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    B cell Stimulation Flow Cytometry

    We used flow cytometry to measure activation of B cells in at-risk individuals (ARI) and healthy controls. B cells were treated with CpG and CD40L or without stimulation for 48 hours. Flow cytometry was performed using a 23 color panel of antibodies and dyes on a Cytek Aurora spectral flow cytometer. Antibodies, fluorophores, dyes, and source information are provided below:

    TargetFluorophoreCloneVendorCat. #
    CD3**PE-Cy7UCHT1BD Biosciences563423
    CD7**PE-Cy7CD7-6B7BioLegend343113/343114
    CD10BV750HI10aBD Biosciences747517
    CD11cFITCBu15BioLegend337214
    CD14*BUV395M5E2BD Biosciences740286
    CD14**PE-Cy7M5E2BC Biosciences557742
    CD20APC-Cy72H7Biolegend302314
    CD21BUV6611048BD Biosciences75018
    CD24PE-Cy5ML5BioLegend311147
    CD27BV786L128BD Biosciences742731
    CD33**PE-Cy7P67.6BioLegend366617/366618
    CD45RBAPCMEM-55Bio-RadMCA1114
    CD56**PE-Cy7B159BD Biosciences557747
    CD61**PE-Cy7VI-PL2BioLegend336415/336416
    CD69BUV737FN50BD Biosciences564364
    CD73BUV805AD2BD Biosciences748584
    CD95BV605DX2BioLegend305628
    CD107aPE-Dazzle594H43ABioLegend328646
    CD235a**PE-Cy7HIR2BioLegend306619/306620
    HLA-DRBV711L243BioLegend307643
    IgAPerCP-Vio700IS11-8E10Miltenyi130-113-478
    IgDBV480IA6-2BD Biosciences566138
    IgGBUV496G18-145BD Biosciences741172
    IgMBUV563UCH-B1BD Biosciences748929
    IL-10BV650JES3-9D7BD Biosciences564051
    IL-6BV421MQ2-13A5BD Biosciences563279
    RANKLPEMIH24BioLegend347504
    TNFaAlexa Fluor 700Mab11BioLegend502928
    ViabilityFVS510nanBD Biosciences564406

    *Included in 1 of 3 batches; Not included in final analyses. 
    ** All PE-Cy7 antibodies are included in the "Lin" channel.

    Data from these flow cytometry experiments are provided in two formats.

    1. A .tar archive file containing .fcs files from each sample suitable for analysis using Flow Cytometry software, along with a .csv table with metadata for each file.
    2. A compressed table (.csv.gz) file containing annotated cell data with scaled expression for each measured marker.

    The columns provided in the metadata table and annotated CSV file are provided below:

    Common columns:
    These columns are available in both the .fcs metadata and annotated cell .csv files.

    flow.fileName: The file name of the .fcs file
    flow.batch: The batch of experimental samples - data was generated in 3 batches of experiments.
    flow.condition: The experimental condition (CpG_CD40_stimulated or unstimulated)

    subject.diseaseGroup: Which group each subject belonged to: Control (HC1); Control (HC2); ACPA+ At-risk (ARI); or ACPA+ Early RA (ERA)
    subject.progressionGroup: For ARI subjects, whether subject was diagnosed with RA during the study period (converted): Progression (CONV) or No Progression (NONC)
    subject.subjectID: An ID for the Subject
    subject.biologicalSex: The biological sex of the Subject
    subject.diagnosisAge: For ARI-CONV subjects, age at diagnosis of RA
    subject.diagnosisBMI: For ARI-CONV subjects, Body Mass Index at diagnosis of RA
    subject.biologicalSex: The biological sex of the Subject
    am.bmi: Body Mass Index (BMI)
    infl.anti_ccp3: Anti-CCP3
    infl.rf_iga_result: RFIgA Result
    infl.rf_igm_result: RFIgM Result
    sample.daysToDiagnosis: Days between sample collection and diagnosis of RA for CONV group
    sample.daysSinceFirstVisit: Days between initial sample collection and this sample draw

    Annotation columns:
    These columns are available only in the annotated cell .csv file.

    flow.cellType: The B cell type assigned to the cell.
    flow.isotype: The isotype of the B cell based on Ig detection (if available)
    TNFa_pos: A boolean value (True or False) for TNFa expression.
    IL_6_pos: A boolean value (True or False) for IL-6 expression.
    IL_10_pos: A boolean value (True or False) for IL-10 expression.
    RANKL_pos: A boolean value (True or False) for RANKL expression.

    Feature columns:
    These columns provide scaled expression values for each feature, and are only present in the annotated cell .csv file. See above for additional antibody and fluorophore information.

    CD45RB
    CD20
    TNFa
    IgG
    IgM
    CD21
    CD69
    CD73
    IL_6
    IgD
    CD95
    IL_10
    HLA_DR
    CD10
    CD27
    CD11c
    Viability
    RANKL
    CD24
    Lin
    CD107a
    IgA

    ALTRA B cell flow cytometry
    File Name Description Download Link
    altra_bcell_clustered_scaled_data.csv.gz Annotated cell dataset .csv
    altra_bcell_fcs.tar FCS files and file metadata