|
| Status |
Public on Apr 11, 2020 |
| Title |
clodronate male PBS2 |
| Sample type |
SRA |
| |
|
| Source name |
Lung homogenate
|
| Organism |
Mus musculus |
| Characteristics |
tissue: lung
strain: C57Bl6/J
Sex: male
treatment: uninfected
|
| Treatment protocol |
Alveolar macrophages were depleted by inoculating intranasally anesthetized mice with 50 μl of either liposome containing clodronate (5 mg/mL) or liposome only controls (Encapsula NanoSciences) 24 h before intranasal infection with 10^7 cfu of A. baumannii 5075.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Lung homogenate was ressuspended in TRIZOL reageant. RNA was extracted from whole lungs using The Direct-zol™ RNA MiniPrep Kit (Zymo Research), following manufacturer's instructions
mRNA was purified from 1 μg of total RNA using poly-T oligo-attached magnetic beads and then fragmented using fragmentation buffer. The first strand of cDNA was synthesized using a random hexamer and M-MuLV reverse transcriptase with the second strand of cDNA synthesized using DNA polymerase I and RNase H. cDNA was purified using AMPure XP beads (Beckman Coulter), converted to blunt ends, adenylated and New England Biolabs (NEB) adaptors ligated.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Analysis was performed using Partek Flow
Reads were trimmed with Phred scores <30, 20bp minimum length and a maximum N of 10%, along with adaptor sequences removed
Trimmed reads were aligned using STAR and unaligned reads further aligned using TopHat2
Combined alignments were quantified to the annotation model
Filtered counts were normalized by adding 1 and using TMM
Differential analysis was conducted using ANOVA and Limma-voom, clodronate males and females were compared either before or after infection
Genome_build: mm9
Supplementary_files_format_and_content: xlsx
|
| |
|
| Submission date |
Jul 24, 2019 |
| Last update date |
Apr 11, 2020 |
| Contact name |
Dane Parker |
| E-mail(s) |
dane.parker@rutgers.edu
|
| Phone |
9739723047
|
| Organization name |
Rutgers New Jersey Medical School
|
| Department |
Pathology, Immunology and Laboratory Medicine
|
| Street address |
205 South Organge Ave, G-1208
|
| City |
Newark |
| State/province |
NJ |
| ZIP/Postal code |
07103 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE134805 |
Biological sex influences susceptibility to Acinetobacter baumannii pneumonia in mice |
|
| Relations |
| BioSample |
SAMN12356456 |
| SRA |
SRX6583696 |
