|
| Status |
Public on Oct 05, 2018 |
| Title |
SAFA (HSV-1 study) |
| Sample type |
SRA |
| |
|
| Source name |
macrophage
|
| Organism |
Mus musculus |
| Characteristics |
cell type: BMDMs
genotype: Safa-/-
infection: control
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
FPKM were calculated. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
|
| |
|
| Submission date |
Oct 04, 2018 |
| Last update date |
Oct 08, 2018 |
| Contact name |
lili Cao |
| E-mail(s) |
caolili@bjmu.edu.cn
|
| Organization name |
Peking university health science center
|
| Street address |
Xueyuan road, haidian district
|
| City |
Beijing |
| ZIP/Postal code |
100191 |
| Country |
China |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE120833 |
Genome wide RNA-seq of wild-type and Safa-/- BMDMs upon HSV-1 infection. |
|
| Relations |
| BioSample |
SAMN10176383 |
| SRA |
SRX4797150 |
