.
- GSM5484405 RNA-seq in wild type mouse alveolar macrophages (vehicle control, rep1)
- GSM5484406 RNA-seq in wild type mouse alveolar macrophages (vehicle control, rep2)
- GSM5484407 RNA-seq in wild type mouse alveolar macrophages (vehicle control, rep3)
- GSM5484408 RNA-seq in EGR2 knock-out mouse alveolar macrophages (vehicle control, rep1)
- GSM5484409 RNA-seq in EGR2 knock-out mouse alveolar macrophages (vehicle control, rep2)
- GSM5484410 RNA-seq in EGR2 knock-out mouse alveolar macrophages (vehicle control, rep3)
- GSM5484411 RNA-seq in wild type mouse alveolar macrophages treated in vivo with 300 μg zymosan (6hr, rep1)
- GSM5484412 RNA-seq in wild type mouse alveolar macrophages treated in vivo with 300 μg zymosan (6hr, rep2)
- GSM5484413 RNA-seq in wild type mouse alveolar macrophages treated in vivo with 300 μg zymosan (6hr, rep3)
- GSM5484414 RNA-seq in wild type mouse alveolar macrophages treated in vivo with 300 μg zymosan (6hr, rep4)
- GSM5484415 RNA-seq in EGR2 knock-out mouse alveolar macrophages treated in vivo with 300 μg zymosan (6hr, rep1)
- GSM5484416 RNA-seq in EGR2 knock-out mouse alveolar macrophages treated in vivo with 300 μg zymosan (6hr, rep2)
- GSM5484417 RNA-seq in EGR2 knock-out mouse alveolar macrophages treated in vivo with 300 μg zymosan (6hr, rep3)
- GSM5484418 RNA-seq in EGR2 knock-out mouse alveolar macrophages treated in vivo with 300 μg zymosan (6hr, rep4)
- GSM5484419 RNA-seq in wild type mouse alveolar macrophages treated in vivo with 300 μg zymosan (24hr, rep1)
- GSM5484420 RNA-seq in wild type mouse alveolar macrophages treated in vivo with 300 μg zymosan (24hr, rep2)
- GSM5484421 RNA-seq in wild type mouse alveolar macrophages treated in vivo with 300 μg zymosan (24hr, rep3)
- GSM5484422 RNA-seq in wild type mouse alveolar macrophages treated in vivo with 300 μg zymosan (24hr, rep4)
- GSM5484423 RNA-seq in EGR2 knock-out mouse alveolar macrophages treated in vivo with 300 μg zymosan (24hr, rep1)
- GSM5484424 RNA-seq in EGR2 knock-out mouse alveolar macrophages treated in vivo with 300 μg zymosan (24hr, rep2)
- GSM5484425 RNA-seq in EGR2 knock-out mouse alveolar macrophages treated in vivo with 300 μg zymosan (24hr, rep3)
- GSM5484426 RNA-seq in EGR2 knock-out mouse alveolar macrophages treated in vivo with 300 μg zymosan (24hr, rep4)
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- GSE271662 RNA-seq of Mouse Spinal Cord after Lateral Compression Spinal Cord Injury followed by Delayed Atorvastatin or Vehicle Treatment [Bulk RNA-seq of mice spinal cords] 16 samples shares treatment, rna-seq, vehicle
- GSE276300 EGR2 O-GlcNAcylation Orchestrates the Development of Protumoral Macrophages to Limit CD8+ T Cell Antitumor Responses. 27 samples shares egr2, macrophages
- GSE332646 Bulk RNA-seq of juvenile mouse liver following NDMA or saline treatment in WT and Mgmt-/- genotypes across multiple timepoints 214 samples shares treatment, rna-seq
- 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, alveolar
- 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, rna-seq
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- GSE285614 Adipocyte death drives fat redistribution from adipocytes to hepatocytes in steatotic liver disease via S100A8+ macrophages [RNA-seq] 34 samples shares macrophages, rna-seq
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.