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Sample GSM7791301 Query DataSets for GSM7791301
Status Public on Sep 24, 2023
Title hCD4_untreated_rep1
Sample type other
 
Source name Blood-derived CD4+ T cells
Organism Homo sapiens
Characteristics cell type: Blood-derived CD4+ T cells
Treatment protocol Following CD4+ T cell isolation, cells were seeded at a concentration of 1x106 cells/ml and activated with αCD3/αCD28 activating beads (ThermoFisher Scientific) for 72h at a concentration of 1 bead/cell in the presence of 100 U/ml IL-2 (PeproTech) in RPMI +/+ (except for mock controls). At the day of infection, cells were spinoculated in 96-well V-bottom plates (MilliporeSigma) in 50 μl RPMI+/+ with 100 ng (HIVDFII) of p24 per 1×106 cells with 5×106 cells total per well for 2 h at 2350 rpm (1173 × g) at 37°C. After spinoculation, all cells were returned to culture in the presence of 30 U/ml IL-2. Pre-stimulated CD4+ T cells stayed in αCD3/αCD28 activating beads during spininfection and subsequent cell culture. Samples were subjected to fluorescence-activated cell sorting 4 days post infection.
Growth protocol Peripheral blood mononuclear cells (PBMCs) were isolated by Ficoll-Hypaque density gradient centrifugation (Corning) at 2000 rpm (~ 850 x g) at RT for 30 min, without brake. PBMCs were immediately processed to isolate CD4+ T cells by negative selection using the EasySep Human CD4+ T Cell Isolation Cocktail (StemCell Technologies) according to manufacturer’s protocol. Purified CD4+ T cells were cultured in RPMI +/+ (supplemented with 10% FBS and 1% Penicillin/Streptomycin) at 37°C, 5% CO2.
Extracted molecule other
Extraction protocol Quantitative RNA and protein expression data were generated using the nCounter Vantage 3D RNA:Protein Immune Cell Profiling Assay (NanoString Technologies) and the nCounter SPRINT profiler (NanoString Technologies), comprising 770 RNA and 30 protein targets as well as positive and negative controls. 100,000 cells were used per sample, which were processed according to the manufacturer’s instructions.
Label nanostring reporter probe
Label protocol NA
 
Hybridization protocol Probe hybridization was performed according to manufacturer's protocol MAN-10066-01_Cell_Surface_Protein_Processing_from_Cell_Suspensions and MAN-10060-03_RNA_Protein_Codeset_Hybridization_Setup
Scan protocol Data was acquired on the nCounter SPRINT profiler (NanoString Technologies).
Description total RNA and protein
Data processing RNA and protein expression values were normalized and analyzed using the nSolver Analysis Software 4.0 and the add-on Advanced Analysis Software 2.0.115 (NanoString Technologies). Samples that did not pass the default control performance and quality parameters were excluded from subsequent analysis.
 
Submission date Sep 19, 2023
Last update date Sep 24, 2023
Contact name Hannah Sabeth Sperber
E-mail(s) Hannahsperber.7@gmail.com
Organization name Essen University Hospital
Department Institute for transaltional HIV Research
Lab Schwarzer Lab
Street address Virchowstr. 171
City Essen
State/province NRW
ZIP/Postal code 45147
Country Germany
 
Platform ID GPL33774
Series (2)
GSE243577 The Hypoxia-regulated Ectonucleotidase CD73 is a Host Determinant of HIV Latency [Array]
GSE244193 The Hypoxia-regulated Ectonucleotidase CD73 is a Host Determinant of HIV Latency

Data table header descriptions
ID_REF
VALUE Normalized linear count data calculated by the Advanced Analysis software 2.0. Normalization probes for each sample were automatically selected by the software based on the geNorm algorithm.

Data table
ID_REF VALUE
4-1BB-protein 132.362527786444
A2M-mRNA 18.3679816022265
ABCB1-mRNA 68.8799310083494
ABL1-mRNA 199.751799924213
ADA-mRNA 94.1359057114108
ADORA2A-mRNA 66.5839333080711
AICDA-mRNA 9.18399080111325
AIRE-mRNA 32.1439678038964
AKT3-mRNA 601.551397472918
ALCAM-mRNA 78.0639218094626
AMBP-mRNA 84.9519149102976
AMICA1-mRNA 537.263461865125
ANP32B-mRNA 681.91131698266
ANXA1-mRNA 966.615031817168
APOE-mRNA 22.9599770027831
APP-mRNA 167.607832120317
ARG1-mRNA 25.2559747030614
ARG2-mRNA 80.3599195097409
ATF1-mRNA 213.527786125883
ATF2-mRNA 264.039735532006

Total number of rows: 761

Table truncated, full table size 20 Kbytes.




Supplementary file Size Download File type/resource
GSM7791301_20180709_30102045921018-01_4_-activation_-DFII-mKO2_01.RCC.gz 8.9 Kb (ftp)(http) RCC

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