|
| Status |
Public on Nov 05, 2023 |
| Title |
mRNA_45 |
| Sample type |
SRA |
| |
|
| Source name |
Primary Lung Fibroblasts, Apex
|
| Organism |
Homo sapiens |
| Characteristics |
participant id: 018A
age: 66
gender: F
smoking history: Never
fvc%: 60
dlco%: 49
disease state: Idiopathic Pulmonary Fibrosis (IPF)
drug treatment: Control
drug concentration: 0uM
|
| Treatment protocol |
Cells were plated at 100,000 cells per mL in growth media and incubated overnight. Following quiescing in 0% FBS media for 24 hours, cells were stimulated with growth media in the presence/absence of the drug ACT001.
|
| Growth protocol |
Cells were cultured in DMEM supplemented with 10% FBS and antibiotics (growth media) in 5% CO2 at 37°C in a humidified atmosphere. Cells at passages 3-4 were used in all experiments. In experiments, growth media is substituted with DMEM and antibiotics without serum (0% FBS).
|
| Extracted molecule |
polyA RNA |
| Extraction 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®
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Ctrl_IPF1
|
| Data processing |
Read alignment using STAR v2.5.2b
featureCounts from subread v1.5.1 for gene quantification
Differential Gene Expression analysis using Degust (DOI: 10.5281/zenodo.3258932)
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: Gene counts table
|
| |
|
| Submission date |
Nov 09, 2021 |
| Last update date |
Nov 05, 2023 |
| Contact name |
Nicholas C Wong |
| E-mail(s) |
nick.wong@monash.edu
|
| Organization name |
Monash University
|
| Department |
Monash Bioinformatics Platform, Central Clinical School
|
| Street address |
Wellington Road
|
| City |
Clayton |
| State/province |
Victoria |
| ZIP/Postal code |
3800 |
| Country |
Australia |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE188464 |
Disease-specific transcriptomic changes induced by NFκB inhibition in idiopathic pulmonary fibrosis |
|
| Relations |
| BioSample |
SAMN23008117 |
| SRA |
SRX13082525 |
