Whole lung gene expression in Tcrd-/- mice after Burkholderia thailandensis infection
RNA-seq (gene expression) · mouse · 16 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
- 16 samples: 16 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.
- Paper
- γδ T Cells Mediate Protection against Neutrophil-associated Lung Inflammation in Pulmonary MelioidosisAmerican journal of respiratory cell and molecular biology · 2024
Read the full summary ↓
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 GSE254868_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 PRJNA1072113 and SRA study SRP487535. 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 16 sample titles: 16 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.
- GSM8059275 Uninfected wild type control, Mouse 1 [NI_WT1]
- GSM8059276 Uninfected wild type control, Mouse 2 [NI_WT2]
- GSM8059277 Uninfected wild type control, Mouse 3 [NI_WT3]
- GSM8059278 Uninfected wild type control, Mouse 4 [NI_WT4]
- GSM8059279 24 hours after B. thailandensis-infection, wild type control, Mouse 1 [Bt88_24_WT1]
- GSM8059280 24 hours after B. thailandensis-infection, wild type control, Mouse 2 [Bt88_24_WT2]
- GSM8059281 24 hours after B. thailandensis-infection, wild type control, Mouse 3 [Bt88_24_WT3]
- GSM8059282 24 hours after B. thailandensis-infection, wild type control, Mouse 4 [Bt88_24_WT4]
- GSM8059283 Uninfected Tcrd-/-, Mouse 1 [NI_GD1]
- GSM8059284 Uninfected Tcrd-/-, Mouse 2 [NI_GD2]
- GSM8059285 Uninfected Tcrd-/-, Mouse 3 [NI_GD3]
- GSM8059286 Uninfected Tcrd-/-, Mouse 4 [NI_GD4]
- GSM8059287 24 hours after B. thailandensis-infection, Tcrd-/-, Mouse 1 [Bt88_24_GD1]
- GSM8059288 24 hours after B. thailandensis-infection, Tcrd-/-, Mouse 2 [Bt88_24_GD2]
- GSM8059289 24 hours after B. thailandensis-infection, Tcrd-/-, Mouse 3 [Bt88_24_GD3]
- GSM8059290 24 hours after B. thailandensis-infection, Tcrd-/-, Mouse 4 [Bt88_24_GD4]
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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.