Early transcriptomic response of innate immune cells to subcutaneous BCG vaccination of mice
RNA-seq (gene expression) · mouse · 24 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
- 24 samples: 24 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
- Early transcriptomic response of innate immune cells to subcutaneous BCG vaccination of miceBMC research notes · 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 GSE261448_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 PRJNA1086964 and SRA study SRP494856. 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 24 sample titles: 24 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.
- GSM8144250 1NK-Control
- GSM8144251 2NK-BCG
- GSM8144252 3NK-Control
- GSM8144253 4NK-BCG
- GSM8144254 5NK-Control
- GSM8144255 6NK-BCG
- GSM8144256 1Neutrophils-Control
- GSM8144257 2Neutrophils-BCG
- GSM8144258 3Neutrophils-Control
- GSM8144259 4Neutrophils-BCG
- GSM8144260 5Neutrophils-Control
- GSM8144261 6Neutrophils-BCG
- GSM8144262 1Monocytes-Control
- GSM8144263 2Monocytes-BCG
- GSM8144264 3Monocytes-Control
- GSM8144265 4Monocytes-BCG
- GSM8144266 5Monocytes-Control
- GSM8144267 6Monocytes-BCG
- GSM8144268 1Bone Marrow-Control
- GSM8144269 2Bone Marrow-BCG
- GSM8144270 3Bone Marrow-Control
- GSM8144271 4Bone Marrow-BCG
- GSM8144272 5Bone Marrow-Control
- GSM8144273 6Bone Marrow-BCG
- GSE264344 Early spatiotemporal evolution of the immune response elicited by adenovirus vector vaccination 195 samples shares vaccination, early
- GSE98600 BCG reprogramming of hematopoietic stem cells generates protective innate immunity against tuberculosis 85 samples shares bcg, innate
- GSE278523 Systems biology mapping of rBCG-LTAK63-induced protection against tuberculosis reveals the significance of autophagy and circadian rhythm regulation by cAMP 126 samples shares bcg
- GSE293097 Pre-existing allergic inflammation alters both innate and adaptive immune responses in mice co-infected with influenza virus 36 samples shares innate
- GSE320238 Lethal Mtb dissemination occurre in the combined absence of lymhocytes and is independent of innate immune response 30 samples shares innate
- GSE297572 Innate immune responses between low DIPs and high DIPs LAIV inoculations in the mouse upper respiratory tract revealed by bulk RNA-seq 22 samples shares innate
- GSE291607 The effect of miR192-LNP on the regulation of innate immune response 18 samples shares innate
- GSE255483 Multiple layers of innate immune response antagonism of SARS-CoV-2 16 samples shares innate
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.