Bulk RNAseq analysis of wildtype and Pim1-/- macrophages
RNA-seq (gene expression) · mouse · 12 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
- 12 samples: 3 × WT control vs 3 × WT oxLDL vs 3 × Pim1-/- control vs 3 × Pim1-/- oxLDLGroups 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.
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 GSE335106_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 PRJNA1477407 and SRA study SRP708762. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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.
- GSM9805879 WT control_1 WT control
- GSM9805880 WT control_2 WT control
- GSM9805881 WT control_3 WT control
- GSM9805882 WT oxLDL_1 WT oxLDL
- GSM9805883 WT oxLDL_2 WT oxLDL
- GSM9805884 WT oxLDL_3 WT oxLDL
- GSM9805885 Pim1-/- control_1 Pim1-/- control
- GSM9805886 Pim1-/- control_2 Pim1-/- control
- GSM9805887 Pim1-/- control_3 Pim1-/- control
- GSM9805888 Pim1-/- oxLDL_1 Pim1-/- oxLDL
- GSM9805889 Pim1-/- oxLDL_2 Pim1-/- oxLDL
- GSM9805890 Pim1-/- oxLDL_3 Pim1-/- oxLDL
- GSE331360 Bulk RNA sequencing of bone marrow-derived macrophages from WT and Ch25h-KO mice under different treatment conditions 24 samples shares macrophages, bulk
- GSE276628 Reciprocal genetic screens identify epigenetics factors controlling epidermal cell activation. [RNAseq_MiniBulk] 41 samples shares bulk
- GSE319614 Bulk RNA-seq transcriptome profiling of hippocampus across 17 autism spectrum disorder mouse models 269 samples shares bulk
- GSE332646 Bulk RNA-seq of juvenile mouse liver following NDMA or saline treatment in WT and Mgmt-/- genotypes across multiple timepoints 214 samples shares bulk
- GSE326452 Bulk RNA-seq of mouse brain following closed head injury: role of IL-1R1 signaling 200 samples shares bulk
- GSE292224 Distinct molecular mechanisms of stress habituation in the mouse hippocampus [bulk RNA-seq] 190 samples shares bulk
- 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
- GSE284808 Bulk RNAseq of sorted fibroblasts from a mouse model of stretch-mediated skin expansion 22 samples shares bulk
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.