Secondary LPS stimulation of BMDMs differentiated from bone marrow of C57B/6J mice treated with 4xLPS, 1xLPS or PBS
RNA-seq (gene expression) · mouse · 18 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
- 18 samples: 18 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 GSE196249_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 PRJNA804097 and SRA study SRP358682. 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 18 sample titles: 18 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.
- GSM5866496 PBS-1-NO
- GSM5866497 PBS-2-NO
- GSM5866498 PBS-3-NO
- GSM5866499 1xLPS-1-NO
- GSM5866500 1xLPS-2-NO
- GSM5866501 1xLPS-3-NO
- GSM5866502 4xLPS-1-NO
- GSM5866503 4xLPS-2-NO
- GSM5866504 4xLPS-3-NO
- GSM5866505 PBS-1-LPS
- GSM5866506 PBS-2-LPS
- GSM5866507 PBS-3-LPS
- GSM5866508 1xLPS-1-LPS
- GSM5866509 1xLPS-2-LPS
- GSM5866510 1xLPS-3-LPS
- GSM5866511 4xLPS-1-LPS
- GSM5866512 4xLPS-2-LPS
- GSM5866513 4xLPS-3-LPS
- GSE302019 Bulk RNA sequencing to investigate transcriptional profiles of lung macrophage subpopulations isolated from wild-type C57BL/6J and Spp1-EGFP knock-in reporter mice subjected to intratracheal administration of bleomycin or PBS. 24 samples shares c57b, pbs
- GSE295334 RNA sequencing data of leptomeningeal/perivascular CAMs and MG following LPS stimulation 8 weeks after repopulation 54 samples shares lps, stimulation
- GSE262107 Next Generation Sequencing to identify the differential expression genes of murine lung tissues upon the stimulation of LPS with/without recombinant TSLP pretreatment 10 samples shares lps, stimulation
- GSE228455 Gene expression profile at single cell level of monocytes sorted from C57BL/6J mouse ear tissue at 3 weeks post Leishmania major infection [scRNA-seq] 218 samples shares c57b
- GSE332798 Transcriptomic profiling of morphine and LPS exposure across mouse brain regions 208 samples shares lps
- GSE228456 Cell-intrinsic effect of IL-7R signaling of monocytes within C57BL/6J mouse ears infected with Leishmania major [bulk RNA-seq] 87 samples shares c57b
- GSE291439 C57BL6 Substrain Differences in Hippocampal-Dependent Learning and Transcriptome 72 samples shares c57b
- GSE181643 Oxygen-dependent changes and lysosome activity-dependent changes of gene expression in BMDM after LPS treatment 72 samples shares lps
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.