|
| Status |
Public on Oct 29, 2018 |
| Title |
Lungs_PA103_1 |
| Sample type |
SRA |
| |
|
| Source name |
Lung
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57Bl/6J
tissue: lung
treatment: water_PA103
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Lung samples were collected in RNAlater (Qiagen) and blood samples were collected in RNAprotect animal blood tubes (Qiagen), both according to the manufacturer protocols. Total RNA was isolated using the RNAeasy Plus Mini kit (Qiagen). An enrichment with poly d(T) beads (New England Biolabs) was used to isolate polyA RNA. A KAPA Stranded Total RNA-Seq kit (Kapa Biosystems) was used to create the cDNA libraries.
The cDNA libraries were made according to the manufacturer protocol. In brief, first strand cDNA was synthesized, following by second strand synthesis and blunt-end formation. After 3’ adenylation, adapters (Bioo Scientific) for multiplexing were ligated, followed by amplification and then purification using Agencourt Ampure XP beads (Beckman Coulter).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Base-calling and de-multiplexing were performed on the Illumina instrument.
fastq file quality control was performed using FastQC v0.11.5 and MultiQC v0.8.dev0
FASTQ files were aligned to the Ensembl murine reference genome using STAR aligner (version 2.5.2B).
Read count tables were generated using HTSeq-count (version 0.6.1p1)
Genome_build: GRCm38.p5 (build 86)
Supplementary_files_format_and_content: The .count files were generated using HTSeq-count and represent read counts.
|
| |
|
| Submission date |
Feb 09, 2018 |
| Last update date |
Oct 30, 2018 |
| Contact name |
Amy H. Lee |
| Organization name |
Simon Fraser University
|
| Department |
Molecular Biology and Biochemistry
|
| Lab |
Amy Lee
|
| Street address |
8888 University Drive
|
| City |
Burnaby |
| State/province |
BC |
| ZIP/Postal code |
V5A1S6 |
| Country |
Canada |
| |
|
| Platform ID |
GPL11002 |
| Series (1) |
| GSE110415 |
Characterization of host responses during Pseudomonas aeruginosa acute lung infection in the lungs and blood and after treatment with the synthetic immunomodulatory peptide IDR-1002 |
|
| Relations |
| BioSample |
SAMN08513895 |
| SRA |
SRX3677886 |
