Activation of alveolar epithelial ER stress by b-coronavirus infection disrupts surfactant homeostasis in mice: implications for COVID-19 respiratory failure
RNA-seq (gene expression) · mouse · 10 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
- 10 samples: 4 × Infected AT2 vs 3 × WT AT2 vs 3 × Transitional AT2Groups 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
- Activation of alveolar epithelial ER stress by β-coronavirus infection disrupts surfactant homeostasis in mice: implications for COVID-19 respiratory failureAmerican 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 GSE244820_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 PRJNA1024962 and SRA study SRP464901. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 4 samples read as cases, 3 as controls.
How we read this: 3 replicated groups read from 10 sample titles; they account for 10 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.
- GSM7830293 WT AT2 - 1 WT AT2
- GSM7830294 WT AT2 - 2 WT AT2
- GSM7830295 WT AT2 - 3 WT AT2
- GSM7830296 Infected AT2 -1 Infected AT2
- GSM7830297 Infected AT2 -2 Infected AT2
- GSM7830298 Infected AT2 -3 Infected AT2
- GSM7830299 Infected AT2 -4 Infected AT2
- GSM7830300 Transitional AT2 -1 Transitional AT2
- GSM7830301 Transitional AT2 -2 Transitional AT2
- GSM7830302 Transitional AT2 -3 Transitional AT2
- GSE326488 Ubiquitin-like proteins NEDD8 and SUMO2 control epithelial homeostasis, regeneration, and inflammation [RNA-Seq mouse] 14 samples shares homeostasis, epithelial
- GSE330351 Ferritin-mediated iron homeostasis regulates fibroblast activation and shapes post-infarction cardiac remodeling 9 samples shares homeostasis, activation
- GSE326641 Ubiquitin-like proteins NEDD8 and SUMO2 control epithelial homeostasis, regeneration, and inflammation [scRNA-seq] 8 samples shares homeostasis, epithelial
- GSE270151 Development of an ideal inactivated vaccine for COVID-19 (mouse lung RNA-seq data) 52 samples shares covid-19
- GSE268810 Fibrin drives thromboinflammation and neuropathology in COVID-19 [Lung] 16 samples shares covid-19
- GSE241089 First cleavage is a manifestation of the geometry of the unfertilized oocyte: implications for monozygotic twinning in mice. 219 samples shares implications
- GSE228579 Chronic stress disrupts hepatic homeostasis and accelerates liver cancer progression through ADRB2 signaling 66 samples shares homeostasis
- GSE279885 Perimenopausal State Oestradiol to Progesterone Imbalance Drives Alzheimer’s Risk via ERRα Dysregulation and Energy Dyshomeostasis 59 samples shares homeostasis
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.