Effect of knockdown of junctional genes JUP and PLEC on Small Airway Epithelial Cells (SAECs) in the context of epithelial desquamation in distal bronchioles of Idiopathic Pulmonary fibrosis (IPF) patients
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: 4 × Scrambled vs 4 × JUP knockdown vs 4 × PLEC knockdownGroups 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.
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 GSE267943_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 PRJNA1113677 and SRA study SRP508830. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 8 samples read as cases, 4 as controls.
How we read this: 3 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.
- GSM8282322 Scrambled1 Scrambled
- GSM8282323 Scrambled2 Scrambled
- GSM8282324 Scrambled3 Scrambled
- GSM8282325 Scrambled4 Scrambled
- GSM8282326 JUP knockdown1 JUP knockdown
- GSM8282327 JUP knockdown2 JUP knockdown
- GSM8282328 JUP knockdown3 JUP knockdown
- GSM8282329 JUP knockdown4 JUP knockdown
- GSM8282330 PLEC knockdown1 PLEC knockdown
- GSM8282331 PLEC knockdown2 PLEC knockdown
- GSM8282332 PLEC knockdown3 PLEC knockdown
- GSM8282333 PLEC knockdown4 PLEC knockdown
- GSE248485 Effects of Antifibrotic Drugs on Transcriptome of Peripheral Blood Mononuclear Cells in Idiopathic Pulmonary Fibrosis [IPF_PBMC] 18 samples shares ipf, idiopathic
- GSE310473 Targeting Fused in Sarcoma (FUS): A Novel Antisense Strategy for Treating Idiopathic Pulmonary Fibrosis [RNA-Seq IPF] 16 samples shares ipf, idiopathic
- GSE284531 Alteration in the transcriptome of lung basal epithelial cells isolated from IPF lungs upon genetic knockdown of SOX9 6 samples shares ipf, epithelial
- GSE282322 JUNB O-GlcNAcylation-mediated Promoter Accessibility of Metabolic Genes Modulates Distinct Epithelial Lineage in Pulmonary Fibrosis [ipf_saec_bulk] 24 samples shares ipf, epithelial
- GSE267521 The MUC5B IPF risk variant promotes a distal airway secretory phenotype and loss of alveolar markers 310 samples shares ipf
- GSE159354 Single-cell RNA-seq of sort human lung explants from IPF and SSc-ILD patients 48 samples shares ipf
- GSE301181 Identification of IPF Specific Genes Expressed by Lung Tissue - Derived Fibroblasts Using Next Generation Sequencing 43 samples shares ipf
- GSE92592 mRNA Sequencing of Ideopathic Pulmonary Fibrosis (IPF) and Control Samples from the Lung Tissue Research Consortium (LTRC) 39 samples shares ipf
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.