Journal: Developmental biology

Article Title: The molecular and cellular basis of variable craniofacial phenotypes and their genetic rescue in Twisted gastrulation mutant mice

doi: 10.1016/j.ydbio.2011.04.026

Figure Lengend Snippet: Human and mouse craniofacial phenotypes associated with genes showing altered expression in Twsg1 −/− mice.

Article Snippet: Reverse transcription was carried out with the Thermoscript RT kit (Invitrogen) priming with random hexamers, followed by quantitative PCR (Q-PCR, MX3000p, Agilent, LaJolla, CA) using expression assays from Applied Biosystems (Foster City, CA) for Bambi (Mm03024088_g1) , Bmp4 (Mm00432087_m1) , Bmpr1b (Mm03023971_m1) , Cyp26a1 (Mm00514486_m1) , Dkk1 (Mm00438422_m1) , Gpr50 (Mm00439147_m1) , Peg3 (Mm00493299_s1) , Plagl1 (Mm00494250_m1), Satb2 (Mm00507337_m) or using published primer sequences with SYBR green RT 2 master mix (SABiosciences, Valencia, CA) for Dlk1 , Igf2 ( Varrault et al., 2006 ), and Msx2 ( Berdal et al., 2009 ).

Techniques: Expressing, Knock-Out, Isolation

Journal: Developmental biology

Article Title: The molecular and cellular basis of variable craniofacial phenotypes and their genetic rescue in Twisted gastrulation mutant mice

doi: 10.1016/j.ydbio.2011.04.026

Figure Lengend Snippet: Photomicrographs of embryos from different phenotype classes, probed by in situ hybridization for (A–C) Dkk1 and (D–F) Msx2, show similar expression levels between WT and class A, but profoundly decreased expression in class C. (G–I) Plagl1, (J–L) Satb2 and (M–O) Peg3 show increased expression in class A and markedly decreased expression in class C. These represent various patterns of differential gene expression as described in the text. Arrowheads indicate expression domains within BA1. Fused mandibular prominences of BA1 are either marked with an asterisk or outlined with a dashed line.

Article Snippet: Reverse transcription was carried out with the Thermoscript RT kit (Invitrogen) priming with random hexamers, followed by quantitative PCR (Q-PCR, MX3000p, Agilent, LaJolla, CA) using expression assays from Applied Biosystems (Foster City, CA) for Bambi (Mm03024088_g1) , Bmp4 (Mm00432087_m1) , Bmpr1b (Mm03023971_m1) , Cyp26a1 (Mm00514486_m1) , Dkk1 (Mm00438422_m1) , Gpr50 (Mm00439147_m1) , Peg3 (Mm00493299_s1) , Plagl1 (Mm00494250_m1), Satb2 (Mm00507337_m) or using published primer sequences with SYBR green RT 2 master mix (SABiosciences, Valencia, CA) for Dlk1 , Igf2 ( Varrault et al., 2006 ), and Msx2 ( Berdal et al., 2009 ).

Techniques: In Situ Hybridization, Expressing, Gene Expression

Journal: Genes

Article Title: Gene Expression in MC3T3-E1 Cells Treated with Diclofenac and Methylprednisolone

doi: 10.3390/genes14010184

Figure Lengend Snippet: Gene and assay ID numbers.

Article Snippet: Satb2 , 4331182 , Mm00507331_m1.

Techniques: Sequencing

Journal: Genes

Article Title: Gene Expression in MC3T3-E1 Cells Treated with Diclofenac and Methylprednisolone

doi: 10.3390/genes14010184

Figure Lengend Snippet: Gene expression in MC3T3-E1 in the presence of DF and MP . Tgfb1 , Alp , Satb2 , and Dlx5 mRNA levels in MC3T3-E1 cells treated with DF ( A , C , E , G ) 0.5 µM, 5 µM, 50 µM (increasing grey scale, respectively) for 24 h, 48 h, 72 h, and 168 h. MC3T3-E1 cells were treated with MP ( B , D , F , H ) 0.5 µM, 5 µM, 50 µM (increasing grey scale, respectively) for 24 h, 48 h, 72 h, and 168 h. Untreated control equals 1 (open bars). Results are presented as geometric means of relative expression. Hprt and B2m were used as reference genes. The significance was evaluated using one-way ANOVA with Tukey’s post hoc test. The significance level was set at 5% ( p < 0.05). Error bars represent ± SEM.

Article Snippet: Satb2 , 4331182 , Mm00507331_m1.

Techniques: Gene Expression, Control, Expressing

Journal: Tissue Engineering Part A

Article Title: Roles of SATB2 in Osteogenic Differentiation and Bone Regeneration

doi: 10.1089/ten.tea.2010.0503

Figure Lengend Snippet: FIG. 4. Effects of SATB2 and Runx2 on the expression level of Osx. (A, B) Murine osteoblast precursor cells in the form of calvarial cells were isolated from Runx2 + / - and Runx2 - / -

Article Snippet: For better comparison, we only blasts were transfected with SATB2 siRNAs or scrambled control siRNAs (Santa Cruz Biotechnology).

Techniques: Expressing, Isolation

Journal: Tissue Engineering Part A

Article Title: Roles of SATB2 in Osteogenic Differentiation and Bone Regeneration

doi: 10.1089/ten.tea.2010.0503

Figure Lengend Snippet: FIG. 6. Histological analysis demonstrated increased bone tissue regeneration and mineralization in bone defects ex- posed to SATB2-overexpressing adult stem cells. (A, B) H&E-stained sections showing bone defects transplanted with control BMSCs (A) or SATB2-overexpressing BMSCs (B). A2 and B2 are exactly the same images as A1 and B1, respectively; however, we showed, in A2 and B2, the area within the original bone lesion assessed by digitizing the reversal line in the bone at the cut margin of the original wound outline. (C) Histomorphometric analysis showed an elevated newly formed bone area in bone defects treated with SATB2-overexpressing BMSCs. Data were represented as mean – SEM. *p < 0.05, SATB2 group versus control group. (D, E) H&E-stained sections showing bone defects trans- planted with control DFCs (D) or SATB2-overexpressing DFCs (E). Again in D2 and E2, we showed the area within the original bone lesion assessed by digitizing the reversal line in the bone at the cut margin of the original wound outline. (F) The newly formed bone area was higher in bone defects treated with SATB2-overexpressing DFCs, as indi- cated by histomorphometric analysis. Data were represented as mean – SEM. *p < 0.05, SATB2 group versus control group. Color images available online at www.liebertonline.com/tea

Article Snippet: For better comparison, we only blasts were transfected with SATB2 siRNAs or scrambled control siRNAs (Santa Cruz Biotechnology).

Techniques: Staining, Control

Journal: Tissue Engineering Part A

Article Title: Roles of SATB2 in Osteogenic Differentiation and Bone Regeneration

doi: 10.1089/ten.tea.2010.0503

Figure Lengend Snippet: FIG. 7. (A) Immunohistochem- ical staining for Luciferase, BSP, and GFP demonstrated increased Luciferase and BSP expression, which indicated enhanced oste- ogenic differentiation in SATB2 groups. Cell counting was per- formed in the whole newly formed bone area as shown in A2, B2, D2, and E2 of Figure 6. Arrow, positively stained cells; arrow head, negatively stained cells. (B–D) Cell counting results indicated that there were more luciferase (B) and BSP (C) posi- tive cells in SATB2 group than in control group. However, there is no significant difference in GFP- positive cell numbers between these two groups (D). Data were represented as mean – SEM. *p < 0.05, SATB2 group versus control group. GFP, green fluorescent protein. Color images available online at www .liebertonline.com/tea

Article Snippet: For better comparison, we only blasts were transfected with SATB2 siRNAs or scrambled control siRNAs (Santa Cruz Biotechnology).

Techniques: Staining, Luciferase, Expressing, Cell Counting, Control

Journal: Nature Communications

Article Title: A method for Boolean analysis of protein interactions at a molecular level

doi: 10.1038/s41467-022-32395-w

Figure Lengend Snippet: Antibodies used for MolBoolean experiments

Article Snippet: Mouse anti-SATB2 Clone CL0323 , 5 μg/mL , Atlas Antibodies, AMAb90682, 03684.

Techniques: Concentration Assay, Transduction