Dissection of influenza infection in vivo by single-cell RNA-sequencing
The influenza virus is a major cause of morbidity and mortality worldwide, yet, the impact of intracellular viral invasion and the cellular response diversity remain uncharacterized. By massively parallel single-cell RNA-seq we comprehensively mapped the host lung response to in-vivo influenza infection in wild-type and Irf7-knockout mice across nine immune and non-immune cell types. We found an unexpected high prevalence of infected cells in all cell types, showed that infection is a characteri...
Provenance — who produced it, who reused it
Linked to 2 papers in the literature. Roles are inferred factual signals (who deposited the data vs who reused it), with counts — never a judgement about any author.
1 further paper cites this accession but reuse could not be confirmed.
Deep data QC
79/100 · CStandardized, field-standard QC computed by touching the data — every metric states how it was obtained · evidence: measured
This dataset is mouse bulk RNA-seq, and the C grade (79/100) reflects a fundamental tension: per-base accuracy is excellent but the quality summary is unusually flat, which tempers confidence. The two metrics steering the grade are mean_base_quality and duplication_rate: a mean Phred of 30 is mediocre-to-borderline for modern Illumina data and is the single biggest drag on the score, signaling that reads carry roughly 1-in-1000 base-call error that can blunt sensitivity for low-frequency variants or precise splice/expression calls, while a 42% duplication rate is moderately high and points to limited library complexity or PCR/optical redundancy that can inflate apparent counts. On the reassuring side, essentially 100% Q20/Q30 base fractions plus negligible adapter (0.03%) and N content indicate clean, well-trimmed reads with little technical contamination, so the data are reusable for standard differential-expression work if you account for duplication. Note, however, that the QC fetch failed (HTTP 429) and several headline numbers (100% Q30 alongside a mean quality of only 30) look internally inconsistent or capped, so this reading should be treated as provisional pending a full measured re-run.
The C grade is a transparent weighted average. Each metric below scored from 0–100% against the published bulk-RNA-seq thresholds, weighted by its importance; nothing is hidden or subjective.
measured = computed from the data · extrapolated/reported = derived or from the repository · dq-1.0
Scientific quality
Based on hands-on reproduction of the papers that use this dataset. A reproducible paper that stands on this data is positive evidence; a flagged one is a prompt to look closer — never a verdict on the dataset itself without the evidence.