Human respiratory organoids sustained reproducible propagation of previously uncultivable human rhinovirus C
RNA-seq (gene expression) · human · 12 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
- Homo sapiens (human)
- Samples
- 12 samples: 6 conditions, mostly in duplicateGroups 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
- Human respiratory organoids sustained reproducible propagation of human rhinovirus C and elucidation of virus-host interactionNature communications · 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 GSE254400_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 PRJNA1070308 and SRA study SRP486401. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 6 replicated groups read from 12 sample titles; they account for 12 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.
- GSM8041523 AwO-Mock-1 AwO-Mock
- GSM8041524 AwO-Mock-2 AwO-Mock
- GSM8041525 AwO-HRVC-1 AwO-HRVC
- GSM8041526 AwO-HRVC-2 AwO-HRVC
- GSM8041527 AwO-HRVC+CYT387-1 AwO-HRVC+CYT387
- GSM8041528 AwO-HRVC+CYT387-2 AwO-HRVC+CYT387
- GSM8041529 NsO-Mock-1 NsO-Mock
- GSM8041530 NsO-Mock-2 NsO-Mock
- GSM8041531 NsO-HRVC-1 NsO-HRVC
- GSM8041532 NsO-HRVC-2 NsO-HRVC
- GSM8041533 NsO-HRVC+CYT387-1 NsO-HRVC+CYT387
- GSM8041534 NsO-HRVC+CYT387-2 NsO-HRVC+CYT387
- GSE311749 Upper Airway Gene Expression in Hospitalized Children with Rhinovirus-induced Respiratory Illnesses 86 samples shares respiratory, rhinovirus
- GSE271148 Human airway submucosal gland organoids to study respiratory inflammation and infection [bulk RNA-seq] 16 samples shares respiratory, organoids
- GSE271264 Human airway submucosal gland organoids to study respiratory inflammation and infection [bulk RNA-seq] 15 samples shares respiratory, organoids
- GSE263272 Human iPS cell-derived respiratory organoids as a model for respiratory syncytial virus infection 12 samples shares respiratory, organoids
- GSE309325 Analysis of SARS-CoV-2 replication using human nasal organoids comprising olfactory and respiratory epithelium 7 samples shares respiratory, organoids
- GSE279753 The respective roles of TMPRSS2 and cathepsins for SARS-CoV-2 infection in human respiratory organoids 6 samples shares respiratory, organoids
- GSE263372 Efficient and reproducible generation of human iPSC-derived cardiomyocytes and cardiac organoids in stirred suspension systems 5 samples shares reproducible, organoids
- GSE325412 Robust generation of distal respiratory airway organoids by an engineered cuboid chip to therapy chronic obstructive pulmonary disease 4 samples shares respiratory, organoids
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.