Innate immune responses between low DIPs and high DIPs LAIV inoculations in the mouse upper respiratory tract revealed by bulk RNA-seq
RNA-seq (gene expression) · mouse · 22 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
- 22 samples: 8 conditions, mostly in triplicateGroups 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
- Live attenuated influenza vaccine with low proportions of defective interfering particles elicits robust immunogenicity and cross-protectionNature communications · 2025
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 GSE297572_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 PRJNA1265208 and SRA study SRP586356. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 22 samples.
How we read this: 8 replicated groups read from 22 sample titles; they account for 22 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.
- GSM8994947 Low DIPs, 8hours, rep1 Low DIPs, 8hours,
- GSM8994948 Low DIPs, 8hours, rep2 Low DIPs, 8hours,
- GSM8994949 Low DIPs, 8hours, rep3 Low DIPs, 8hours,
- GSM8994950 High DIPs, 8hours, rep1 High DIPs, 8hours,
- GSM8994951 High DIPs, 8hours, rep2 High DIPs, 8hours,
- GSM8994952 High DIPs, 8hours, rep3 High DIPs, 8hours,
- GSM8994953 Low DIPs, 2days, rep1 Low DIPs, 2days,
- GSM8994954 Low DIPs, 2days, rep2 Low DIPs, 2days,
- GSM8994955 High DIPs, 2days, rep1 High DIPs, 2days,
- GSM8994956 High DIPs, 2days, rep2 High DIPs, 2days,
- GSM8994957 Low DIPs, 4days, rep1 Low DIPs, 4days,
- GSM8994958 Low DIPs, 4days, rep2 Low DIPs, 4days,
- GSM8994959 Low DIPs, 4days, rep3 Low DIPs, 4days,
- GSM8994960 High DIPs, 4days, rep1 High DIPs, 4days,
- GSM8994961 High DIPs, 4days, rep2 High DIPs, 4days,
- GSM8994962 High DIPs, 4days, rep3 High DIPs, 4days,
- GSM8994963 Low DIPs, 6days, rep1 Low DIPs, 6days,
- GSM8994964 Low DIPs, 6days, rep2 Low DIPs, 6days,
- GSM8994965 Low DIPs, 6days, rep3 Low DIPs, 6days,
- GSM8994966 High DIPs, 6days, rep1 High DIPs, 6days,
- GSM8994967 High DIPs, 6days, rep2 High DIPs, 6days,
- GSM8994968 High DIPs, 6days, rep3 High DIPs, 6days,
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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.