|
| Status |
Public on Jul 15, 2020 |
| Title |
Control_4 |
| Sample type |
SRA |
| |
|
| Source name |
Left lung post lavage
|
| Organism |
Mus musculus |
| Characteristics |
strain: BALB/c
tissue: Left Lung
exposure: Control
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Lungs were lavaged with 2x 1mL of saline and then removed. The left lung was placed into RNAlater (Qiagen) and stored at 4 degrees Celcius for 24 hours after which time it was flash frozen in liquid nitrogen and stored at -80 degrees celcius.
cDNA libraries were constructed for sequencing using a KAPA Stranded Total RNA Kit (Kapa Biosystems)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Base-calling and de-multiplexing were done using built-in software on the Illumina HiSeq 2500
fastq file quality control was performed using FastQC v0.11.5 and MultiQC v0.8.dev0
fastq files were aligned to the mouse genome using STAR v2.5
read count tables were generated from bam files using htseq-count v.2.5
Significance and fold changes calculated in R using DEseq2 package with Likelihood Ratio Test
Genome_build: Ensebml GRCm38
Supplementary_files_format_and_content: tab delimited files containing uniquely mapped reads per gene for each sample
|
| |
|
| Submission date |
Jul 11, 2018 |
| Last update date |
Jul 15, 2020 |
| Contact name |
Christopher Pascoe |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Manitoba
|
| Department |
Physiology & Pathophysiology
|
| Street address |
602-715 McDermot Avenue, Children's Hospital Research Institute of Manitoba
|
| City |
Winnipeg |
| State/province |
MB |
| ZIP/Postal code |
R3E 3P4 |
| Country |
Canada |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE116967 |
Effects of endotoxin abundance in house dust mite on the molecular phenotype of inflammation and tissue response in mouse lung |
|
| Relations |
| BioSample |
SAMN09643765 |
| SRA |
SRX4381955 |
