A mouse model of human coronavirus HCoV-NL63 infection: comparison with rhinovirus-A1B
RNA-seq (gene expression) · mouse · 18 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
- 18 samples: 6 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
- Developing a mouse model of human coronavirus NL63 infection: comparison with rhinovirus-A1B and effects of prior rhinovirus infectionAmerican journal of physiology. Lung cellular and molecular physiology · 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 GSE254967_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 PRJNA1072722 and SRA study SRP487846. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 16 samples.
How we read this: 6 replicated groups read from 18 sample titles; they account for 16 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.
- GSM8061470 RV1B d6 NL63 d2, rep 1 RV1B d6 NL63 d2,
- GSM8061471 RV1Bd2, rep 1
- GSM8061472 RV1B d2, rep 2 RV1B d2,
- GSM8061473 RV1B d2, rep 3 RV1B d2,
- GSM8061474 Sham d2, rep 1 Sham d2,
- GSM8061475 Sham d2, rep 2 Sham d2,
- GSM8061476 NL63 d2, rep 1 NL63 d2,
- GSM8061477 NL63 d2, rep 2 NL63 d2,
- GSM8061478 RV1B d6 NL63 d2, rep 2 RV1B d6 NL63 d2,
- GSM8061479 RV1B d6 NL63 d2, rep 3 RV1B d6 NL63 d2,
- GSM8061480 sham d2, rep 3
- GSM8061481 NL63 d2, rep 3 NL63 d2,
- GSM8061482 NL63 d4, rep 1 NL63 d4,
- GSM8061483 NL63 d4, rep 2 NL63 d4,
- GSM8061484 NL63 d4, rep 3 NL63 d4,
- GSM8061485 RV1B d4, rep 1 RV1B d4,
- GSM8061486 RV1B d4, rep 2 RV1B d4,
- GSM8061487 RV1B d4, rep 3 RV1B d4,
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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.