. 2021 Mar 9;10:e56088. doi: 10.7554/eLife.56088

Table 2. Mixed effects model investigating changes in FNR density between total chloroplast sub-compartments of three individuals each from Arabidopsis genotypes WT, fnr1 mutant and expressing ZmFNR1; ZmFNR2 and ZmFNR3 in the fnr1 background.

Analysis of data presented in Figure 3. Fixed effects taking either label density in the stroma as the intercept or label density in the margins/lamellae as the intercept. Linear mixed model fit by REML. Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘’ 1.

Wt Deletion test carried out using Satterthwaite’s method with the R package lmerTest (Kuznetsova, Brockhoff & Christensen 2017). The model is a mixed effects model with random intercepts. The square root of response is the response variable, tissue is the fixed effect, and individual the random effect.
Fixed effect deleted	Sum Sq	Mean Sq	Num DF	Den DF	F value	Pr (>F)
Sub-compartment	4.991	1.6637	3	6	36.152	0.0003089	***
Model summary:
Random effects:
Groups	Name	Variance	Std. Dev.
Individual	(Intercept)	0.21097	0.4593
Residual		0.04602	0.2145
Number of obs: 12, groups: individual, 3
Fixed effects when stroma is set as the intercept:
		Estimate	Std. Error	DF	t value	Pr (>\|t\|)
(Intercept)		1.1743	0.2927	2.6475	4.012	0.034961	*
Grana		0.3104	0.1752	6	1.772	0.126711
Lamellae		1.4748	0.1752	6	8.42	0.000153	***
Margin		1.3736	0.1752	6	7.842	0.000227	***
Fixed effects when lamellae is set as the intercept:
		Estimate	Std. Error	DF	t value	Pr (>\|t\|)
(Intercept)		2.6491	0.2927	2.6475	9.051	0.004601	**
Grana		−1.1644	0.1752	6	−6.648	0.00056	***
Margin		−0.1012	0.1752	6	−0.578	0.584522
Stroma		−1.4748	0.1752	6	−8.42	0.000153	***
*fnr1* Deletion test carried out using Satterthwaite’s method with the R package lmerTest (Kuznetsova, Brockhoff & Christensen 2017). The model is a mixed effects model with random intercepts. The square root of response is the response variable, tissue is the fixed effect, and individual the random effect.
Fixed effect deleted	Sum Sq	Mean Sq	Num DF	Den DF	F value	Pr (>F)
Sub-compartment	5.6516	1.8839	3	6	26.204	0.000759	***
Model summary:
Random effects:
Groups	Name	Variance	Std. Dev.
Individual	(Intercept)	0.07521	0.2742
Residual		0.07189	0.2681
Number of obs: 12, groups: individual, 3
Fixed effects when stroma is set as the intercept:
	Estimate	Std. Error	DF	t value	Pr (>\|t\|)
(Intercept)	1.2117	0.2214	4.4836	5.472	0.003875	**
Grana	−0.1584	0.2189	6	−0.724	0.496563
Lamellae	0.9353	0.2189	6	4.272	0.005251	**
Margin	1.5161	0.2189	6	6.925	0.000449	***

Fixed effects when lamellae is set as the intercept:
	Estimate	Std. Error	DF	t value	Pr (>\|t\|)
(Intercept)	2.1469	0.2214	4.4836	9.695	0.000356	***
Grana	−1.0937	0.2189	6	−4.996	0.002463	**
Margin	0.5808	0.2189	6	2.653	0.037882	*
Stroma	−0.9353	0.2189	6	−4.272	0.005251	**
fnr1:ZmFNR1 Deletion test carried out using Satterthwaite’s method with the R package lmerTest (Kuznetsova, Brockhoff & Christensen 2017). The model is a mixed effects model with random intercepts. The square root of response is the response variable, tissue is the fixed effect, and individual the random effect.
Fixed effect deleted	Sum Sq	Mean Sq	Num DF	Den DF	F value	Pr (>F)
Sub-compartment	4.5242	1.5081	3	6.01	23.558	0.001009	**
Model summary:
Random effects:
Groups	Name	Variance	Std. Dev.
Individual	(Intercept)	0.0005984	0.02446
Residual		0.064017	0.25302
Number of obs: 12, groups: individual, 3
Fixed effects when stroma is set as the intercept:
	Estimate	Std. Error	DF	t value	Pr (>\|t\|)
(Intercept)	1.1754	0.1468	7.9979	8.009	4.34⁻⁰⁵	***
Relevel grana	0.2318	0.2066	6.01	1.122	0.304712
Relevel lamellae	1.3774	0.2066	6.01	6.668	0.000547	***
Relevel margin	1.2849	0.2066	6.01	6.22	0.000793	***
Fixed effects when lamellae is set as the intercept:
	Estimate	Std. Error	DF	t value	Pr (>\|t\|)
(Intercept)	2.55285	0.14676	7.9979	17.395	1.22⁻⁰⁷	***
Relevel grana	−1.14567	0.20659	6.01002	−5.546	0.001444	**
Relevel margin	−0.09252	0.20659	6.01002	−0.448	0.669949
Relevel stroma	−1.37744	0.20659	6.01002	−6.668	0.000547	***
fnr1:ZmFNR2
Deletion test carried out using Satterthwaite’s method with the R package lmerTest (Kuznetsova, Brockhoff & Christensen 2017). The model is a mixed effects model with random intercepts. The square root of response is the response variable, tissue is the fixed effect, and individual the random effect.
Fixed effect deleted	Sum Sq	Mean Sq	Num DF	Den DF	F value	Pr (>F)
Sub-compartment	5.4414	1.8138	3	6	22.849	0.001106	**
Model summary:
Random effects:
Groups	Name	Variance	Std. Dev.
Individual	(Intercept)	0.02741	0.1656
Residual		0.07938	0.2817
Number of obs: 12, groups: individual, 3
Fixed effects when stroma is set as the intercept:
	Estimate	Std. Error	DF	t value	Pr (>\|t\|)
(Intercept)	1.1886	0.1887	6.6796	6.3	0.000488	***
Grana	0.4864	0.23	6	2.114	0.078885	.
Lamellae	1.8298	0.23	6	7.954	0.00021	***
Margin	0.9239	0.23	6	4.016	0.006989	**
Fixed effects when lamellae is set as the intercept:
	Estimate	Std. Error	DF	t value	Pr (>\|t\|)
(Intercept)	3.0184	0.1887	6.6796	15.998	1.42⁻⁰⁶	***
Grana	−1.3434	0.23	6	−5.84	0.00111	**
Margin	−0.9059	0.23	6	−3.938	0.00764	**
Stroma	−1.8298	0.23	6	−7.954	0.00021	***
fnr1:ZmFNR3
Deletion test carried out using Satterthwaite’s method with the R package lmerTest (Kuznetsova, Brockhoff & Christensen 2017). The model is a mixed effects model with random intercepts. The square root of response is the response variable, tissue is the fixed effect, and individual the random effect.
Fixed effect deleted	Sum Sq	Mean Sq	Num DF	Den DF	F value	Pr (>F)
Sub-compartment	9.0046	3.0015	3	8	25.416	0.0001923	***

Model summary:
Random effects:
Groups	Name	Variance	Std. Dev.
Individual	(Intercept)	0	0
Residual		0.1181	0.3436
Number of obs: 12, groups: individual, 3
Fixed effects when stroma is set as the intercept:
	Estimate	Std. Error	DF	t value	Pr (>\|t\|)
(Intercept)	1.06794	0.19841	8	5.383	0.00066	***
Grana	0.06284	0.28059	8	0.224	0.828395
Lamellae	1.99447	0.28059	8	7.108	0.000101	***
Margin	1.44343	0.28059	8	5.144	0.00088	***
Fixed effects when lamellae is set as the intercept:
	Estimate	Std. Error	DF	t value	Pr (>\|t\|)
(Intercept)	3.0624	0.1984	8	15.435	3.09⁻⁰⁷	***
Grana	−1.9316	0.2806	8	−6.884	0.000127	***
Margin	−0.551	0.2806	8	−1.964	0.085144	.
Stroma	−1.9945	0.2806	8	−7.108	0.000101	***