U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

SRX13082544: GSM5683394: mRNA_187; Homo sapiens; RNA-Seq
1 ILLUMINA (Illumina NovaSeq 6000) run: 22.6M spots, 6.8G bases, 2Gb downloads

Submitted by: NCBI (GEO)
Study: Disease-specific transcriptomic changes induced by NF?B inhibition in idiopathic pulmonary fibrosis
show Abstracthide Abstract
Idiopathic pulmonary fibrosis (IPF) is a progressive fibrotic lung disease of unknown etiology and poor prognosis. In IPF, aberrant extracellular matrix production by activated, hyperproliferative fibroblasts drives disease progression but the exact mechanisms by which this occurs remains undefined. We previously showed that inhibition of transcription factor nuclear factor kappa-B (NF?B) with ACT001 reduced pro-fibrotic fibroblast behaviors such as fibroblast-to-myofibroblast transition. The aim of this follow-up study was to characterize the transcriptional profile of primary fibroblasts treated with ACT001 and identify differences between cells from patients with IPF and non-diseased control donors. Primary lung fibroblasts derived from eight patients with IPF and eight age-matched non-diseased controls (NDC) were treated with 0, 3 or 10 µM ACT001 in the presence/absence of pro-fibrotic cytokine transforming growth factor (TGF)-ß1 for 24 hours after which whole genome RNA sequencing was performed. Gene set enrichment analysis (GSEA) of the Hallmark gene sets was also completed. Although the majority of genes differentially expressed after ACT001 treatment were the same in NDC and IPF cells, several genes were uniquely changed in IPF. GSEA indicated that ACT001 treatment most upregulates the reactive oxygen species pathway. ACT001 is a water-soluble compound with a stable half-life in plasma, thus making it an attractive candidate for further investigation as a therapeutic in IPF. This study adds to the growing body of literature that demonstrates anti-fibrotic activity of NF-?B inhibition in the context of IPF. Overall design: Primary cultered human fibroblasts from 16 individuals, 8 with idiopathic pulmonary fibrosis (IPF) and 8 age-matched controls
Sample: mRNA_187
SAMN23008136 • SRS11019443 • All experiments • All runs
Organism: Homo sapiens
Library:
Instrument: Illumina NovaSeq 6000
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: PAIRED
Construction protocol: After 24 hours, cells were lysed in RNA lysis buffer (Qiagen, Aus) and stored at -80°C until further extraction for transcriptomic analyses. RNA was extracted using the Quick-RNA MiniPrep Kit (Zymo, Australia) according to manufacturer's instructions. RNA was extracted in groups of two patient samples per group per round to reduce batch effects. RNA was eluted into 30 μL RNase-free water and 24 μL was sent for sequencing NEBNext® Ultra Directional RNA Library Prep Kit for Illumina®
Experiment attributes:
GEO Accession: GSM5683394
Links:
Runs: 1 run, 22.6M spots, 6.8G bases, 2Gb
Run# of Spots# of BasesSizePublished
SRR1688978422,635,2336.8G2Gb2023-11-06

ID:
17791150

Supplemental Content

Search details

See more...

Recent activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...