Next Generation Sequencing to identify the differential expression genes of murine lung tissues upon the stimulation of LPS with/without recombinant TSLP pretreatment
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: 4 × Lung, LPS+TSLP, vs 3 × Lung,Vehicle, vs 3 × Lung, LPS,Groups 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 GSE262107_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 PRJNA1090399 and SRA study SRP496927. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 10 samples.
How we read this: 3 replicated groups read from 10 sample titles; they account for 10 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.
- GSM8157621 Lung,Vehicle, rep1 Lung,Vehicle,
- GSM8157622 Lung,Vehicle, rep2 Lung,Vehicle,
- GSM8157623 Lung,Vehicle, rep3 Lung,Vehicle,
- GSM8157624 Lung, LPS, rep1 Lung, LPS,
- GSM8157625 Lung, LPS, rep2 Lung, LPS,
- GSM8157626 Lung, LPS, rep3 Lung, LPS,
- GSM8157627 Lung, LPS+TSLP, rep1 Lung, LPS+TSLP,
- GSM8157628 Lung, LPS+TSLP, rep2 Lung, LPS+TSLP,
- GSM8157629 Lung, LPS+TSLP, rep3 Lung, LPS+TSLP,
- GSM8157630 Lung, LPS+TSLP, rep4 Lung, LPS+TSLP,
- GSE295334 RNA sequencing data of leptomeningeal/perivascular CAMs and MG following LPS stimulation 8 weeks after repopulation 54 samples shares lps, stimulation
- GSE279383 Transcriptome profiles of RAW264.7 cells under fibroblast coculture with or without LPS sitimulation and tryptophan metabolites intervention 24 samples shares lps, without
- GSE196249 Secondary LPS stimulation of BMDMs differentiated from bone marrow of C57B/6J mice treated with 4xLPS, 1xLPS or PBS 18 samples shares lps, stimulation
- GSE296026 Spatial distribution and chromatin accessibility determine the therapeutic capacity of microglial subsets during neurodegeneration [scRNAseq1_LPS_ABX] 12 samples shares lps, generation
- GSE332798 Transcriptomic profiling of morphine and LPS exposure across mouse brain regions 208 samples shares lps
- GSE181643 Oxygen-dependent changes and lysosome activity-dependent changes of gene expression in BMDM after LPS treatment 72 samples shares lps
- GSE277696 Role of endothelial SOCS3 in the transcriptional response to LPS 45 samples shares lps
- GSE250279 25-hydroxycholesterol mediates brain cytokine production and neutrophil infiltration in a mouse model of LPS-induced neuroinflammation. 40 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.