Description

This track shows intensities of a microarray spotted with short peptides derived from the S protein. Fifty-five sera from convalescent COVID-19 patients and 18 control sera were screened on the peptide microarray for both IgG and IgM responses. When comparing the microarry tracks, note that they are from patients at difference stages of the infection.

A total of 211 peptides were synthesized and conjugated to BSA. The conjugates along with control proteins were prepared in triplicate at three dilutions.

Display Conventions and Configuration

This track contains two composite tracks, for IgG and IgM. It also contains two signal (wiggle) tracks, that show the "response frequency", roughly calculated as described in the paper, for IgG and IgM separately.

Genomic locations of peptides that were spotted on the array are highlighted. Because these peptides overlap, the tracks default to dense mode and the sequence is shown as labels drawn onto the rectangles, but only visible on high zoom levels. Put any track into pack mode to fully see the sequence and also the triplicates. Since every peptide was spotted in three concentrations, every peptide is shown three times in pack mode.

The color is assigned based on the log of the fluorescent signal, with all negative values replaced by 0. The fluorescent signal was restricted to the range 0-15, scaled to 0-1.0 and the viridis color palette was used to assign a color intensity. This color palette is different from the one used in the original paper, to make the quantitative data easier to see.

The two signal tracks show the "response frequency", as defined in the paper. The response frequency is the share of Covid samples at a position that exceed the threshold mean(x)+3*stdev(y), with x being all values at a position and y being the negative controls. At positions where two peptides overlap, the two values are summed up, which means that the result on the Genome Browser can exceed 1.0.

Methods

Supplemental files were received from the authors, converted from Excel, rearranged and run through the command line script bigHeat to create a heatmap-like display. 0.285 for positive values. For better visibility, colormap viridis from matplotlib was used. Like all tracks, the exact commands are documented in our makeDoc text files.

Data Access

The raw data can be explored interactively with the Table Browser or combined with other datasets in the Data Integrator tool. For automated analysis, the genome annotation is stored in a bigBed file that can be downloaded from the download server.

Annotations can be converted from binary to ASCII text by our command-line tool bigBedToBed. Instructions for downloading this command can be found on our utilities page. Please refer to our mailing list archives for questions, or our Data Access FAQ for more information.

References

Li Y, Lai DY, Zhang HN, Jiang HW, Tian X, Ma ML, Qi H, Meng QF, Guo SJ, Wu Y et al. Linear epitopes of SARS-CoV-2 spike protein elicit neutralizing antibodies in COVID-19 patients. Cell Mol Immunol. 2020 Oct;17(10):1095-1097. PMID: 32895485; PMC: PMC7475724