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Sample GSM2778749 Query DataSets for GSM2778749
Status Public on Feb 22, 2018
Title d002_non-adherent_us1_infected.TTTCAGA
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 SAMN07626347
SRA SRX3173854

Supplementary file Size Download File type/resource
GSM2778749_d002_non-adherent_us1_infected.TTTCAGA.gene_counts.txt.gz 3.5 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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