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Sample GSM2252676 Query DataSets for GSM2252676
Status Public on Aug 31, 2017
Title F71_A82V_T230A_6hr
Sample type SRA
Source name F71_MDDCs_A82V_T230A
Organism Homo sapiens
Characteristics donor id: healthy donor #F71
cell type: monocyte-derived dendritic cells (MDDCs)
stimulation: 6 hour stimulation with A82V/T230A M-EBOV
Treatment protocol MDDCs were seeded at 5x10^5 cells per well in 24-well plates and incubated with 100ul HIV-derived lentiviral vector pseudotyped with M-EBOV founder or A82V-containing Ebola virus glycoprotein. These challenges were performed in a total volume of 250ul culture medium. Cells were harvested at times indicated postinnoculation with virus.
Growth protocol Peripheral blood mononuclear cells (PBMCs) were isolated by gradient centrifugation on Histopaque-1077 and CD14+ mononuclear cells were enriched via positive selection using anti-CD14 antibody MicroBead conjugates, according to the manufacturer’s protocol. CD14+ cells were then plated at a density of 1 to 2 x 106 cells/ml in RPMI-1640 supplemented with 5% heat inactivated human AB+ serum, 20 mM L-glutamine, 75 mM HEPES pH 7.2, 1 mM sodium pyruvate, and 1 x MEM non-essential amino acids. Differentiation of the CD14+ monocytes into dendritic cells (MDDCs) was promoted by addition of recombinant human GM-CSF and human IL-4; cytokines were produced from HEK293 cells stably transduced with pAIP-hGMCSF-co or pAIP-hIL4-co, respectively, as previously described (C. Reinhard et al., Retrovirology, 2014) with each cytokine supernatant added at a dilution of 1:100.
Extracted molecule total RNA
Extraction protocol Qiagen RNeasy Miniplus
Nugen Ovation FFPE RNA-seq
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
Data processing Because of their lower quality, the first and last base of all reads was trimmed, we then used trimmomatic-0.32 to trim by quality, removing 5’ or 3’ stretches of bases having average quality of less than 20 in a window size 10
Only reads longer than 36 bases were kept for further analysis. After quality trimming reads were aligned to the human ribosomal RNA using Bowtie2 v 2.2.3 with parameters -p 2 -N 1 --no-unal
All reads mapped to rRNA were discarded from further analysis. To estimate gene and isoform expression in Transcripts per Million (TPM) units and raw counts (expected_count), we used RSEM v1.2.28
Genome_build: hg19
Supplementary_files_format_and_content: tsv, read counts and tpm normalized counts
Submission date Jul 26, 2016
Last update date May 15, 2019
Contact name Alper Kucukural
Phone 7743124493
Organization name UMass Medical School
Department Program in Molecular Medicine
Lab Biocore
Street address 364 Plantation Street
City Worcester
State/province MA
ZIP/Postal code 01605
Country USA
Platform ID GPL18573
Series (1)
GSE84865 Ebola virus glycoprotein variant with increased infectivity for human cells dominated the 2013-2016 outbreak
BioSample SAMN05441377
SRA SRX1978370

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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