A time-resolved proteomic and prognostic map of COVID-19
Ontology highlight
ABSTRACT:
INSTRUMENT(S): TripleTOF 6600
ORGANISM(S): Homo Sapiens (human)
TISSUE(S): Blood Plasma
DISEASE(S): Covid-19
SUBMITTER: 
Michael Mülleder
LAB HEAD: Markus Ralser
PROVIDER: PXD025752 | Pride | 2021-07-19
REPOSITORIES: Pride
Publications
A time-resolved proteomic and prognostic map of COVID-19.
Demichev Vadim V Tober-Lau Pinkus P Lemke Oliver O Nazarenko Tatiana T Thibeault Charlotte C Whitwell Harry H Röhl Annika A Freiwald Anja A Szyrwiel Lukasz L Ludwig Daniela D Correia-Melo Clara C Aulakh Simran Kaur SK Helbig Elisa T ET Stubbemann Paula P Lippert Lena J LJ Grüning Nana-Maria NM Blyuss Oleg O Vernardis Spyros S White Matthew M Messner Christoph B CB Joannidis Michael M Sonnweber Thomas T Klein Sebastian J SJ Pizzini Alex A Wohlfarter Yvonne Y Sahanic Sabina S Hilbe Richard R Schaefer Benedikt B Wagner Sonja S Mittermaier Mirja M Machleidt Felix F Garcia Carmen C Ruwwe-Glösenkamp Christoph C Lingscheid Tilman T Bosquillon de Jarcy Laure L Stegemann Miriam S MS Pfeiffer Moritz M Jürgens Linda L Denker Sophy S Zickler Daniel D Enghard Philipp P Zelezniak Aleksej A Campbell Archie A Hayward Caroline C Porteous David J DJ Marioni Riccardo E RE Uhrig Alexander A Müller-Redetzky Holger H Zoller Heinz H Löffler-Ragg Judith J Keller Markus A MA Tancevski Ivan I Timms John F JF Zaikin Alexey A Hippenstiel Stefan S Ramharter Michael M Witzenrath Martin M Suttorp Norbert N Lilley Kathryn K Mülleder Michael M Sander Leif Erik LE Ralser Markus M Kurth Florian F
Cell systems 20210614 8
COVID-19 is highly variable in its clinical presentation, ranging from asymptomatic infection to severe organ damage and death. We characterized the time-dependent progression of the disease in 139 COVID-19 inpatients by measuring 86 accredited diagnostic parameters, such as blood cell counts and enzyme activities, as well as untargeted plasma proteomes at 687 sampling points. We report an initial spike in a systemic inflammatory response, which is gradually alleviated and followed by a protein ...[more]
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2014-07-02 | E-GEOD-55962 | biostudies-arrayexpress
Project description:(1) qPCR Gene Expression Data The THP-1 cell line was sub-cloned and one clone (#5) was selected for its ability to differentiate relatively homogeneously in response to phorbol 12-myristate-13-acetate (PMA) (Sigma). THP-1.5 was used for all subsequent experiments. THP-1.5 cells were cultured in RPMI, 10% FBS, Penicillin/Streptomycin, 10mM HEPES, 1mM Sodium Pyruvate, 50uM 2-Mercaptoethanol. THP-1.5 were treated with 30ng/ml PMA over a time-course of 96h. Total cell lysates were harvested in TRIzol reagent at 1, 2, 4, 6, 12, 24, 48, 72, 96 hours, including an undifferentiated control. Undifferentiated cells were harvested in TRIzol reagent at the beginning of the LPS time-course. One biological replicate was prepared for each time point. Total RNA was purified from TRIzol lysates according to manufacturerâs instructions. Genespecific primer pairs were designed using Primer3 software, with an optimal primer size of 20 bases, amplification size of 140bp, and annealing temperature of 60°C. Primer sequences were designed for 2,396 candidate genes including four potential controls: GAPDH, beta actin (ACTB), beta-2-microglobulin (B2M), phosphoglycerate kinase 1 (PGK1). The RNA samples were reverse transcribed to produce cDNA and then subjected to quantitative PCR using SYBR Green (Molecular Probes) using the ABI Prism 7900HT system (Applied Biosystems, Foster City, CA, USA) with a 384-well amplification plate; genes for each sample were assayed in triplicate. Reactions were carried out in 20μL volumes in 384-well plates; each reaction contained: 0.5 U of HotStar Taq DNA polymerase (Qiagen) and the manufacturerâs 1à amplification buffer adjusted to a final concentration of 1mM MgCl2, 160μM dNTPs, 1/38000 SYBR Green I (Molecular Probes), 7% DMSO, 0.4% ROX Reference Dye (Invitrogen), 300 nM of each primer (forward and reverse), and 2μL of 40-fold diluted first-strand cDNA synthesis reaction mixture (12.5ng total RNA equivalent). Polymerase activation at 95ºC for 15 min was followed by 40 cycles of 15 s at 94ºC, 30 s at 60ºC, and 30 s at 72ºC. The dissociation curve analysis, which evaluates each PCR product to be amplified from single cDNA, was carried out in accordance with the manufacturerâs protocol. Expression levels were reported as Ct values. The large number of genes assayed and the replicates measures required that samples be distributed across multiple amplification plates, with an average of twelve plates per sample. 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Calculate differences between consecutive Ct values: difference1 = Ct2 â Ct1 and difference2 = Ct3 â Ct2. 2. Four regions are defined (where Region4 overrides the other regions): Region1: difference ⦠0.2, Region2: 0.2 < difference ⦠1.0, Region3: 1.0 < difference, Region4: one of the Ct values in the difference calculation is 40 If difference1 and difference2 fall in the same region, then the three replicate Ct values are averaged to give a final representative measure. If difference1 and difference2 are in different regions, then the two replicate Ct values that are in the small number region are averaged instead. This particular filtering method is specific to the data set we used here and does not represent a part of the normalization procedure itself; Alternate methods of filtering can be applied if appropriate prior to normalization. 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(α1, â¦, αs) then represents the vector of rank-invariant average expression values for all conditions 1 to s iv) We calculate the scale f The THP-1 cell line was sub-cloned and one clone (#5) was selected for its ability to differentiate relatively homogeneously in response to phorbol 12-myristate-13-acetate (PMA) (Sigma). THP-1.5 was used for all subsequent experiments. THP-1.5 cells were cultured in RPMI, 10% FBS, Penicillin/Streptomycin, 10mM HEPES, 1mM Sodium Pyruvate, 50uM 2-Mercaptoethanol. THP-1.5 were treated with 30ng/ml PMA over a time-course of 96h. Total cell lysates were harvested in TRIzol reagent at 1, 2, 4, 6, 12, 24, 48, 72, 96 hours, including an undifferentiated control. Total RNA was purifed from TRIzol lysates according to manufacturerâs instructions. The RNA samples were reverse transcribed to produce cDNA and then subjected to quantitative PCR using SYBR Green (Molecular Probes) using the ABI Prism 7900HT system (Applied Biosystems, Foster City, CA,USA) with a 384-well amplification plate; genes for each sample were assayed in triplicate.
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