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Sample GSM6056602 Query DataSets for GSM6056602
Status Public on Dec 14, 2023
Title M27, MDA5 KD, Mock, 48h
Sample type SRA
 
Source name Monocyte-derived dendritic cells
Organism Homo sapiens
Characteristics cell type: Monocyte-derived dendritic cells
donor number: M27
genotype: MDA5 KD
infection: Mock
time: 48h
Treatment protocol CD14+ mononuclear cells, isolated from 3 different human blood donors, were transduced with shRNA-encoding lentivectors targeting either Luc or MDA5. Upon differentiation into MDDCs, cells were either challenged with HIV-1 for 48 hours, or left uninfected.
Growth protocol Peripheral blood mononuclear cells (PBMCs) were isolated from leukopaks by gradient centrifugation on Lymphoprep. To generate dendritic cells, CD14+ mononuclear cells were enriched by positive selection using anti-CD14 antibody microbeads. Enriched CD14+ cells were plated in RPMI-1640, supplemented with 5% heat-inactivated human AB+ serum, 20 mM GlutaMAX, 1 mM sodium pyruvate, 1x MEM non-essential amino acids and 25 mM HEPES pH 7.2 (RPMI−HS complete), at a density of 2 x 10^6 cells/ml. To differentiate CD14+ cells into dendritic cells, 1:100 human granulocyte-macrophage colony stimulating factor (hGM-CSF) and 1:100 human interleukin-4 (hIL-4)-conditioned media was added. Cells were cultured in humidified, 5% CO2 incubators at 37°C.
Extracted molecule total RNA
Extraction protocol Cells were lysed and RNA from these samples was isolated by using Rneasy Plus Mini kit (Qiagen) following manufacturer's protocol.
Poly(A)-selected RNA-seq libraries were generated by Genewiz, using standard Illumina protocol.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Description genes_expression_expected_count_hg38.tsv
genes_expression_expected_count_hg38_HIV.tsv
Data processing Reads were aligned to human genome assembly hg38 (Gencode v34 transcript set) and gene expression was quantified via RSEM (v1.3.1) software's rsem-calculate-expression command, utilizing STAR aligner (v2.6.1) with default parameters to create the "expected gene counts" files.
Reads were aligned to human genome assembly hg38 (Gencode v34 transcript set) concatenated to HIV genome plasmid (pUC57mini_NLBN_dEnv_GFP) and human and HIV genes were quantified via RSEM (v1.3.1) software's rsem-calculate-expression command, utilizing STAR aligner (v2.6.1) with default parameters to create the "expected gene counts" files.
Assembly: hg38
Supplementary files format and content: Matrix table with raw (expected) gene counts for every gene and every sample
 
Submission date Apr 21, 2022
Last update date Dec 14, 2023
Contact name Jeremy Luban
Organization name UMass Medical School
Street address 373 Plantation Street Biotech 2, Suite 319
City Worcester
State/province Massachusetts
ZIP/Postal code 01605
Country USA
 
Platform ID GPL20301
Series (1)
GSE201250 Analysis of monocyte-derived dendritic cell transcriptome upon HIV-1 challenge and effect of MDA5 knockdown
Relations
BioSample SAMN27727304
SRA SRX14954646

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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