The soluble factor milieu in IPF and in COPD exacerbations dysregulates epithelial differentiation
RNA-seq (gene expression) · mouse · 30 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
- 30 samples: 17 distinct titles, 1 of them repeatedGroups 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
- The disruptive effects of COPD exacerbation-associated factors on epithelial repair responsesFrontiers in immunology · 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 GSE245259_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 PRJNA1027466 and SRA study SRP466033. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 30 sample titles: 17 distinct titles with little repetition. 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.
- GSM7839535 105096-001-025
- GSM7839536 105096-001-026
- GSM7839537 105096-001-027
- GSM7839538 105096-001-028
- GSM7839539 105096-001-029
- GSM7839540 105096-001-030
- GSM7839541 105096-001-031
- GSM7839542 105096-001-032
- GSM7839543 105096-001-033R
- GSM7839544 105096-001-034R
- GSM7839545 105096-001-035R
- GSM7839546 105096-001-036R
- GSM7839547 105096-001-037R
- GSM7839548 105096-001-038R
- GSM7839549 105096-001-039R
- GSM7839550 105096-001-040R
- GSM7839551 105096-001-041R
- GSM7839552 105096-001-042R
- GSM7839553 105096-001-043R
- GSM7839554 105096-001-044R
- GSM7839555 105096-001-045R
- GSM7839556 105096-001-046R
- GSM7839557 105096-001-047R
- GSM7839558 105096-001-048R
- GSM7839559 105096-001-049
- GSM7839560 105096-001-050
- GSM7839561 105096-001-051
- GSM7839562 105096-001-052
- GSM7839563 105096-001-053
- GSM7839564 105096-001-054
- GSE277533 Interpretable machine learning uncovers epithelial transcriptional rewiring and a role for Gelsolin in COPD 8 samples shares copd, epithelial
- GSE268757 Reproducible lung protective effects of a TGFβR1/ALK5 inhibitor in the bleomycin-induced and spirometry-confirmed mouse model of IPF 75 samples shares ipf
- GSE287944 Adenine Nucleotide translocase 1 (ANT1) Deficiency Impairs Macrophage Metabolism and Migration, Protecting Against Emphysema in COPD 12 samples shares copd
- GSE289559 Adenine Nucleotide translocase 1 (ANT1) Deficiency Impairs Macrophage Metabolism and Migration, Protecting Against Emphysema in COPD [6 months] 12 samples shares copd
- GSE336580 γ-Tocopherol attenuates COPD-associated macrophage inflammation through the PSEN1–SYT7–PI3K/Akt axis 9 samples shares copd
- GSE239537 A Japanese herbal medicine, Hochuekkito (TJ-41), has anti-inflammatory effects on the COPD mouse model 8 samples shares copd
- GSE317792 Transcriptomic analysis of Platycodin D (PD)-improved idiopathic pulmonary fibrosis (IPF) mice 8 samples shares ipf
- GSE280059 Mice with Lymphatic Dysfunction Develop Pathogenic Lung Tertiary Lymphoid Organs that Model an Autoimmune Emphysema Phenotype of COPD 6 samples shares copd
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.