|
| Status |
Public on Jun 19, 2013 |
| Title |
Macrophages from flu-treated mice |
| Sample type |
SRA |
| |
|
| Source name |
lung
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57Bl/6
cell type: Macrophages
tissue: lung
treatment: flu-treated
|
| Treatment protocol |
Mice were treated with 106 pfu of NS1-GFP flu virus and sacrificed 12h later
|
| Extracted molecule |
total RNA |
| Extraction protocol |
CD103+ dendritic cells and alveolar macrophages were cell-sorted from lungs of untreated and flu-treated mice. Total RNA was extracted from sorted cells following Qiazol protocol. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
MO_flu
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
Sequence reads were filtered for low quality and mapped to the mm9 genome.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated following the protocol from Mortazavi et al, Nat Methods, 2008. Briefly, all reads falling in the exons of a given gene were counted and normalized by the length of the gene and the total reads of the run.
Supplementary_files_format_and_content: RPKM abundance
|
| |
|
| Submission date |
Jun 20, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Brian Brown |
| E-mail(s) |
[email protected]
|
| Organization name |
Icahn School of Medicine at Mount Sinai
|
| Department |
Genetics and Genomic Sciences
|
| Street address |
1470 Madison Avenue
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10029 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE38838 |
Cross-presenting CD103+ dendritic cells are protected from influenza virus infection |
|
| Relations |
| SRA |
SRX155465 |
| BioSample |
SAMN01057037 |
