Table 3 Results of gene expression analyses from the ipsilateral cortex at 24 h post-CCI in male and female mice

Neuroinflammation

 GFAP

0.00 ± 0.39

0.17 ± 0.53

1.00 ± 0.42

0.91 ± 0.17

CCI

− 0.03

[− 0.68, 0.70]

0.87

[0.65, 1.64]

1.94

[1.78, 2.37]

2.09

[1.89, 2.18]

3 > 1, 4 > 1

 CD45

0.00 ± 0.19

3.00 ± 0.77

1.08 ± 0.33

3.41 ± 0.91

TG, CCI

0.00 ± 0.30

2.27 ± 0.92

1.56 ± 0.96

3.59 ± 0.57

TG, CCI

 CD86

0.00

[− 0.11, 0.11]

2.51

[2.21, 2.94]

0.50

[0.42, 0.62]

3.26

[2.49, 3.60]

2 > 1, 4 > 1

0.12

[− 0.27, 0.20]

2.08

[0.93, 2.71]

0.59

[0.37, 1.15]

3.22

[2.59, 3.38]

2 > 1, 4 > 1

 CD206

− 0.24

[− 0.67, 0.79]

1.11

[0.98, 1.33]

0.86

[0.39, 1.50]

0.88

[0.64, 1.37]

ns

0.00 ± 0.51

0.63 ± 0.34

0.28 ± 0.44

0.67 ± 0.50

TG

 TREM2

0.00 ± 0.22

1.39 ± 0.64

0.43 ± 0.27

1.72 ± 0.72

TG

0.00 ± 0.12

1.00 ± 0.61

0.19 ± 0.42

1.65 ± 0.38

TG, CCI

 CCR5

0.00 ± 0.25

1.15 ± 0.52

0.56 ± 0.28

1.75 ± 0.73

TG, CCI

0.00 ± 0.43

1.23 ± 0.70

1.06 ± 0.35

2.36 ± 0.29

TG, CCI

 IBA1

0.00 ± 0.14

2.40 ± 0.67

0.66 ± 0.24

2.79 ± 0.66

TG, CCI

0.10

[− 0.18, 0.13]

1.83

[0.76, 2.42]

0.76

[0.57, 0.85]

2.67

[2.49, 3.07]

2 > 1, 4 > 1

 TMEM119

0.00 ± 0.36

0.84 ± 0.68

− 0.02 ± 0.18

0.89 ± 0.52

TG

0.03

[− 0.17, 0.15]

0.52

[0.06, 1.30]

− 0.08

[− 0.62, 0.01]

0.93

[0.59, 1.15]

4 > 3

 GATA3

− 0.04

[− 1.34, 1.36]

5.88

[5.17, 6.84]

0.95

[− 0.02, 1.96]

6.25

[5.46, 6.73]

2 > 1, 4 > 1, 4 > 3

0.00 ± 0.78

4.30 ± 0.96

1.01 ± 0.93

5.20 ± 0.86

TG, CCI

 CXCR3

0.20

[− 1.12, 1.02]

6.18

[5.67, 7.17]

0.68

[0.32, 1.13]

6.51

[5.79, 6.95]

2 > 1, 4 > 1,

4 > 3, 2 > 3

0.09

[− 0.21, 0.16]

4.62

[4.04, 6.28]

− 0.12

[− 0.70, 0.88]

5.65

[5.41, 7.14]

4 > 1, 4 > 3

 STAT1

0.01

[− 0.17, 0.16]

3.46

[3.12, 4.26]

0.45

[0.37, 0.78]

3.81

[3.26, 4.29]

2 > 1, 4 > 1

0.09

[− 0.28, 0.23]

2.79

[1.59, 3.62]

0.37

[0.28, 0.54]

3.23

[2.96, 3.67]

2 > 1, 4 > 1

 SOCS1

0.00 ± 0.53

2.14 ± 0.87

0.16 ± 0.30

2.92 ± 1.24

TG

− 0.16

[− 0.41, 0.49]

1.08

[0.20, 2.88]

0.18

[0.14, 0.41]

2.38

[2.04, 2.98]

4 > 1

 FOXP3

− 0.32

[− 0.41, 0.57]

1.62

[0.77, 3.07]

− 0.04

[− 0.61, 0.37]

2.68

[2.04, 3.61]

4 > 1, 4 > 3

0.00 ± 1.11

1.96 ± 1.45

0.76 ± 0.79

3.27 ± 0.91

TG, CCI

 TSPO

0.00 ± 0.38

1.18 ± 1.35

0.73 ± 0.23

2.61 ± 0.77

TG, CCI

0.08

[− 0.17, 0.13]

0.93

[0.09, 2.04]

0.57

[− 0.76, 0.80]

2.49

[2.24, 2.79]

4 > 1, 4 > 3

 NLRP3

0.00 ± 0.30

1.65 ± 0.50

0.85 ± 0.30

2.10 ± 0.67

TG, CCI

0.00 ± 0.48

1.33 ± 0.84

1.12 ± 0.47

2.09 ± 0.27

TG, CCI

 IL1β

0.00 ± 0.91

2.06 ± 1.51

1.16 ± 0.70

3.02 ± 1.39

TG, CCI

0.00 ± 1.22

1.63 ± 1.80

2.23 ± 0.91

3.43 ± 0.82

TG, CCI

 IL2

− 0.22

[− 0.48, 0.59]

3.32

[2.36, 4.61]

0.46

[0.11, 0.67]

4.02

[2.70, 4.88]

2 > 1, 4 > 1, 4 > 3

0.13

[-0.49, 0.43]

2.60

[1.93, 3.91]

0.09

[− 0.33, 1.76]

2.66

[1.71, 4.12]

ns

 IL6

0.00 ± 0.89

0.56 ± 1.47

2.12 ± 0.81

2.72 ± 1.00

CCI

0.00 ± 0.96

1.06 ± 1.71

3.37 ± 1.74

4.02 ± 0.94

CCI

 IL10

0.00 ± 0.56

4.94 ± 0.93

1.06 ± 1.02

5.59 ± 1.26

TG

− 0.24

[− 0.89, 1.01]

3.32

[0.88, 3.79]

0.29

[− 0.54, 1.96]

4.94

[4.58, 5.29]

4 > 1, 4 > 3

 IL12p40

0.61

[− 1.13, 0.83]

6.17

[5.74, 7.64]

1.39

[− 0.15, 1.59]

7.27

[5.55, 8.33]

2 > 1, 4 > 1, 4 > 3

0.00 ± 0.97

4.24 ± 1.98

0.49 ± 1.88

5.83 ± 0.94

TG

 IL33

0.14

[− 0.41, 0.34]

− 0.15

[− 0.37, 0.23]

0.33

[− 0.17, 0.98]

0.32

[0.10, 0.67]

ns

0.00 ± 0.24

0.60 ± 0.41

1.21 ± 0.33

1.37 ± 0.24

TG, CCI

 TNFα

0.00 ± 0.54

2.38 ± 0.85

1.29 ± 0.49

3.73 ± 1.15

TG, CCI

0.00 ± 1.45

2.92 ± 1.59

3.10 ± 0.40

4.94 ± 0.59

TG, CCI

 CSF1

0.00 ± 0.21

0.81 ± 0.68

0.63 ± 0.36

1.21 ± 0.47

TG, CCI

0.00 ± 0.25

0.61 ± 0.49

0.69 ± 0.59

1.18 ± 0.22

TG, CCI

 CSF2

0.00 ± 1.12

4.26 ± 1.10

1.71 ± 1.38

4.53 ± 1.05

TG

0.00 ± 0.95

2.15 ± 1.15

0.72 ± 1.57

3.23 ± 0.82

TG

 CXCL10

0.00 ± 0.87

4.57 ± 1.16

1.12 ± 0.91

6.09 ± 0.85

TG, CCI

0.00 ± 1.56

4.66 ± 2.13

2.17 ± 0.24

6.54 ± 0.33

TG, CCI

 IFNγ

− 0.05

[− 0.32, 0.34]

8.44

[7.57, 10.08]

0.77

[0.58, 0.92]

8.97

[7.04, 10.68]

2 > 1, 4 > 1

− 0.21

[− 0.31, 0.42]

6.70

[5.32, 8.88]

0.05

[− 0.14, 1.95]

7.50

[7.23, 8.66]

2 > 1, 4 > 1, 4 > 3

 TGFβ

− 0.12

[− 0.66, 0.72]

0.86

[0.36, 1.75]

0.55

[0.22, 0.97]

1.80

[1.06, 2.41]

4 > 1

0.00 ± 0.90

1.03 ± 0.70

1.64 ± 0.95

2.87 ± 0.46

TG, CCI

 ARG1

0.00 ± 0.78

− 1.73 ± 1.37

3.05 ± 0.98

3.15 ± 1.43

CCI

0.00

[− 2.01, 2.01]

− 0.29

[− 1.31, 0.26]

4.81

[4.52, 5.51]

5.98

[4.57, 6.84]

4 > 1, 3 > 2, 4 > 2

 CCL2

0.00 ± 0.34

1.51 ± 1.36

1.77 ± 0.60

3.91 ± 0.92

TG, CCI

0.00 ± 1.45

2.79 ± 2.26

3.66 ± 0.58

5.62 ± 0.61

TG, CCI

 CCL4

0.00 ± 0.81

1.42 ± 1.18

2.66 ± 0.80

3.26 ± 0.75

TG, CCI

− 0.62

[− 1.27, 1.58]

1.61

[0.48, 3.28]

4.54

[4.22, 5.02]

5.03

[4.34, 5.16]

3 > 1, 4 > 1

 CCL5

0.22

[− 0.48, 0.37]

6.70

[6.07, 7.75]

1.29

[0.92, 1.85]

6.92

[6.06, 8.58]

2 > 1, 4 > 1

0.13

[− 0.37, 0.31]

5.30

[3.55, 6.87]

0.86

[0.36, 1.64]

6.67

[5.98, 7.97]

2 > 1, 4 > 1, 4 > 3

 CCL12

− 0.12

[− 0.33, 0.39]

1.05

[− 0.03, 1.70]

0.56

[0.24, 1.02]

1.80

[1.24, 3.14]

4 > 1

0.00 ± 1.62

2.30 ± 1.64

2.59 ± 0.95

3.89 ± 0.50

TG, CCI

Neuronal cell markers

 MAP2

0.00

[− 0.20, 0.19]

0.19

[0.08, 0.30]

0.18

[0.06, 0.24]

− 0.18

[− 0.53, − 0.09]

2 > 4

− 0.04

[− 0.14, 0.16]

0.07

[− 0.08, 0.11]

− 0.01

[− 0.26, 0.30]

− 0.36

[− 0.61, − 0.23]

2 > 4

Oxidative stress

 IDO1

− 0.16

[− 0.42, 0.50]

6.59

[5.62, 7.56]

0.52

[0.17, 0.73]

7.50

[5.54, 8.78]

2 > 1, 4 > 1, 4 > 3

0.13

[− 0.49, 0.43]

5.47

[3.99, 6.67]

− 0.14

[− 0.33, 1.76]

7.68

[7.04, 8.53]

4 > 1, 4 > 3

 NOS2

0.03

[− 0.39, 0.38]

2.80

[1.94, 4.78]

0.59

[0.48, 0.94]

4.43

[2.03, 5.60]

2 > 1, 4 > 1

− 0.09

[− 0.31, 0.35]

1.17

[0.01, 3.87]

0.68

[0.33, 1.24]

2.66

[2.01, 3.41]

4 > 1

 CYBB

0.15

[− 0.37, 0.30]

5.22

[4.50, 6.01]

1.13

[1.07, 1.24]

5.66

[4.47, 6.32]

2 > 1, 4 > 1

0.19

[− 0.46, 0.36]

4.04

[2.70, 5.24]

0.96

[0.90, 1.64]

5.43

[4.85, 6.39]

2 > 1, 4 > 1, 4 > 3

Glutamate pathway

 PHGDH

0.00 ± 0.49

0.41 ± 0.61

0.40 ± 0.31

0.33 ± 0.31

ns

0.00 ± 0.51

0.08 ± 0.14

− 0.07 ± 0.27

− 0.39 ± 0.17

CCI

 GLT1

0.00 ± 0.36

0.17 ± 0.45

0.04 ± 0.23

− 0.38 ± 0.34

ns

0.12

[− 0.34, 0.28]

− 0.08

[− 0.11, 0.02]

− 0.36

[− 0.86, − 0.13]

− 0.91

[− 1.17, − 0.66]

1 > 4, 2 > 4

 GLUL

0.00 ± 0.58

1.00 ± 0.30

0.27 ± 0.38

0.23 ± 0.34

TG, *

0.00 ± 0.62

0.14 ± 0.27

− 0.49 ± 0.50

− 0.78 ± 0.31

CCI

 GRIN2B

0.00 ± 0.20

0.36 ± 0.25

0.32 ± 0.32

− 0.08 ± 0.34

*

− 0.01

[− 0.38, 0.39]

0.04

[− 0.03, 0.26]

− 0.06

[− 0.24, 0.07]

− 0.41

[− 0.82, − 0.12]

ns

 GAD1

0.00 ± 0.22

− 0.42 ± 0.55

− 0.34 ± 0.29

− 0.78 ± 0.39

TG

0.05

[− 0.24, 0.21]

− 0.18

[− 0.31, 0.02]

− 0.30

[− 0.45, 0.09]

− 0.55

[− 1.12, − 0.19]

ns

 GLAST

0.00 ± 0.17

0.75 ± 0.61

0.29 ± 0.22

0.63 ± 0.26

TG

0.00 ± 0.24

0.26 ± 0.20

− 0.10 ± 0.31

0.26 ± 0.10

TG

 PPARγ

0.00 ± 0.30

− 0.15 ± 0.17

− 0.41 ± 0.27

− 0.45 ± 0.35

CCI

0.00 ± 0.15

− 0.27 ± 0.23

− 0.38 ± 0.17

− 0.43 ± 0.40

CCI