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. Author manuscript; available in PMC: 2019 Jun 1.
Published in final edited form as: Arthritis Rheumatol. 2018 May 3;70(6):841–854. doi: 10.1002/art.40453

Table 1.

Patient and Sample Information. Anti-CCP-cyclic citrullinated peptide; ESR-Erythrocyte Sedimentation Rate; DAS-Disease Activity Score; CDAI-Clinical Disease Activity Index; RAPID-Routine Assessment of Patient Index Data; PGA-Physician Global Assessment; HAQ-Health Assessment Questionnaire; TJC-tender joint count; SJC-swollen joint count. Treatment is divided by medication type and whether the patient is currently taking or has previously taken the medication. Standard deviation or percent of population is reported for patient information and treatment. Histological Scoring of Synovial Tissue. All slides were scored by same physician blinded to the origin of the samples. The amount of synovial tissue in each biopsy was estimated by structure, lining and leukocyte content. The number of CD45- and CD68-positive cells were scored on modified scale from 0-4. SEM is reported for Histology and RNA-seq library stats.

Patient Information
Age (years) 57.5 ± 11.4
Gender (female) 29 (71 %)
Gender (Male) 12 (29%)
Disease duration, years n=40 9.3 ± 8.4
Early disease (<2 years), n= 40 9 (23%)
Positive Rheumatoid Factor (RF) n=40 23 (58%)
Positive Anti-CCP n=36 19 (53%)
ESR (mm/hour) n=14 33.5 ± 21.7
DAS28 n=17 4.7 ± 1.3
CDAI n=20 21.5 ± 10.6
RAPID3 n=25 11.4 ± 7.4
PGA n=24 4.7 ± 3.1
HAQ n=18 0.7 ± 0.5
TJC n=31 5.8 ± 6.0
SJC n=31 7.1 ± 4.9

Treatment (n=31)
no Treatment (naïve) 3 (10%)
Methotrexate, current 15 (48%)
Methotrexate, past 9 (29%)
TNF-inhibitor, current 12 (38%)
TNF-inhibitor, past 17 (55%)
IL-6 inhibitor, current 2 (6%)
IL-6 inhibitor, past 2 (6%)
JAK-inhibitor, current 3 (10%)
JAK-inhibitor, past 5 (16%)
Other treatment, current 11 (35%)
Other treatment, past 12 (39%)
Prednisone, <5 mg, current 1 (3%)
Prednisone, 5-10 mg, current 6 (19%)

Histology-RA Synovial Biopsy (n=30)
% Synovial Tissue 36.0 ± 5.6
CD45 score (0-4) 1.7 ± 0.2
CD68 score (0-4) 1 ± 0.1

RNA-seq Stats
Whole Tissue Samples (RA=9, OA=9)
RIN# RA 6.7 ± 0.5
OA 8.0 ± 0.2
# aligned reads (Million) RA 9.2 ± 0.7
OA 12.9 ± 1.1
% of total reads aligned RA 81 9 ± 1.2
OA 85.3 ± 1.2
% Complexity RA 54.8 ± 1.7
OA 56.2 ± 1.9

Sorted Macrophage Samples (RA=15, OA=9)
Cells sorted RA 1642 ± 1178
OA 77414 ± 26413
# aligned reads (Million) RA 21.0 ± 4.2
OA 21.1 ± 6.8
% of total reads aligned RA 53 9 ± 6.0
OA 65.2 ± 1.5
% Complexity RA 37.2 ± 2.7
OA 38.1 ± 2.2