Identification of differentially expressed genes in lesional versus nonlesional skin of patients with atopic dermatitis by using high-throughput transcriptome-wide RNA sequencing

2019 ◽  
Vol 52 (10) ◽  
Keyword(s):  
Atopic Dermatitis ◽  
Rna Sequencing ◽  
Differentially Expressed Genes ◽  
High Throughput ◽  
Differentially Expressed

scholarly journals Comparison of the Transcriptomic Signatures in Pediatric and Adult CML

Cancers ◽  
2021 ◽  
Vol 13 (24) ◽  
pp. 6263
Author(s):  
Minyoung Youn ◽  
Stephanie M. Smith ◽  
Alex Gia Lee ◽  
Hee-Don Chae ◽  
Elizabeth Spiteri ◽  
...  
Keyword(s):  
Chronic Myeloid Leukemia ◽  
Rna Sequencing ◽  
Differentially Expressed Genes ◽  
High Throughput ◽  
Myeloid Leukemia ◽  
Differentially Expressed ◽  
Molecular Characteristics ◽  
Healthy Controls ◽  
Cd34 Cells ◽  
Transcriptomic Signature

Children with chronic myeloid leukemia (CML) tend to present with higher white blood counts and larger spleens than adults with CML, suggesting that the biology of pediatric and adult CML may differ. To investigate whether pediatric and adult CML have unique molecular characteristics, we studied the transcriptomic signature of pediatric and adult CML CD34+ cells and healthy pediatric and adult CD34+ control cells. Using high-throughput RNA sequencing, we found 567 genes (207 up- and 360 downregulated) differentially expressed in pediatric CML CD34+ cells compared to pediatric healthy CD34+ cells. Directly comparing pediatric and adult CML CD34+ cells, 398 genes (258 up- and 140 downregulated), including many in the Rho pathway, were differentially expressed in pediatric CML CD34+ cells. Using RT-qPCR to verify differentially expressed genes, VAV2 and ARHGAP27 were significantly upregulated in adult CML CD34+ cells compared to pediatric CML CD34+ cells. NCF1, CYBB, and S100A8 were upregulated in adult CML CD34+ cells but not in pediatric CML CD34+ cells, compared to healthy controls. In contrast, DLC1 was significantly upregulated in pediatric CML CD34+ cells but not in adult CML CD34+ cells, compared to healthy controls. These results demonstrate unique molecular characteristics of pediatric CML, such as dysregulation of the Rho pathway, which may contribute to clinical differences between pediatric and adult patients.

scholarly journals Identifying Candidate Genes for Hypoxia Adaptation of Tibet Chicken Embryos by Selection Signature Analyses and RNA Sequencing

Genes ◽  
2020 ◽  
Vol 11 (7) ◽  
pp. 823
Author(s):  
Xiayi Liu ◽  
Xiaochen Wang ◽  
Jing Liu ◽  
Xiangyu Wang ◽  
Haigang Bao
Keyword(s):  
Candidate Genes ◽  
Rna Sequencing ◽  
Differentially Expressed Genes ◽  
Gallus Gallus ◽  
Differentially Expressed ◽  
Tibet Plateau ◽  
Embryonic Liver ◽  
Selection Signature ◽  
Chicken Embryos ◽  
Hypoxia Adaptation

The Tibet chicken (Gallus gallus) lives on the Qinghai–Tibet Plateau and adapts to the hypoxic environment very well. The objectives of this study was to obtain candidate genes associated with hypoxia adaptation in the Tibet chicken embryos. In the present study, we used the fixation index (Fst) and cross population extended haplotype homozygosity (XPEHH) statistical methods to detect signatures of positive selection of the Tibet chicken, and analyzed the RNA sequencing data from the embryonic liver and heart with HISAT, StringTie and Ballgown for differentially expressed genes between the Tibet chicken and White leghorn (Gallus gallus, a kind of lowland chicken) embryos hatched under hypoxia condition. Genes which were screened out by both selection signature analysis and RNA sequencing analysis could be regarded as candidate genes for hypoxia adaptation of chicken embryos. We screened out 1772 genes by XPEHH and 601 genes by Fst, and obtained 384 and 353 differentially expressed genes in embryonic liver and heart, respectively. Among these genes, 89 genes were considered as candidate genes for hypoxia adaptation in chicken embryos. ARNT, AHR, GSTK1 and FGFR1 could be considered the most important candidate genes. Our findings provide references to elucidate the molecular mechanism of hypoxia adaptation in Tibet chicken embryos.

Identification of Differentially Expressed Genes in Atopic Dermatitis-Prone NC/Nga Mouse

2002 ◽  
pp. 379-383
Author(s):  
Itadaki Yamaguchi ◽  
Seiji Kawamoto ◽  
Tsunehiro Aki ◽  
Seiko Shigeta ◽  
Osamu Suzuki ◽  
...  
Keyword(s):  
Atopic Dermatitis ◽  
Differentially Expressed Genes ◽  
Differentially Expressed
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