RNA sequencing of wild type or calcineurin-deficient mouse bone marrow-derived dendritic cells stimulated with or without lipoarabinomannan (LAM) from Mycobacterium tuberculosis Aoyama-B
RNA-seq (gene expression) · mouse · 10 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
- 10 samples: 10 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.
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 GSE189297_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 PRJNA782470 and SRA study SRP347185. 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 10 sample titles: 10 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.
- GSM5697120 WT_0h
- GSM5697121 CnKO_0h
- GSM5697122 WT_2h
- GSM5697123 CnKO_2h
- GSM5697124 WT_4h
- GSM5697125 CnKO_4h
- GSM5697126 WT_8h
- GSM5697127 CnKO_8h
- GSM5697128 WT_12h
- GSM5697129 CnKO_12h
- GSE294832 Modular neuroinflammatory network discovery from large-scale phenotypic screening in genetically heterogeneous mice [part10] 1000 samples shares lam
- GSE294911 Modular neuroinflammatory network discovery from large-scale phenotypic screening in genetically heterogeneous mice [part14] 1000 samples shares lam
- GSE294535 Modular neuroinflammatory network discovery from large-scale phenotypic screening in genetically heterogeneous mice[part5] 1000 samples shares lam
- GSE294849 Modular neuroinflammatory network discovery from large-scale phenotypic screening in genetically heterogeneous mice [part13] 1000 samples shares lam
- GSE327057 Systematically characterizing the roles of E3-ligase family members in inflammatory responses with massively parallel Perturb-seq 169 samples shares lam
- GSE302188 Multi-omics analysis highlights the link of aging-related cognitive decline with systemic inflammation and alterations of tissue-maintenance 165 samples shares lam
- GSE303256 A spatial and projection-based transcriptomic atlas of paraventricular hypothalamic cell types 131 samples shares lam
- GSE176506 Synergistic behavioral and neuroinflammatory effects of amyloid neuropathology and sepsis survival in a murine model of Alzheimer’s disease 112 samples shares lam
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.