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8 protocols using pooled normal human plasma

1

Characterization of LPS Interactions

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Highly pure rough LPS from E. coli K12 strain LCD25 was obtained from List biological labs. The FITC labelled LPS from E. coli 014 (Ra) and 3H/14C labelled LPS from Salmonella enterica sv. Typhimurium PR122 (Rc) were kind gift from Prof. Robert Munford (NIAID). Pooled normal human plasma was from Innovative Research. Endotoxin free water was from GE Healthcare Life Sciences. Fluorescein isothiocyanate (FITC), Alexa 488 hydrazide and Alexa 594 NHS were obtained from Molecular Probes. Purified apo-A1 from human plasma was obtained from Athens Research & Technology. The rabbit anti-apoA1 antibody was from Abcam. The TNF-α ELISA kit was from R&D. Chromogenic LAL Endotoxin Assay Kit was from Genscript. Recombinant human LBP protein was from R&D.
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2

Thrombomodulin Functionalized PEG Conjugation

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All solvents, chemicals and reagents were purchased from commercial sources and were used unless otherwise noted. pET39b vector, pET28b vector and competent cells were purchased from EMD Chemicals. Kanamycin sulfate and IPTG (Isopropyl-beta-D-thiogalactopyranoside) were purchased from Calbiochem. The mouse monoclonal antibody specific to human TM, rabbit monoclonal antibody specific to Polyethylene glycol (PEG), goat anti-mouse IgG H&L (HRP) and goat anti-rabbit IgM mu chain (HRP) were purchased from Abcam. Human protein C, human thrombin and human antithrombin III were obtained from Haematologic Technologies Inc. Chromogenic thrombin substrate BIOHPEN CS-01(38) and bovine serum albumin (BSA) were from Fisher Scientific. Heparin, Aprotinin and Trypsin were purchased from Sigma. Pooled normal human plasma was from Innovative Research. NH2-Gly-Gly-PEG3-azide and NH2-Gly-Gly-NH-PEG5000-OMe were purchased from CarboSynUSA. DBCO-Cy5 and DBCO-mPEG5000-OMe were purchased from Click Chemistry Tools.
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3

Sensitive EGFR Mutation Detection

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DNA oligonucleotides including PCR primers and padlock probe DNA were chemically synthesized and purified by high performance liquid chromatography (Bionics, Korea). The padlock probe DNA that can hybridize to the sequence of EGFR exon 19-del site was modified with phosphate at the 5’-end to be ligated into a circular template for subsequent RCA. The sequences of the oligonucleotides are listed in Table S1. Ex Taq polymerase and dNTPs mixture (dATP, dGTP, dCTP, and dTTP) was purchased from Takara Korea Biomedical Inc. (Korea). Thioflavin T (ThT) was purchased from Sigma-Aldrich Korea (Korea). Phi29 DNA polymerase and Taq DNA ligase were purchased from New England Bio-labs (USA). Pooled normal human plasma was purchased from Innovative Research (Novi, MI, USA).
The A549 cell line was from the American Type Culture Collection (ATCC, CCL-185, USA) and PC9 cell line was from the European Collection of Authenticated Cell Cultures (ECACC, 90071810, UK). A549 cells possess the wild-type EGFR exon 19 gene, whereas PC9 cells contain EGFR exon 19 deletion mutation (E746-A750). All cells were cultured in DMEM high glucose (Hyclone, USA) supplemented with 10% fetal bocine serum (Hyclone) and 100 U/ml penicillin (WelGene, Korea) in a humidified incubator under 5% CO2 at 37°C.
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4

Global Quality Control with Pooled Plasma

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Pooled normal human plasma was purchased from Innovative Research (Novi, MI, USA; Lot 26,393) and was used for global quality control (gQC). The other chemicals and reagents used are described in previous studies [15 (link), 16 (link), 21 (link), 22 (link)].
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5

IdeS Treatment Serum and Plasma Samples

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Serum samples (blood collected with modified CAT serum vacutainer tubes (BD Diagnostics, Franklin Lakes, NJ) containing 2 mm iodoacetic acid) from healthy individuals treated with IdeS were from the Phase I trial NCT01802697 (23 (link)). Briefly, subjects were intravenously injected with IdeS (at the following doses: 0.01, 0.04, 0.12, or 0.24 mg IdeS/kg bodyweight), followed by a time-course collection of serum samples. Plasma samples from septic patients were from (48 (link)) (blood collected with vacutainer sodium citrate tubes). Plasma samples from healthy individuals were from (49 (link)) (blood collected with vacutainer sodium citrate tubes) or were purchased from Innovative Research (pooled normal human plasma, Novi, MI). Swabs and scrapes from local infections from patients with diagnosed S. pyogenes infection were collected at Skåne University Hospital or at Laurentiikliniken (a primary health clinic), both in Lund, Sweden. Tonsillar swabs from healthy individuals were obtained at Lund University, Lund Sweden. The medical ethics committee of Lund University approved this study (protocol numbers 2005/790 and 2015/14) and informed consent was obtained from all subjects. The samples were transported at −20 °C and stored at −80 °C until further processing. A compilation of patients, control and IdeS clinical phase I study samples is in supplemental Table S1.
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6

Serum Albumin and Plasma Fibrinogen

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Albumin from human serum (A3782) and fibrinogen from human plasma (F4883) were obtained from Sigma. Pooled normal human plasma from healthy donors was purchased from Innovative Research (MI, USA).
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7

Multiplex Serological Profiling of SARS-CoV-2 and Other Viral Infections

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We obtained serum and plasma specimens from 2 study cohorts in Africa and 1 in Thailand. Cohorts in Africa included the RV329 African Cohort Study (RV329/AFRICOS), which predominantly enrolled PLHIV with chronic infection, and study RV466 of the Joint West Africa Research Group (RV466/JWARG), which was designed to diagnose acute febrile illnesses in Nigeria. The cohort in Thailand was from the RV254 South East Asia Research Collaboration in HIV (RV254/SEARCH 010) study, which enrolls persons with acute HIV-1 infection. For negative controls, we used prepandemic plasma samples, including Zika Negative Plasma (SeraCare, https://www.seracare.com), Pooled Normal Human Plasma (Innovative Research, https://www.innov-research.com), and 2 human serum coronavirus panels, MSRM-CR1 and HMSRM-CR22 (BioIVT, https://bioivt.com). For positive controls, we used 2 SARS-CoV-2–positive plasma samples with high neutralization titers and 2 serum panels, HMSRM-COVIDPOS and HMSRM-COVIDREC (BioIVT). We also used 12 matched SARS-CoV-2 patient convalescent serum and plasma samples (Innovative Research). We divided 51 antigens into custom panels, including panels for coronaviruses (SARS-CoV-2, SARS-CoV-1, MERS-CoV, OC43, NL63, HKU1, 229E), flaviviruses, and HIV-1 (Appendix Table 1). We included an alphavirus, chikungunya Envelope 1 antigen (E1), in the flavivirus panel.
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8

Isotopic Labeling of Rifampicin for Quantification

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Standard RIF, RPT, and 2,4,6-trihydroxyacetophenone (THAP) were obtained from Sigma-Aldrich (St. Louis, MO). Ethanol (200 proof) was acquired from Pharco-AAPER (Brookfield, CT), and 18 MΩ water was obtained from a Milli-Q water purification system (Millipore, Billerica, MA). Pooled normal human plasma was purchased from Innovative Research (Novi, MI). Isotopically labeled 13C1,2H1-RIF was synthesized as described previously.32 (link)
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