|
| Status |
Public on May 05, 2017 |
| Title |
MDM-520_H5N1_MOI2_12h_2 |
| Sample type |
SRA |
| |
|
| Source name |
MDM-520_H5N1_MOI2_12h
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Human Monocyte-Derived Macrophages (MDM)
donor id: 520
infection: A/Vietnam/1203/04 (H5N1) HALo, MOI 2
time point: 12h
biological replicate: 2
|
| Treatment protocol |
For infection, growth medium was replaced with virus diluted to the appropriate concentration in serum-free RPMI 1640 medium at a total volume of 2 mL. Dishes were incubated in a cell culture incubator with gentle rocking every 15 minutes. After 60 minutes, the inoculum was removed and cells were washed twice washed gently with 5 mL serum-free RPMI 1640. 10 mL of RPMI 1640 + 10% fetal bovine serum and Penicillin-Streptomycin was added and cells were incubated for the specified length of time.
|
| Growth protocol |
Human CD14+ monocytes, isolated from healthy donor blood, were plated at a density of 3 x 10^6 cells in a 10 cm dish and cultured for 10 days in RPMI 1640 + 10% fetal bovine serum, Penicillin-Streptomycin, and 1000U/ml GM-CSF.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
1 ml Trizol was added to 5-10 x 10^6 cells and the homogenate was incubated at room temperature for 5 minutes. 200 μl chloroform were added per ml of Trizol, shaken vigorously for 15-30 seconds and incubated at room temperature for 15 minutes. Samples were centrifuged for 15 minutes at 4˚C and 12,000 rcf. The aqueous phase was carefully collected in a separate tube. 500 μl isopropanol was added per 1 ml Trizol, inverted to mix and incubated at room temperature for 5-10 minutes. Samples were transferred to Qiagen RNeasy Spin Columns and RNA was isolated according to the manufacturer’s instructions.
Libraries were constructed using the Illumina TruSeq Stranded Total RNA Library Prep Kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
1-0126-2/2-BR
|
| Data processing |
Raw sequencing reads were aligned to the human hg38 genome with STAR
Read counts per gene were calculated using FeatureCounts
DESeq2 was used to generate FPKM values
Genome_build: hg38
Supplementary_files_format_and_content: comma-separated values containing FPKM quantification for all samples; gene-level quantification (FPKM normalization)
|
| |
|
| Submission date |
Apr 12, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Max Chang |
| E-mail(s) |
mchang@ucsd.edu
|
| Organization name |
University of California, San Diego
|
| Street address |
9500 Gilman Drive
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE97672 |
Human monocyte-derived macrophage (MDM) cell transcriptome response to infection with H1N1, H3N2, and H5N1 influenza virus. |
|
| Relations |
| BioSample |
SAMN06711203 |
| SRA |
SRX2733713 |
