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Sample GSM8441231 Query DataSets for GSM8441231
Status Public on Aug 06, 2024
Title D29 T1 Prot_S stimulated
Sample type RNA
 
Source name Whole blood - 24 hours - 37°C - anti-CD28+anti-CD49d+SARS-CoV-2 Prot_S
Organism Homo sapiens
Characteristics tissue: Whole blood
date 1st dose bnt162b2: 2021-01-26
date 2nd dose bnt162b2: 2021-02-19
date 3rd dose bnt162b2 (booster): 2021-11-18
date timepoint 0 (pre-booster): 2021-11-18
date timepoint 1 month post-booster: 2021-12-09
date timepoint 3 months post-booster: 2022-02-16
date timepoint 6 months post-booster: 2022-05-11
gender: Male
age at timepoint 0: 63
Treatment protocol As published previously (Lauruschkat et al., 2021, J Fungi), 2.7-mL blood collection tubes without anticoagulant were pre-loaded with co-stimulatory antibodies α-CD28 and α-CD49d (10 µg/mL, Miltenyi Biotec, Bergisch Gladbach, Germany) plus either no antigen (negative control) or SARS-CoV-2 spike peptides (Prot_S, 0.6 nmol per peptide/mL, Miltenyi Biotec, Bergisch Gladbach, Germany). 0.5 mL blood lithium-heparin blood was added and stimulation tubes were incubated for 20 – 24 h at 37 °C. Samples were transferred to 1.5 mL tubes and centrifuged at 2000 g for 20 min. After preservation of the supernatant for LegendPlex cytokine assays, the residual cell pellet underwent erythrocyte lysis using Buffer EL (Qiagen, Hilden, Germany) and was then cryopreserved in 1 mL RNAprotect buffer (Qiagen, Hilden, Germany).
Growth protocol Not applicable
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using the RNeasy Plus Mini Kit according to the manufacturer's instructions (Qiagen, Hilden, Germany).
Label n/a
Label protocol Hybridisation with labelled probes was performed according to the manufacturer's instructions (Nanostring, Seattle, USA): RNA concentration was normalized to 50 ng in 5 µL water. The lyophilyzed Reporter Code set was reconstitued using 70 µL Hybridisation Buffer. 50 ng of RNA was mixed with 8 µL of Reporter Codeset solution and 2 µL of (ready-to-use) Capture Probe Set.
 
Hybridization protocol Hybridisation was performed for 16-24 h at 65 °C.
Scan protocol 17 µL water was added to the hybridized samples. 30 µL of each sample was loaded onto a Nanostring nCounter Sprint Cartridge and analyzed using an nCounter Sprinter device (Nanostring, Seattle, USA).
Description nCounter Immune Exhaustion Panel Reporter CodeSet
Data processing Data was analyzed using the nSolver Analysis Software (Nanostring, Seattle, USA), with background thresholding to the median of negative controls and normalization to the panel’s 12 internal reference genes (geometric mean).
mRNA counts normalized to internal reference genes by the nSolver Analysis Software (Nanostring, Seattle, USA).
 
Submission date Aug 05, 2024
Last update date Aug 06, 2024
Contact name Lukas Page
Organization name University Hospital of Augsburg
Department Institute for Laboratory Medicine and Microbiology
Lab Reinhard Hoffmann
Street address Stenglinstrasse 2
City Augsburg
State/province Bavaria
ZIP/Postal code 86156
Country Germany
 
Platform ID GPL33412
Series (1)
GSE273994 Antigen-specific T helper cells predict intensity and longevity of immune responses to SARS-CoV-2 booster vaccination

Data table header descriptions
ID_REF
VALUE normalized

Data table
ID_REF VALUE
ACACA 22
ACADL 18
ACADVL 727.53
ACAT2 118.95
ACOT1/2 35.85
ACSL3 43.99
ACSL4 538.52
ACSL6 49.7
ADH1A/B/C 18
ADH6 18
ADORA2A 100.21
ADORA2B 20.37
AHR 756.04
AIFM1 52.96
AK4 210.19
AKT1 139.31
AKT2 452.97
AKT3 655.02
ALDH1A1 422.83
ALDH1A3 18

Total number of rows: 785

Table truncated, full table size 9 Kbytes.




Supplementary file Size Download File type/resource
GSM8441231_D29_T1_Prot_S_stimulated.RCC.gz 9.1 Kb (ftp)(http) RCC

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