|
| Status |
Public on Jun 20, 2020 |
| Title |
20-Lung-steady-state-AM-KO |
| Sample type |
SRA |
| |
|
| Source name |
Lung Alveolar macrophage mTOR{delta}APC
|
| Organism |
Mus musculus |
| Characteristics |
genotype/variation: mTOR {delta}APC
treatment: Steady-state
tissue: Lung
cell type: Alveolar macrophage
|
| Treatment protocol |
HDM - house dust mite allergy treatment. Mice were anesthetized with Isoflurane, and vaccinated intranasally (i.n.) with 25µL house dust mite extract (HDM) (1mg/mL protein content, Greer Labs). Injections were performed thrice weekly and mice were analyzed after 18d.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was purified using RNAeasy Micro Kit (Qiagen). Standard quality control steps were included to determine total RNA quality using Agilent 2100 Bioanalyzer (RNA integrity number (RIN) >8.5; Eukaryote Total RNA Pico Kit, Agilent, USA)
RNA libraries were prepared for sequencing using standard Clontech laboratory and Illumina NexteraXT protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1000 |
| |
|
| Data processing |
Reads were demultiplexed to Illumina BaseSpace with FastQ version 1.0.0
Read were mapped to mm10 reference using the STAR aligner (v2.3.1s) via the BaseSpace RNAExpress App v1.0
Abundance estimation of raw read counts was performed with Htseq-count via the BaseSpace RNAExpress App v1.0
Normalized expression (normalized read counts) was performed with DESeq2 (v1.10.1)
Genome_build: UCSC mm10 (mouse)
Supplementary_files_format_and_content: tab delimited text file containing normalized read counts for each sample (in columns) and each annotated transcript (in rows).
|
| |
|
| Submission date |
Jun 21, 2017 |
| Last update date |
Jun 20, 2020 |
| Contact name |
Gregory K Tharp |
| E-mail(s) |
gktharp@emory.edu
|
| Phone |
404-727-7797
|
| Organization name |
Yerkes National Primate Research Center
|
| Department |
Developmental and Cognitive Neuroscience
|
| Lab |
Genomics Core
|
| Street address |
954 Gatewood Dr
|
| City |
Atlanta |
| State/province |
GA |
| ZIP/Postal code |
30329-4208 |
| Country |
USA |
| |
|
| Platform ID |
GPL15103 |
| Series (1) |
| GSE100316 |
RNA-seq analysis of mTOR{delta}APC and WT lung and spleen APC subsets |
|
| Relations |
| BioSample |
SAMN07261467 |
| SRA |
SRX2941551 |
