scholarly journals Combination of Linkage Mapping and Microarray-Expression Analysis Identifies NF-κB Signaling Defect as a Cause of Autosomal-Recessive Mental Retardation

2009 ◽  
Vol 85 (6) ◽  
pp. 903-908 ◽  
Author(s):  
Orianne Philippe ◽  
Marlène Rio ◽  
Astrid Carioux ◽  
Jean-Marc Plaza ◽  
Philippe Guigue ◽  
...  
Bone ◽  
2012 ◽  
Vol 50 (5) ◽  
pp. 1081-1091 ◽  
Author(s):  
Carmen E. Macsai ◽  
Kristen R. Georgiou ◽  
Bruce K. Foster ◽  
Andrew C.W. Zannettino ◽  
Cory J. Xian

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Keisuke Adachi ◽  
Yosuke Asada ◽  
Toshiaki Hirakata ◽  
Miki Onoue ◽  
Satoshi Iwamoto ◽  
...  

Abstract To clarify the early alterations of gene expression using a mouse model of glaucoma filtration surgery, we carried out microarray expression analysis. Using BALB/c mice, a filtration surgery model was made by incision of the limbal conjunctiva, followed by the insertion of a 33G needle tip into the anterior chamber, and 11-0 nylon sutures. Subgroups of mice were treated intraoperatively with 0.4 mg/ml mitomycin-C (MMC). At day 3 after surgery the bleb was maintained. The bleb region tissue was sampled 3 days after the filtration surgery, and gene expression analysis was carried out using a mouse Agilent 8 × 60 K array. We found 755 hyperexpressed transcripts in the bleb region compared to control conjunctiva. The hyperexpressed transcripts included epithelial cell metaplasia-related (Il1b, Krt16, Sprr1b), inflammation-related (Ccl2, Il6) and wound healing-related (Lox, Timp1) genes. We also found downregulation of a goblet cell marker gene (Gp2) in the bleb conjunctiva. MMC treatment suppressed elastin (Eln) gene expression and enhanced keratinization-related gene expression (Krt1, Lor) in the bleb region. Our results suggest the importance of epithelial wound healing after filtration surgery, and this filtration surgery model will be a useful tool for further pathophysiological analysis.


2007 ◽  
Vol 418 (1) ◽  
pp. 38-43 ◽  
Author(s):  
Liu Yang ◽  
Dai Li ◽  
Jinmao Chen ◽  
Jinnan Yang ◽  
Liping Xue ◽  
...  

2009 ◽  
Vol 69 (14) ◽  
pp. 5946-5953 ◽  
Author(s):  
Narasimharao V. Marella ◽  
Kishore S. Malyavantham ◽  
Jianmin Wang ◽  
Sei-ichi Matsui ◽  
Ping Liang ◽  
...  

2012 ◽  
Vol 45 (1) ◽  
pp. 462-468 ◽  
Author(s):  
Teresa Botta-Orfila ◽  
Eduard Tolosa ◽  
Ellen Gelpi ◽  
Alex Sànchez-Pla ◽  
Maria-José Martí ◽  
...  

2013 ◽  
Vol 59 (4) ◽  
pp. 667-674 ◽  
Author(s):  
Hans G Thormar ◽  
Bjarki Gudmundsson ◽  
Freyja Eiriksdottir ◽  
Siyoen Kil ◽  
Gudmundur H Gunnarsson ◽  
...  

BACKGROUND The causes of imprecision in microarray expression analysis are poorly understood, limiting the use of this technology in molecular diagnostics. Two-dimensional strandness-dependent electrophoresis (2D-SDE) separates nucleic acid molecules on the basis of length and strandness, i.e., double-stranded DNA (dsDNA), single-stranded DNA (ssDNA), and RNA·DNA hybrids. METHODS We used 2D-SDE to measure the efficiency of cDNA synthesis and its importance for the imprecision of an in vitro transcription–based microarray expression analysis. RESULTS The relative amount of double-stranded cDNA formed in replicate experiments that used the same RNA sample template was highly variable, ranging between 0% and 72% of the total DNA. Microarray experiments showed an inverse relationship between the difference between sample pairs in probe variance and the relative amount of dsDNA. Approximately 15% of probes showed between-sample variation (P < 0.05) when the dsDNA percentage was between 12% and 35%. In contrast, only 3% of probes showed between-sample variation when the dsDNA percentage was 69% and 72%. Replication experiments of the 35% dsDNA and 72% dsDNA samples were used to separate sample variation from probe replication variation. The estimated SD of the sample-to-sample variation and of the probe replicates was lower in 72% dsDNA samples than in 35% dsDNA samples. CONCLUSIONS Variation in the relative amount of double-stranded cDNA synthesized can be an important component of the imprecision in T7 RNA polymerase–based microarray expression analysis.


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