|
| Status |
Public on Apr 30, 2020 |
| Title |
THP-GFPhigh_S8 |
| Sample type |
SRA |
| |
|
| Source name |
THP-1
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: CMV
culture conditions: 100 ng/ml PMA-stimulated
passage: passage 3
virus strain: TB40/E-5
|
| 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. RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiniSeq |
| |
|
| Description |
Bulk RNA-seq for THP-1 infected with CMV
RNA.raw.cnt.table.txt
THP-GFPhigh_S8
|
| 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
Transcript abundance was calculated using Htseq
Single-cell libraries were aligned to hg19 reference genome and UMI count files were generated using the Illumina BaseSpace SureCell application
Genome_build: hg19
|
| |
|
| Submission date |
May 31, 2019 |
| Last update date |
Apr 30, 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 |
GPL22790 |
| Series (1) |
| GSE132048 |
Linking Indirect Effects of Cytomegalovirus to Modulation of Monocyte Innate Immune Function |
|
| Relations |
| BioSample |
SAMN11918251 |
| SRA |
SRX5940138 |
