The largest database of trusted experimental protocols

82 protocols using qifikit

1

Quantifying Cell Surface Antigen Density

Check if the same lab product or an alternative is used in the 5 most similar protocols
The cells were prepared as described in the Flow Cytometry section. The QIFIKIT (Dako, Glostrup, Denmark) bead populations with defined quantities of antibody molecules attached per a single bead were incubated with FITC-labeled secondary antibody (goat anti-mouse IgG conjugated with FITC included in the QIFIKIT or goat anti-mouse IgM, in which case the antibody binding capacities were corrected for differences in fluorophore to protein ratios). The calibration beads were then analyzed by flow cytometry and the data were used for plotting the calibration curves (mean fluorescence intensity versus antibody binding capacity). The cells were then analyzed by flow cytometry and the antigen density was calculated by interpolation from the calibration curve as described in the manufacturer’s protocol. The cells stained with the respective control were analyzed using the same protocol.
+ Open protocol
+ Expand
2

Quantification of MSLN and MUC16 Binding

Check if the same lab product or an alternative is used in the 5 most similar protocols
MSLN and MUC16 binding capacity of tumour cell lines was quantified by DAKO QIFIKIT (DAKO Cytomation), according to the manufacturer’s protocol. Briefly, tumour cells were first labelled with anti-MSLN mAb K1 (150 nM, Genetex) or anti-CA125 mAb X75 (100 nM, ThermoFisher Scientific) on ice for 60 min. After several washes in PBS-BSA 2%, FITC-conjugated goat anti-mouse F(ab’)2 antibody diluted 1:50 (QIFIKIT, Agilent Dako) was used for labelling of both calibration and set-up beads (QIFIKIT, Agilent Dako) as well as tumour cells. Set-up beads were used to establish the window of analysis and the calibration beads were used to construct a calibration curve. The MSLN or MUC16 densities were determined by extrapolation on the calibration curve and expressed as specific antibody-binding capacity units after subtracting the background from the isotype control.
+ Open protocol
+ Expand
3

Quantification of Surface Mesothelin Molecules

Check if the same lab product or an alternative is used in the 5 most similar protocols
To quantify surface mesothelin molecules, adherent cells were washed with DPBS, coated with Versene and incubated at 37°C for ~15 min. After incubation, flasks were tapped vigorously to promote complete detachment. The cells were diluted with DBPS at 1:2 ratio (Versene:DPBS) and counted. A total of 300,000 cells were centrifuged at 500×g for 5 min. Cells were resuspended in 300 µL 1× FACS buffer (DPBS +1% BSA). One hundred microliters of aliquot was divided into two v-bottom wells. Cells were washed one more time with 100 µL FACS buffer, then stained with 100 µL of anti-MSLN antibody at 10 µg/mL (R&D Systems, clone 618923) on ice for 30 min. After the primary stain, 50 µL of calibration beads from the QIFIKIT (Agilent) were added. The mixture was washed with 100 µL FACS buffer twice, then stained with 100 µL of anti-mouse F(ab′)2-Goat Alexa Fluor 647 (Invitrogen) antibody diluted 2000× in FACS buffer for 45 min on ice. The stained cells and beads were washed 2× with 100 µL FACS buffer, then resuspended in 100 µL FACS buffer to measure fluorescence. The calibration curve plotting median fluorescence intensity of each bead population versus number of molecules was plotted according to the manufacturer’s protocol provided by the QIFIKIT (Agilent). The number of endogenous MSLN molecules was determined using the cell’s MFI and the calibration curve generated with the QIFIKIT beads.
+ Open protocol
+ Expand
4

CEACAM5 and CD47 Expression in Cancer Cells

Check if the same lab product or an alternative is used in the 5 most similar protocols
CEACAM5-positive colorectal, lung, or gastric cancer cell lines were purchased from ATCC (SK-CO-1, SNU-C1, H508, LS174T, SNU-16, H727, H2122) or DSMZ (MKN-45), and cultured according to the respective datasheets. CEACAM5-negative A549 cells (ATCC), and two primary epithelial cell lines, i.e., HBEpiC (ScienCell Research Laboratories) and CCD841CoN (ATCC), were used as controls. The number of CEACAM5 and CD47 antigens/cell was determined by QIFIKIT (Agilent DAKO) according to the manufacturer’s instruction as previously described (41 (link)).
MC38 (Kerafast) were silenced for mouse CD47 cell surface expression and were afterwards stably transfected to express human CD47 and human CEACAM5. A stable clone named 3C12 was isolated by cell sorting (Beckman #Cytoflex SRT) and cultured like mentioned in the original MC38 datasheet. The number of human CEACAM5 (203’000 molecules/cell) and human CD47 (40’000 molecules/cell) expressed at the surface of the clone was determined by QIFIKIT (Agilent DAKO) according to the manufacturer’s instruction as previously described (41 (link)).
+ Open protocol
+ Expand
5

Quantification of Cell Surface HER2 and EGFR

Check if the same lab product or an alternative is used in the 5 most similar protocols
Cell surface HER2 and EGFR were quantified using the Dako QIFIKIT according to the manufacturers’ protocol. Three different passages of C4-2B cells were grown in complete T-medium without phenol red and detached with TrypLE Express (Gibco). A total of 1×105 C4-2B cells were analyzed in triplicate. HER2 binding sites were saturated with anti-HER2 (R&D Systems 191924 10μg/mL) and EGFR sites with anti-EGFR (LSBio 225 10μg/mL) as primary antibodies. Alexa Fluor 488 goat anti-mouse IgG (H+L) (Invitrogen 1:400) was utilized as the secondary antibody. The median fluorescence intensity (MFI) was analyzed by flow cytometry (Accuri BD analyzer) and the number of molecules per cell calculated by FlowJo and subsequent extrapolation of the samples’ MFI into a standard curve based on the calibration beads MFI.
+ Open protocol
+ Expand
6

Quantifying GPC-1 Expression in Glioblastoma

Check if the same lab product or an alternative is used in the 5 most similar protocols
The expression of GPC-1 by GBM cells was quantified using the murine version of Miltuximab®, antibody MIL-38 (GlyTherix Ltd., Sydney, Australia), and QIFIKIT (Quantitative Immunofluorescence Intensity kit, Dako) as per the manufacturer’s protocol. Briefly, the U-87, U-251, and Raji cells were incubated with an anti-GPC-1 antibody MIL-38 and then a secondary FITC-conjugated goat antimouse antibody from the kit. QIFIKIT beads with known number of antibody molecules on the surface were incubated with the same secondary FITC-conjugated goat antimouse antibody. Both cells and beads were analyzed by BD Fortessa X20 (BD Biosciences, Franklin Lakes, NJ, USA) flow cytometer. The fluorescence data from the beads were used to produce a calibration curve. The number of bound antibody molecules on the cell surface was then interpolated from the calibration curve.
+ Open protocol
+ Expand
7

Cell Line Authentication and Characterization

Check if the same lab product or an alternative is used in the 5 most similar protocols
HEK293, HeLa and Skov-3 cells were purchased from ATCC (American Type Culture Collection (ATCC)), MDA-MB-231 NLR were purchased from Essen Bioscience (Cat.# 4487), human bronchial epithelial cells (HBEpiC, 3210) and human renal cortical epithelial cells (HrcEpiC, 4110) were purchased from ScienCell Research Laboratories, AsPC-1 (ECACC, 96020930) cells were obtained from the European Collection of Cell Cultures (ECACC) and NCI H596 cells were provided by Roche Innovation Center Munich. Jurkat NFAT-cells were purchased from Promega. All cells were routinely cultured at 37 °C and 5% CO2 and tested for mycoplasma contamination. The cell identity of all tumor cell lines was verified by FTA cell authentication service provided by the ATCC64 . Antigen-binding sites were determined using QIFIKIT® (Dako) according to the manufacturer’s instructions.
+ Open protocol
+ Expand
8

Quantitative Analysis of MET Expression

Check if the same lab product or an alternative is used in the 5 most similar protocols
MET antigen expression on the surface of the human tumor cell lines was determined with a mouse anti-human HGFR/MET antibody (R&D systems, Bio-Techne) and a FITC-conjugated goat anti-Mouse F(ab')2 as detection antibody as described in the manufacturer's protocol of the Qifi kit (DAKO, Agilent).
+ Open protocol
+ Expand
9

Quantifying Cell Surface Receptor Density

Check if the same lab product or an alternative is used in the 5 most similar protocols
Receptor density was quantified following manufacturer’s instruction (QIFIKIT®, Dako). Briefly, following incubation with Fc Receptor (FcR) Blocking reagent (Miltenyi Biotec, cat # 130-059-901), primary Abs (50 µg/mL) anti-hCD19 (BD Biosciences, cat # 555410), -hCD47 (eBiosciences, cat # 11-0478-42) and -hCD20 (R&D Systems, cat # MAB4225) were added to the samples (whole blood or cells) for 30 min at 4°C. 100 µL of Calibration beads were washed along with the cells and treated identically. 100 µL of secondary Ab (1/50 in PBS BSA 2 %) were added for 30 min at 4°C. Cells were washed and resuspended in 130 µL of CellFix (Becton Dickinson (BD) Biosciences) and acquired on FACS Calibur (BD Biosciences). Analysis was performed and Mean Fuorescence Intensity (MFI) was determined. A linear regression was performed using MFI values from the calibration beads. Receptor density per cell was extrapolated from this regression line.
+ Open protocol
+ Expand
10

Flow Cytometry Analysis of Immunoligand Binding

Check if the same lab product or an alternative is used in the 5 most similar protocols
Flow cytometry was performed on a Navios flow cytometer (Beckman Coulter) as described earlier [30 (link)]. For binding studies, the immunoligands were applied at a concentration of 50 μg/ml. An Alexa Fluor 488-coupled anti-penta His secondary antibody (Qiagen) was employed for detection. To demonstrate simultaneous binding, SK-BR-3 cells were reacted with the immunoligands at 50 μg/ml and then incubated with an Fc-fusion protein containing the corresponding NK cell receptor (i.e. NKp30-Fc, NKp80-Fc, or DNAM-1-Fc) at 100 μ g/ml and subsequently with polyclonal FITC-coupled anti-human IgG F(ab’)2 fragments (Beckman Coulter). Receptor expression levels were quantitated by determination of specific antigen binding capacities (SABC) employing Qifikit (DAKO) according to manufacturer's protocols.
+ Open protocol
+ Expand

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required

Sign up now

Revolutionizing how scientists
search and build protocols!