This README.txt file was generated on 2021-05-31 by Jessica Kleer GENERAL INFORMATION 1. Title of Dataset: EPITOPE-SPECIFIC ANTI-C1Q AUTOANTIBODIES IN SYSTEMIC LUPUS-ERYTHEMATOSUS 2. Author Information Principal Investigator Contact Information Name: Jessica Susann Kleer Institution: Division of Internal Medicine, University Hospital Basel Email: Jessicasusann.kleer@usb.ch Alternate Contact Information Name: Prof. Marten Trendelenburg Institution: Division of Internal Medicine, University Hospital Basel Email: marten.trendelenburg@usb.ch 3. Date of data and sample collection: Data from SSCS 2010-10 - 2018-06, Date of epitope-Mapping:2018-12 & 2019-09, Date of peptide- ELISA Measurement 2020-12 - 2021-02 4. Geographic location of data collection: Switzerland 5. Information about funding sources that supported the collection of the data: - SNF Project No. 320030_200423 - Association of the Swiss Systemic Lupus Erythematosus Cohort Study (ASSCS) SHARING/ACCESS INFORMATION 1. Licenses/restrictions placed on the data: Collection of Serum-Samples of the Lupus-Cohort as well as collection of corresponding data was financed by the Association of the Swiss Systemic Lupus Erythematosus Cohort Study (ASSCS). Those data are therefore not included in this data set. 2. Links to publications that cite or use the data: https://pubmed.ncbi.nlm.nih.gov/32111865/ DATA & FILE OVERVIEW 1. File List: Rawdata_Epitopemapping_Dryad_kleer.xlsx Pipetting scheme and ODs.zip MASTERFILE_Dryad_kleer_2021.xlsx Tableone_Dryad.Rmd Boxplots_and_Cutoffs_Dryad.Rmd Correlation_plot_Dryad.Rmd logistic_regression_Dryad.Rmd ROC_Curves_Dryad.Rmd multivariate_logistic_regression.Rmd 2. Relationship between files, if important: The raw data in the form of measured absolute ODs are shown, sorted by date and ELISA, in the folder "Pipetting scheme and ODs.zip". Note that A-Chain derived Peptides were initial named differently: A09 = A08, A15 =A08shift, A86 = A90. The document "Cohort Measurement and raw data_Dryad.xlsx" (contained in "Pipetting scheme and ODs.zip") contains the pipetting schemes and an overview of the interpolated values. The other folders are named according the respective peptide and show the absolute measured ODs. MASTERFILE_Dryad_kleer_2021.xlsx includes the interpolated values and clinical data of studied SLE patients and healthy controls. 3. Additional related data collected that was not included in the current data package: collection of demographical and clinical data of the Lupus cohort was financed by the Association of the Swiss Systemic Lupus Erythematosus Cohort Study (ASSCS). Those data are therefore not included in this data set. 4. Are there multiple versions of the dataset? no METHODOLOGICAL INFORMATION Methods for processing the data: - raw data of epitope mapping (Rawdata_Epitopemapping_Dryad_kleer.xlxs (showing magnitude of binding intensity to certain peptides)) were shown as Heat-map using GraphPad Prism Version 9.1.0. - For the Peptide ELISA, the signal obtained from incubating every patient-serum with diluting-buffer was considered background and this optical density (OD) value was subtracted from the specific signal. For the anti-C1q ELISA, background binding of secondary antibody to C1q was subtracted from the specific signal. Obtained ODs were standardised by expressing the data in units relative to the OD values obtained from reference SLE sera, that showed high levels of binding in the peptide ELISA or in the anti-C1q ELISA and that were included in each experiment. Calibration curves were fitted using a sigmoidal four-parameter logistic model (GraphPad Prism Version 9.1.0) 3. Instrument- or software-specific information needed to interpret the data: R software version 4.0.2. and GraphPad Prism Version 9.1.0. necessary packages to run scripts: tableone, ggplot2, ggcorrplot, psych, pROC 6. Describe any quality-assurance procedures performed on the data: Dates/Codes of all blood samples were checked again after retrieval from the biobank before further use in this project. 7. People involved with sample collection, processing, analysis and/or submission: - Samples used for epitope mapping were selected by oel Leonardi and Marten Trendelenburg. - Peptide microarrays were manufactured and performed by PEPperPRINT (Heidelberg, Germany). - Serum samples from 378 SLE patients were provided by the Swiss Systemic Lupus Erythematosus Cohort Study (SSCS). Samples and data from SLE patients were collected cross-sectionally between October 2010 and June 2018. Laboratory parameters were assessed by the individual centers. - Plasma from healthy blood donors were obtained from the blood donation center in Basel. - the protocol of the peptide ELISAS was established by Jessica Weiss,Jessica Kleer and Marten Trendelenburg. - anti-C1q- and Peptide ELISAs were performed by Denise Dubler (lab technician) and Jessica Kleer. - data processing and analysis was performed by Pascal Rabatscher, Severin Vogt, Jessica Kleer and Marten Trendelenburg. DATA-SPECIFIC INFORMATION FOR: Rawdata_Epitopemapping_Dryad_kleer.xlxs Results of Epitopemapping were digitised from optical density (OD)to arbitrary fluorescence units, which are present in this document.To display the data, a heat map was created using Prism. All values above 1000 were set to 1000 for better comparability. DATA-SPECIFIC INFORMATION FOR: pipetting scheme and ODs.zip raw data (optical densities =OD) obtained from Peptide ELISAs. A-Chain derived Peptides were initial named differently: A09 = A08, A15 =A08shift, A86 = A90. Excel Files show the raw data, sorted according to tested peptide and date. To evaluate the ELISA, the duplicate value was calculated in each case and then background was subtracted from foreground. The values calculated in this way were then interpolated using a standard curve (Prism Version 9.1.0; "Sigmoidal, 4PL, X is concentration"). DATA-SPECIFIC INFORMATION FOR: MASTERFILE_Dryad_kleer_2021.xlsx 1. Number of variables: 16 2. Number of cases/rows: 492 3. Variable List: Pat.Numb. = Patient Number (Patient 11,105,191,206,207,213,222,236,243,304,326,354,356,372 were excluded due to ineligibility or insufficient data) Group: SLE = systemic Lupus erythematosus, NHS= healthy control Group sex: Female, Male Age (at time point of blood sampling) DDXBE= time duration between Diagnosis and Blood sampling ENBG:ethnical Background, 1=Caucasian, 2= Asian, 3= African, 4= Native American, 5= other A08 =A09 A08shift =A15 A90 = A86 B41 B43 B83 antiC1q NARCR= Number of ACR-Criteria PGA= Physicians global Assessment SELENA= Systemic Lupus Erythematosus Disease Activity Index (SLEDAI) score with the Safety of Estrogens in Lupus Erythematosus National Assessment (SELENA) modification 4. Missing data codes: empty cells DATA-SPECIFIC INFORMATION FOR: Tableone_Dryad.Rmd Summary statistics for demographic and clinical characteristics of patients with systemic lupus erythematosus and control group DATA-SPECIFIC INFORMATION FOR: Boxplots_and_Cutoffs_Dryad.Rmd Distribution of anti-C1q, anti-A15, anti-A09, anti-A86, anti-B41, anti-B43 and anti-B83 Antibodies in SLE patients and control group. Selected Cutoff for positivity. DATA-SPECIFIC INFORMATION FOR: Correlation_plot_Dryad.Rmd Correlation plot, that shows Correlation of autoantibodies to peptides among each other DATA-SPECIFIC INFORMATION FOR: logistic_regression_Dryad.Rmd Univariate logistic regression to examine the relationship between positivity in ELISAs and serological and clinical manifestations of SLE-disease, taking the serological measures as predictors and the presence of different disease-features as dependent variable - Disease-activity Features (SLEDAI): Evaluated at the time of blood collection - different Items of ACR-Criteria: evaluated at entry into the study or symptom onset; usually not subsequently documented. Create data.frame for export of Odds Ratios and Confidence Intervals in .txt file (to make forest plots with prism Version 9.1.0) 99% CI Intervals were taken into consideration, but intervals have not been adjusted for multiplicity in the final analysis DATA-SPECIFIC INFORMATION FOR: ROC_Curves_Dryad.Rmd ROC-Curves to compare diagnostic performance of certain ELISAS regarding discrimination between SLE patients and normal blood donors, active Disease vs. Inactive Disease and Proteinuria DATA-SPECIFIC INFORMATION FOR: multivariate_logistic_regression.Rmd multivariate logistic regression, adjusting for disease activity