Molecular analyses of zebrafish V0v spinal interneurons and identification of transcriptional regulators downstream of Evx1 and Evx2 in these cells

England, Samantha J.; Rusnock, Amber K.; Mujcic, Amra; Kowalchuk, Angelica; de Jager, Sarah; Hilinski, William C.; Juárez-Morales, José L.; Smith, Matthew E.; Grieb, Ginny; Banerjee, Santanu; Lewis, Katharine E.

doi:10.1186/s13064-023-00176-w

Neural Development

Table 6 Differential expression analysis of genes downregulated in evx1;evx2 Mutant Group 1 and 2 V0v spinal interneurons

From: Molecular analyses of zebrafish V0v spinal interneurons and identification of transcriptional regulators downstream of Evx1 and Evx2 in these cells

A
Gene Symbol	Hurdle Model Fold-Change
Gene Symbol	Mutant 1 + 2 vs WT 1 + 2	Mutant 3 vs Mutant 1 + 2	Mutant 1 vs WT 1	Mutant 2 vs WT 2	Mutant 3 vs WT 1 + 2	WT 1 vs WT 2	Mutant 1 vs Mutant 2
ccdc3a	↓1.71***	↑1.01	↓1.74***	↓1.64***	↓1.68**	↑1.16***	↑1.09
dachc	↓1.73***	↑1.15	↓1.83***	↓1.63***	↓1.50	↑1.27***	↑1.13**
luzp1	↓1.70***	↑1.60***	↓1.71***	↓1.63***	↓1.06	↓1.25***	↓1.31***
mycb	↓1.97***	↑3.76***	↓1.40*	↓2.85***	↑1.92***	↓1.70***	↑1.20
nr5a2	↓37.70***	↑1.88***	↓7.47***	↓151.81***	↓19.83***	↓19.58***	↑1.04
pou3f1	↓2.43***	↑2.09***	↓1.80***	↓3.47***	↓1.16*	↓1.83***	↑1.05
pou3f2b	↓25.86***	↑1.12	↓32.33***	↓17.28***	↓22.90***	↓1.61***	↓3.01***
pou3f3b	↓47.31***	↑1.86*	↓45.00***	↓47.63***	↓25.32***	↓1.53**	↓1.44***
scrt2	↓2.41***	↑3.38***	↓2.58***	↓1.80***	↑1.40	↓2.34***	↓3.36***
pou2f2a	↓8.56***	↓2.15*	↓28.23***	↓1.17***	↓18.39***	↓6.83***	↓163.63***
pou2f2b	↓6.78***	↓4.47***	↓13.05***	↓1.50***	↓30.31***	↓12.38***	↓107.28***
mafba	↓15.72***	↓1.21	↓16.24***	↓9.56***	↓18.90***	↓3.36***	↓5.69***
pbx1b	↓4.70***	↓1.20	↓9.17***	↓1.68***	↓5.65***	↓2.09***	↓11.35***
scrt1a	↓3.86***	↓4.17***	↓4.13***	↓2.60***	↓16.10***	↓6.70***	↓10.61***
zfhx3b	↓5.43***	↓3.78***	↓17.11***	↓1.78***	↓20.52***	↓3.89***	↓37.40***
nr2f5	↓6.23***	↓1.19	↓2.07***	↓20.77***	↓7.42***	↓24.31***	↓2.42***
ebf1a	↓2.66***	↑2.76***	↓12.54***	↓1.13***	↑1.04**	↑14.27***	↑1.28
pitx2	↓1.64***	↑1.01	↓10.67***	↓1.06*	↓1.63*	↑9.95***	↓1.02
B
Gene Symbol	ANOVA Fold-Change
Gene Symbol	Mutant 1 + 2 vs WT 1 + 2	Mutant 3 vs Mutant 1 + 2	Mutant 1 vs WT 1	Mutant 2 vs WT 2	Mutant 3 vs WT 1 + 2	WT 1 vs WT 2	Mutant 1 vs Mutant 2
ccdc3a	↓6.93***	↓1.03	↓5.59***	↓11.62***	↓7.16***	↑1.69	↑3.50
dachc	↓4.18***	↓1.61	↓4.44***	↓3.77***	↓2.59*	↑1.88*	↑1.60
luzp1	↓1.89***	↑1.62**	↓3.04***	↓1.40***	↓1.17	↓1.06	↓2.31
mycb	↓2.32***	↑4.63***	↓1.55*	↓3.54***	↑1.99**	↓1.44***	↑1.58
nr5a2	↓75.12***	↑15.38***	↓32.40***	↓129.88***	↓4.88***	↓3.13***	↑1.28
pou3f1	↓5.40***	↑5.97***	↓3.82***	↓7.04***	↑1.10	↓1.78***	↑1.04
pou3f2b	↓3.65***	↓1.08	↓6.93***	↓2.49***	↓3.94***	↓1.02***	↓2.83***
pou3f3b	↓6.54***	↑1.40*	↓9.14***	↓5.26***	↓4.69***	↓1.16**	↓2.02
scrt2	↓1.34***	↑1.62***	↓2.79***	↑1.02**	↑1.21	↓1.41***	↓4.01***
pou2f2a	↓1.10***	↓1.66***	↓7.34***	↑1.33	↓1.83***	↓1.84***	↓17.92***
pou2f2b	↓1.17***	↓2.25***	↓5.14***	↑1.16**	↓2.64***	↓2.19***	↓13.01***
mafba	↓3.00***	↓1.34	↓7.93***	↓2.00***	↓4.04***	↓1.24***	↓4.92***
pbx1b	↓1.52***	↓1.57	↓3.91***	↓1.00*	↓2.38***	↓1.18***	↓4.60***
scrt1a	↓1.27***	↓3.09***	↓2.15***	↓1.04***	↓3.93***	↓1.86***	↓3.86***
zfhx3b	↓1.49***	↓1.58***	↓3.49***	↓1.09***	↓2.36***	↓1.54***	↓4.94***
nr2f5	↓4.09***	↓3.27*	↓6.08***	↓3.87***	↓13.34***	↓6.01***	↓9.42***
ebf1a	↓4.27***	↑4.38***	↓6.44***	↑1.03	↑1.03	↑10.15***	↑1.52
pitx2	↓175.87***	↑1.16	↓416.72***	↓7.19	↓152.16***	↑40.61***	↓1.43

Gene-specific analyses of differential expression, created through (A) Hurdle model and (B) ANOVA statistical comparisons between distinct cell clusters in our 48 h evx1^i232/+;evx2^sa140/+ heterozygote incross single-cell atlas (see Fig. 9A and also Methods for experimental details and rationale for using both statistical methods). For these comparisons, the Hurdle model is probably the most statistically robust method as there are sufficient cell numbers in each group to effectively model the variance (see Methods for more information). We also provide the ANOVA data for completeness and comparison. Column 1 shows the gene symbol. Columns 2–8 show fold-change values. ↑ = fold-change increase, ↓ = fold-change decrease in the antecedent (first) population compared to the consequent (second) population in each comparison. Statistically significant (P < 0.05) values are indicated in bold. *** P < 0.001, ** P < 0.01, * P < 0.05. Mutant Groups 1 + 2 combined, Mutant Group 3, Mutant Group 1, Mutant Group 2, Mutant Group 3, WT Group 1, and Mutant Group 1 are the antecedent populations for columns 2, 3, 4, 5, 6, 7 and 8 respectively. WT Groups 1 + 2 combined, Mutant Groups 1 + 2 combined, WT Group 1, WT Group 2, WT Groups 1 + 2 combined, WT Group 2 and Mutant Group 2 are the consequent populations for columns 2, 3, 4, 5, 6, 7 and 8 respectively. Additional data for each comparison are available in Supp. Data Tables 2 (Hurdle model data) and 3 (ANOVA data)

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