|
| Status |
Public on Feb 22, 2018 |
| Title |
d130_non-adherent_us1_infected.CTTGGAA |
| Sample type |
SRA |
| |
|
| Source name |
monocyte-derived macrophage
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: monocyte-derived macrophage
phenotype: Siglec-1 hi CD4+
hiv-1 infection status: Infected
|
| Treatment protocol |
For HIV-1 infection, polybrene (2mg/ml) was added to the MDM cultures during the last 30 minutes of the in vitro culture, before subsequent exposure to HIV-1.
|
| Growth protocol |
PBMCs from healthy HIV-1 seronegative donors were isolated by Ficoll density gradient centrifugation and monocytes were enriched from the PBMCs by plastic adherence in 24-well plates, and differentiated into monocyte-derived macrophages (MDM) in 1ml M-CSF media The non-adherent MDM were isolated from their adherent counterparts by repeated gentle washes with monocyte media. The non-adherent MDM were gently aspirated, and collected in 50ml tubes. Accutase (500μl) was added to the remaining adherent MDM, and the cultures were incubated at 37oC/5%CO2 for 20 minutes, to detach the cells. The detached MDM were transferred into 50ml tubes, and washed with monocyte media.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from uninfected and HIV-1 infected MDM using the Qiagen RNeasy Mini Kit
Clontech Smarter
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
non-adherent_us1_infected
|
| Data processing |
Basecalling with Illumina RTA 1.9
Demultiplexing with custom demultiplexer written in python
Alignments performed with STAR 2.0.4b
Gene counts dervied with Subread:featureCount 1.45 and normalized with CPM and RPKM transformations
Genome_build: Ensembl GRCh38.76
Supplementary_files_format_and_content: Gene Counts
|
| |
|
| Submission date |
Sep 08, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Mangala Rao |
| E-mail(s) |
mrao@hivresearch.org
|
| Phone |
301-319-7699
|
| Organization name |
WRAIR
|
| Street address |
503 Robert Grant Avenue
|
| City |
Silver Spring |
| State/province |
MD |
| ZIP/Postal code |
20910 |
| Country |
USA |
| |
|
| Platform ID |
GPL21290 |
| Series (1) |
| GSE103666 |
Human primary macrophages derived in vitro from circulating monocytes comprise adherent and non-adherent subsets with differential expression of Siglec-1 and CD4 and permissiveness to HIV-1 infection |
|
| Relations |
| BioSample |
SAMN07626339 |
| SRA |
SRX3173862 |
