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| Status |
Public on Dec 23, 2015 |
| Title |
Donor 97 SLAN DC |
| Sample type |
SRA |
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| Source name |
Blood derived APC_SLAN DC
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| Organism |
Homo sapiens |
| Characteristics |
group: Healthy controls
donor id: Donor 97
tissue: Blood
cell type: Dendritic cell
cell subtype: slan(+) Dendritic cells
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| Extracted molecule |
total RNA |
| Extraction protocol |
PBMC were isolated by Ficoll-Paque density gradient centrifugation (GE Healthcare, Chalfont St. Giles, United Kingdom) from healthy buffy coats obtained from the Australian Red Cross. PBMC were further separated into three populations by counter-current elutriation using Beckman J-6 M/E centrifuge equipped with a JE 5.0 rotor (Beckman Coulter, Pasedena, CA, USA). The three fractions were isolated at rates of 12 (small lymphocytes), 16 (large lymphocytes) and 20 (DC/Monocytes fractions) ml/min. dendritic cells and monocytes were islated from the large cell fraction. The large cell fraction was first stained with antibodies specific for the DC subsets, which included CD1c-APC (Miltenyi), CD141-VioBlue (Miltenyi), CD123-PE (BD BioSciences, Franklin Lakes, NJ, USA) and SLAN-FITC (Miltenyi), and labeled with anti-IgG beads (Miltenyi). DC were then isolated using an AutoMACS (Miltenyi) into positive and negative fractions. The positive fraction (DC enriched) was further sorted into four DC subsets: CD1c+ mDC, SLAN+ DC, CD141+ mDC and CD123+ pDC, using a FACSAria (BD BioSciences). The negative fraction (DC depleted/mono) was stained with anti-CD14-FITC and anti-CD16-PE (BD Biosciences) antibodies, labeled with IgG beads (Miltenyi) and a positive selection performed using an AutoMACS (Miltenyi) to obtain a bulk monocyte population. These cells were further sorted to obtain the CD14+CD16- (CD14+) and CD16+CD14lo (CD16+) monocyte subsets using a FACSAria. Cell populations with a purity ≥90% were used, as determined by flow cytometry (LSR II or FACSAria; BD Bioscience).
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
SM_97-SLAN_RP_1_1_MDC8
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| Data processing |
Reads were trimmed for adaptors and quality using Trimmomatic
Reads were mapped against Human reference GRCh37using bowtie2
BAM files were converted to counts per gene using htseq-count counting reads mapping to exons
Genome_build: Ensembl GRCh37
Supplementary_files_format_and_content: CSV file containing raw read counts per gene
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| Submission date |
Jun 22, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
David Richard Powell |
| E-mail(s) |
david.powell@monash.edu
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| Organization name |
Monash University
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| Department |
Bioinformatics Platform
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| Street address |
Wellington Road
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| City |
Clayton |
| State/province |
VIC |
| ZIP/Postal code |
3800 |
| Country |
Australia |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE70106 |
The role of antigen presenting cells in the induction of HIV-1 latency in resting CD4+ T-cells |
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| Relations |
| BioSample |
SAMN03785019 |
| SRA |
SRX1067703 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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