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Status |
Public on Jul 15, 2019 |
Title |
HIV_specific_CD4_ T cells_EC4 |
Sample type |
RNA |
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Source name |
CD154+ CD69+ HIV-specific CD4 T cells from PBMCs
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Organism |
Homo sapiens |
Characteristics |
disease status: Elite Controller cell type: PBMCs
|
Treatment protocol |
A CD40 blocking antibody (Miltenyi Biotec, clone HB14) was added 15 minutes prior to stimulation with a gag peptide pool. Following a 9 hr incubation, HIV-specific CD4 T cells were identified based on the co-upregulation of CD40L and CD69 and were live-sorted directly in RLT lysis buffer (Qiagen).
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Growth protocol |
Cryopreserved PBMCs were thawed and rested at 37°C for 3 hours.
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Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was purified using the RNeasy Plus Micro Kit (Qiagen) according to manufacturer's instructions.
|
Label |
biotin
|
Label protocol |
Sense-strand cDNA was synthesized from total RNA using a fixed volume of 3µL. Fragmentation and labeling were performed to produce ss-DNA with the Applied Biosystems™ GeneChip® WT Pico Terminal Labeling Kit according to manufacturer’s instructions (Applied Biosystems™).
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Hybridization protocol |
5 µg DNA target was hybridized on GeneChip® Clariom™ D, human (ThermoFisher Scientific) and incubated at 450C in the Genechip® Hybridization oven 640 (Affymetrix) for 17 hours at 60 rpm. GeneChips were then washed in a GeneChips® Fluidics Station 450 (Affymetrix) using Applied Biosystems™ Hybridization Wash and Stain kit according to the manufacturer’s instructions (Applied Biosystems™)
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Scan protocol |
The microarrays were finally scanned on a GeneChip® scanner 3000 (Affymetrix).
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Data processing |
The preprocessing of the microarray data was done in R v3.3.3 using the oligo package47 v1.38.0 using rma function.
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Submission date |
Apr 16, 2019 |
Last update date |
Jul 16, 2019 |
Contact name |
Daniel Elias Kaufmann |
Organization name |
CRCHUM
|
Street address |
900 Rue St. Denis
|
City |
Montreal |
State/province |
Quebec |
ZIP/Postal code |
H2X 0A9 |
Country |
Canada |
|
|
Platform ID |
GPL23126 |
Series (2) |
GSE128297 |
Transcriptional analysis of HIV-specific CD4+ T cells |
GSE129872 |
Transcriptional analysis of HIV-specific CD4+ T cells in progressive disease and in spontaneously controlled infection. |
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