|
Status |
Public on Feb 22, 2018 |
Title |
d130_adherent_uninfected.TTCGCTG |
Sample type |
SRA |
|
|
Source name |
monocyte-derived macrophage
|
Organism |
Homo sapiens |
Characteristics |
tissue: monocyte-derived macrophage phenotype: Siglec-1 low CD4- hiv-1 infection status: Uninfected
|
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 |
adherent_uninfected
|
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) |
[email protected]
|
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 |
SAMN07626342 |
SRA |
SRX3173859 |