|
| Status |
Public on Nov 10, 2022 |
| Title |
COPD nasopharyngal organoids, No infection, 6h post infection NRMK6 |
| Sample type |
SRA |
| |
|
| Source name |
Nasopharyngal organoids
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Nasopharyngal organoids
disease state: COPD
treatment: No infection
time: 6h post infection
|
| Treatment protocol |
Non-diseased or COPD nasopharyngeal organoids were either mock-treated or infected with Pseudomonas aeruginosa for 6 hours
|
| Growth protocol |
Human nasopharyngeal epithelial cells were isolated from NP swab or BALF, respectively from healthy volunteers or COPD patients, and cultured until confluency was reached. Cells were seeded on transwell inserts and differentiated at air-liquid interface for 2 weeks. Cells from ALI at 2 weeks were detached from the transwell membrane and embedded on matrigel for 3D differentiation for further 4-6 weeks to achieve maturation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Organoids were lysed with Qiagen RLT plus buffer and RNA was isolated using Qiagen Rneasy Plus Mini Kit. Stranded mRNA library preparation with oligo dT purification using Illumina TruSeq Stranded mRNA Kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
COPD nasopharyngal organoids, No infection, 6h post infection
|
| Data processing |
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trimmomatic-0.39 (parameter- /trimmomatic-0.39/adapters/TruSeq3-PE-2.fa:2:30:10:1:TRUE LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:30)
Quality check of sequencing reads using FastQC v0.11.8
Trimmed sequence reads were mapped to hg38 using align function available in Rsubread v2.6.4, which was run in R v4.1.0 software (parameters- type: rna)
Feature count extraction was performed using featureCounts function available in Rsubread v2.6.4, which was run in R v4.1.0 software (parameters- annot.ext: hg38.ensGene.gtf, isGTFAnnotationFile: TRUE, isPairedEnd: TRUE)
Assembly: hg38
Supplementary files format and content: Tab-delimited text files that contain the features and counts for each sample
|
| |
|
| Submission date |
Apr 25, 2022 |
| Last update date |
Nov 10, 2022 |
| Contact name |
Fransiskus Xaverius Ivan |
| E-mail(s) |
[email protected]
|
| Organization name |
Nanyang Technological University
|
| Department |
Lee Kong Chian School of Medicine
|
| Street address |
11 Mandalay Road
|
| City |
Singapore |
| ZIP/Postal code |
308232 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE201465 |
Gene expression in COPD and non-diseased nasopharyngeal organoids following Pseudomonas aeruginosa infection |
|
| Relations |
| BioSample |
SAMN27764269 |
| SRA |
SRX14991501 |
