Wild type (WT) and Aconitate decarboxylase 1 knockout (Acod1-/-) BMDM treated with Imiquimod for 12h
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: 6 × BMDM_WT vs 6 × BMDM_WT_IMQ12hGroups 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
- The aconitate decarboxylase 1/itaconate pathway modulates immune dysregulation and associates with cardiovascular disease markers in SLEmedRxiv : the preprint server for health sciences · 2024
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 GSE250384_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 PRJNA1053787 and SRA study SRP478467. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 2 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.
- GSM7978169 BMDM_WT_rep1 BMDM_WT
- GSM7978170 BMDM_WT_rep2 BMDM_WT
- GSM7978171 BMDM_WT_rep3 BMDM_WT
- GSM7978172 BMDM_WT_rep4 BMDM_WT
- GSM7978173 BMDM_WT_rep5 BMDM_WT
- GSM7978174 BMDM_WT_rep6 BMDM_WT
- GSM7978175 BMDM_WT_IMQ12h_rep1 BMDM_WT_IMQ12h
- GSM7978176 BMDM_WT_IMQ12h_rep2 BMDM_WT_IMQ12h
- GSM7978177 BMDM_WT_IMQ12h_rep3 BMDM_WT_IMQ12h
- GSM7978178 BMDM_WT_IMQ12h_rep4 BMDM_WT_IMQ12h
- GSM7978179 BMDM_WT_IMQ12h_rep5 BMDM_WT_IMQ12h
- GSM7978180 BMDM_WT_IMQ12h_rep6 BMDM_WT_IMQ12h
- GSE248885 Wild-type and GLO2 knockout BMDMs with infection of VSV 4 samples shares bmdm, knockout, wild
- GSE279654 BMDM from Young and Aged Mice Treated with β-glucan 42 samples shares bmdm, treated
- GSE252101 The effect of STING knockout on gene expression in DMXAA-induced BMDMs and BMDCs 24 samples shares bmdm, knockout
- GSE249266 Transcriptomics of PLXDC2 knockdown BMDM treated with PTEN 24 samples shares bmdm, treated
- GSE78849 Investigation of the effect of succinate and dimethyl malonate on murine bone-marrow derived macrophages (BMDMs) treated with or without LPS 21 samples shares bmdm, treated
- GSE196249 Secondary LPS stimulation of BMDMs differentiated from bone marrow of C57B/6J mice treated with 4xLPS, 1xLPS or PBS 18 samples shares bmdm, treated
- GSE327962 Effects of CRISPR-mediated knockout of Mitf, Tfe3 and Tfeb on the transcriptome of mouse BMDMs from WT and Grn KO animals [hex001130] 16 samples shares bmdm, knockout
- GSE249265 Transcriptomics of BMDM treated with PTEN in the presence or absence of STAT1 inhibitors 16 samples shares bmdm, treated
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.