|
| Status |
Public on Aug 15, 2020 |
| Title |
CT00B CD14+ high VL |
| Sample type |
SRA |
| |
|
| Source name |
monocyte/CD14+
|
| Organism |
Homo sapiens |
| Characteristics |
gender: F
immune status: heart transplant
virus strain: clinically infected with CMV
|
| Treatment protocol |
THP-1 cells were stimulated with PMA at 100 ng/ml for 48 hours prior to infection with TB40/E-5. Human peripheral blood mononuclear cells (PBMC) were isolated from CMV IgG negative immunocompetent donors and cultured ex vivo in donor autologous serum and infected with TB40/E-5.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Desired monocyte populations for sorted by flow cytometry and RNA was harvested using Qiagen RNeasy micro kit and on column Dnase digestion was performed. RNA quantity and quality was analyzed on Agilent Bioanalyzer.
Lexogen QuantSeq Kit was used for the construction of bulk sequencing libraries. SureCell WTA 3' Library Prep Kit was used for the construction of single-cell sequencing libraries for in vitro infections. The inDrop platform was used for the construction of single-cell sequencing libraries from transplant patients. RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
raw data at dbGAP
|
| Data processing |
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to reference genome hg19 using STAR
Gene-count matrices were calculated using scumi
Downstream analysis was performed using Pegasus
Genome_build: hg19
|
| |
|
| Submission date |
Aug 14, 2020 |
| Last update date |
Aug 15, 2020 |
| Contact name |
Pritha Sen |
| E-mail(s) |
[email protected]
|
| Organization name |
Massachusetts General Hospital
|
| Street address |
149 13th street
|
| City |
Charlestown |
| State/province |
Massachusetts |
| ZIP/Postal code |
02129 |
| Country |
USA |
| |
|
| Platform ID |
GPL21697 |
| Series (1) |
| GSE132048 |
Linking Indirect Effects of Cytomegalovirus to Modulation of Monocyte Innate Immune Function |
|
| Relations |
| BioSample |
SAMN15824569 |
