Table 1 Baseline characteristics of participants, their SF samples and association of these factors with IPS

Feature	Description	Spun OA Samples (N)	Mean (SD) or N	Reference Group	Strength and Direction of Association of IPS (regression coefficient)		Adjusted p-values
					Cohort included as a random intercept		Cohort included as a random intercept
					Yes	No	Yes	No
Age	Participant age at the time of sampling (year)	1133	64.46 (11.00)	__	2.01e^-05	1.47e^-04	7.01e^-01	2.64e^-01
Sex	Biological sex	1134	Female: N = 596 Male: N = 538	Female	-5.47e^-03	-6.29e^-03	2.42e^-02*	1.22e^-02*
BMI	Participant body mass index at the time of sampling	1045	30.68 (5.92)	__	4.11e^-05	7.87e^-05	8.09e^-01	7.59e^-01
Smoking History	Current or past smoker at the time of the baseline sampling	926	Never Smoked: N = 510 Ever Smoked: N = 416	Never Smoked	1.38e^-03	7.26e^-04	7.01e^-01	7.59e^-01
WOMAC Pain Score	Scale of 0-100, where 100 is the worst possible knee pain	748	44.91 (21.08)	__	2.63e^-05	3.81e^-05	7.01e^-01	7.59e^-01
Advanced Radiographic Status	Binary indicator for the presence of advanced radiographic knee OA (KL grades 3-4)	1096	Non-Advanced: N = 264 Advanced: N = 832	Non-Advanced OA (KL grades 0-2)	1.07e^-02	1.09e^-02	4.36e^-04*	2.18e^-04*
Visual Blood Staining Grade	Grading of SF blood staining (BS) prior to centrifugation (if known). Scale of 1-4, with larger grades corresponding to greater degrees of blood staining	515	Grade 1: N = 394Grade 2: N = 77Grade 3: N = 26Grade 4: N = 18	BS = 1	BS = 2, 1.50e^-02 BS = 3, 3.48e^-02 BS = 4, 5.54e^-02	BS = 2, 1.59e^-02 BS = 3, 3.60e^-02 BS = 4, 5.68e^-02	8.53e⁻¹³*	6.51e^-13*

Association testing was carried out between IPS and core demographic, clinical and technical features in spun OA samples where relevant data were available. Linear regression models were constructed with log scaled IPS (i.e. IPS that was transformed using natural logarithms) as the outcome with each feature listed in the table used as a univariate exposure. Adjusted models where cohort was included as a random intercept are also shown. Asterisks (bold) denote statistical significance at Benjamini-Hochberg cutoff (adjusted p-value ≤ 0.05).
OA osteoarthritis, SF synovial fluid, IPS intracellular protein score, BS blood staining, KL Kellgren Lawrence, SD standard deviation, BMI body mass index, WOMAC Western Ontario and McMaster Universities Osteoarthritis Index, ‘advanced’ (KL grades: 3-4), ‘non-advanced’ (KL grades: 0-2).

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