|
| Status |
Public on Feb 01, 2023 |
| Title |
3-Parenchyma-PBS (X102) |
| Sample type |
SRA |
| |
|
| Source name |
Parenchyma
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Parenchyma
strain: Balb/C
age: 18-20 weeks
Sex: Female
exposure: PBS
|
| Treatment protocol |
Experimental asthma: Some mice were sensitized and challenged intranasally with house dust mite (HDM) extract 5 days per week for 3 weeks. In other mice, this was HDM treatment 3 times/week from weeks 4-11. Controls received phosphate buffered saline (PBS).
Experimental chronic obstructive pulmonary disease (COPD): Mice were exposed to cigarette smoke (CS) twice per day, 5 days per week for 8 weeks. Control mice were exposed to normal air (AIR).
Experimental asthma-COPD overlap (ACO): Mice were sensitized and challenged intranasally with HDM or PBS. From weeks 4-11, mice were also exposed to CS or AIR.
Treatment with dexamethasone (DEX): Separate groups of mice were treated with DEX during week 11.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was prepared using TRizol (Invitrogen) extraction method following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 Spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
RNAseq (3 week PBS parenchyma)
|
| Data processing |
Image analysis was performed in real time by the NovaSeq Control Software (NCS) v1.6.0 and Real Time Analysis (RTA) v3.4.4, running on the instrument computer. RTA performs real-time base calling on the NovaSeq instrument computer.
Then the Illumina bcl2fastq 2.20.0.422 pipeline was used to generate the sequence data.
Read libraries were mapped to the mouse genome using STAR (v2.5.1b), followed by gene quantitation with RSEM (v1.2.31) and Kallisto (v0.44.0).
Assembly: mm10
Supplementary files format and content: raw gene counts comma separated
|
| |
|
| Submission date |
Mar 31, 2022 |
| Last update date |
Feb 01, 2023 |
| Contact name |
Emma de Jong |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Western Australia
|
| Street address |
35 Stirling Hwy
|
| City |
Crawley, Perth |
| State/province |
WA |
| ZIP/Postal code |
6009 |
| Country |
Australia |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE199853 |
Airway and parenchyma RNA sequencing in a mouse model of asthma chronic obstructive pulmonary disease overlap |
|
| Relations |
| BioSample |
SAMN27123089 |
| SRA |
SRX14687452 |
