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| Status |
Public on Dec 14, 2023 |
| Title |
M29, MDA5 KD, HIV1, 48h |
| Sample type |
SRA |
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| Source name |
Monocyte-derived dendritic cells
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| Organism |
Homo sapiens |
| Characteristics |
cell type: Monocyte-derived dendritic cells
donor number: M29
genotype: MDA5 KD
infection: HIV1
time: 48h
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| 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.
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| 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.
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
genes_expression_expected_count_hg38.tsv
genes_expression_expected_count_hg38_HIV.tsv
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| 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
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| Submission date |
Apr 21, 2022 |
| Last update date |
Dec 14, 2023 |
| Contact name |
Jeremy Luban |
| Organization name |
UMass Medical School
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| Street address |
373 Plantation Street Biotech 2, Suite 319
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| City |
Worcester |
| State/province |
Massachusetts |
| ZIP/Postal code |
01605 |
| Country |
USA |
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| Platform ID |
GPL20301 |
| Series (1) |
| GSE201250 |
Analysis of monocyte-derived dendritic cell transcriptome upon HIV-1 challenge and effect of MDA5 knockdown |
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| Relations |
| BioSample |
SAMN27727293 |
| SRA |
SRX14954657 |
| 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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