Journal: Molecular Cytogenetics

Article Title: Genetic testing for hearing loss in the United States should include deletion/duplication analysis for the deafness/infertility locus at 15q15.3

doi: 10.1186/1755-8166-6-19

Figure Lengend Snippet: Array CGH results demonstrating a homozygous deletion on 15q15.3 in the proband (A) that includes the full STRC and CATSPER2 genes as well as a portion of CKMT1B as shown by the red rectangle (B). Both parents were found to be heterozygous carriers of this deletion ( C ).

Article Snippet: Each mixture was then applied to an Agilent 4 × 180 K oligonucleotide array CGH slide and incubated while rotating at 65°C for 24 hours.

Techniques:

Journal: Redox Biology

Article Title: BRCA1 haploinsufficiency promotes chromosomal amplification under Fenton reaction-based carcinogenesis through ferroptosis-resistance

doi: 10.1016/j.redox.2022.102356

Figure Lengend Snippet: Expression microarray analysis at the subacute phase of Fe-NTA-induced renal carcinogenesis sorts out mitochondrial and iron metabolisms as candidate responsible pathways in Brca1 MUT(L63X/+) rat. (A) Results of hierarchical clustering and GO term analysis for the genes differentially expressed between WT and Brca1 MUT at 3 weeks in the Fe-NTA-induced renal carcinogenesis protocol (refer to ). (B) Renal Brca1 expression during the subacute phase of Fe-NTA-induced renal carcinogenesis protocol with qPCR (left panel; means ± SD) and immunoblot analysis (right panels). (C) Examples of altered metabolisms and mitochondrial dysfunction with expression microarray analysis specifically in the kidney of Brca1 MUT rats during the subacute phase of Fe-NTA-induced renal carcinogenesis (n = 3; * P < 0.05, ** P < 0.01, *** P < 0.001 vs wild-type Fe-NTA renal carcinogenesis protocol at 3 weeks). Refer to text for details.

Article Snippet: We labeled DNA from 16 rat primary RCCs (4 in wild-type without metastasis, 4 in wild-type with pulmonary metastasis, 4 in Brca1-MUT rat without metastasis, and 4 in Brca1-MUT rat with pulmonary metastasis; randomly selected from RCC samples of appropriate size [diameter >15 mm] without massive necrosis and obtained by scheduled autopsy; ) with Cy-5 and the corresponding control DNA with Cy-3, which were applied to the aCGH microarray slides (SurePrint G3 Rat CGH 4 × 180k Microarray, G4826A#27064, Agilent Technologies, Santa Clara, CA) according to the Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis protocol Ver.7.3.

Techniques: Expressing, Microarray, Western Blot

Journal: bioRxiv

Article Title: LncRNA Dnmt3aos regulates Dnmt3a expression leading to aberrant DNA methylation in macrophage polarization

doi: 10.1101/514307

Figure Lengend Snippet: (a-b) LncRNA microarray expression data from BMDMs incubated in distinct polarizing conditions. A total of 1,251 differentially-expressed lncRNAs were identified between the M(LPS+IFN-γ) and M(IL-4) macrophages. (a) Scatter plots show the variation in lncRNA expression between the M(LPS+IFN-γ) and M(IL-4) macrophages. The values of the X and Y axes in the scatter plot are the averaged normalized values in each group (log2-scaled). (b) Heat maps of lncRNAs expression profiles between the two groups. “Red” indicates high relative expression and “green” indicates low relative expression. One ANOVA test was used for statistical analysis. LncRNA with expression fold change > 2 and with FDR-adiusted P value < 0.05 was considered statistically significant. (c) Confirmation of the differential expression of lncRNAs by RT-qPCR. Four differentially expressed lncRNAs were validated by RT-qPCR. The y-axis represents the log2-transformed median fold-change in expression. (d) LncRNA Dnmt3aos locates on the Dnmt3a opposite strand on mouse chromosome 12. (e) RT-qPCR detection of Dnmt3aos level in cellular fractions from BMDMs. U6 and GAPDH were the nuclear and cytoplasmic controls, respectively. Data were expressed as the means ± SD of three independent experiments. (f) Dnmt3aos expression in BMDMs detected by RNA-FISH. Scale bar, 20 mm.

Article Snippet: Each SBC mouse (4*180K) LncRNA microarray slide (Agilent Technologies Inc.) was hybridized with 1.65 μg Cy3-labeled cRNA using a gene expression hybridization kit (Agilent Technologies, Inc.).

Techniques: Microarray, Expressing, Incubation, Quantitative RT-PCR, Transformation Assay