Genome-wide maps of gene expression in liver of alkaline sphingomyelinase knockout mice
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ABSTRACT:
PROVIDER: PRJNA527215 | ENA |
REPOSITORIES: ENA
Dataset's files
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| SRR8732813.fastq.gz | Fastqsanger.gz | |||
| SRR8732814.fastq.gz | Fastqsanger.gz | |||
| SRR8732815.fastq.gz | Fastqsanger.gz | |||
| SRR8732816.fastq.gz | Fastqsanger.gz | |||
| SRR8732817.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Genome-wide maps of gene expression in alkaline sphingomyelinase knockout mice
| PRJNA471908 | ENA
Project description:Intestinal alkaline sphingomyelinase (alk-SMase) generates ceramide and inactivates platelet-activating factor and associated with digestion and inhibition of cancer. There is few study to analyze the correlated function and characterize the genes related to alk-SMase comprehensively. In this work, deep RNA sequencing was performed to investigate the function of alk-SMase. Our RNA-seq data found 239 differentially expressed mRNAs between the wild type (WT) mice and alk-SMase (gene NPP7) knockout (KO) mice, in which 73 were significantly up-regulated and 166 were down-regulated, including protein coding genes, non-coding RNAs. Notably, the results of gene ontology functional enrichment analysis indicated that differentially expressed genes were functionally associated with the immune response, regulation of cell proliferation and development related terms using DAVID. Additionally, an integrated PPI and KEGG network was chose to study the relationship of differentially expressed genes, it was shown that some modules was significantly related to alk-SMase and with accordance of previously results. We chose 6 of these genes randomly were validated the accuracy of RNA-seq technology using quantitative real-time polymerase chain reaction (qPCR) and 2 genes showed difference significantly (P<0.05).
2020-01-01 | GSE128349 | GEO
Project description:Intestinal alkaline sphingomyelinase (alk-SMase) generates ceramide and inactivates platelet-activating factor and associated with digestion and inhibition of cancer. There is few study to analyze the correlated function and characterize the genes related to alk-SMase comprehensively. In this work, deep RNA sequencing was performed to investigate the function of alk-SMase. Our RNA-seq data found 239 differentially expressed mRNAs between the wild type (WT) mice and alk-SMase (gene NPP7) knockout (KO) mice, in which 73 were significantly up-regulated and 166 were down-regulated, including protein coding genes, non-coding RNAs. Notably, the results of gene ontology functional enrichment analysis indicated that differentially expressed genes were functionally associated with the immune response, regulation of cell proliferation and development related terms using DAVID. Additionally, an integrated PPI and KEGG network was chose to study the relationship of differentially expressed genes, it was shown that some modules was significantly related to alk-SMase and with accordance of previously results. We chose 6 of these genes randomly were validated the accuracy of RNA-seq technology using quantitative real-time polymerase chain reaction (qPCR) and 2 genes showed difference significantly (P<0.05).
2019-01-01 | GSE114608 | GEO
Project description:Alkaline sphingomyelinase (alk-SMase) is phospholipase that creates ceramides and inactivates platelet activating factors during metabolism, and is linked to digestion and cancer prevention. There have been few studies that completely investigate the linked function and identify the genes related to alk-SMase. In this work, RNA sequencing was performed to investigate the function of alk-SMase. Using RNA-seq data, we discovered 95 differentially expressed genes in the liver of wild type (WT) mice and alk-SMase (gene NPP7) knockout (KO) mice. Differentially expressed genes were functionally associated with the inflammatory response, steroid metabolic process and TNF signaling pathway related terms, regulation of carbohydrate biosynthetic process, and Cytochrome P450-arranged by substrate type using Metascape, according to the results of gene ontology functional enrichment analysis. In addition, an integrated PPI and KEGG network was used to investigate the relationship of differentially expressed genes, It was discovered that one module, which contained 21 nodes and 23 interactions, was significantly related to Cytochrome P450 family, which as mediator of phospholipase. To corroborate the RNAseq results, we identified 12 important genes with high expression levels and significant differences in RNAseq for quantitative real-time polymerase chain reaction (qPCR) verification; 7 genes showed difference significantly (P < 0.05). Our research is the first to conduct a comprehensive genome-wide analysis of the alk-SMase knockout model. Alk-SMase is involved in sphingomyelin hydrolysis. In liver tissues lacking alk-SMase expression, the expression levels of seven genes, including Cyp4a14 and Cyp4a10, were altered.
| S-EPMC8961189 | biostudies-literature
Project description:The purpose of this protocol is to develop a detailed MRI technique and haemodynamic maps enabling early detection of colorectal metastases in the liver.
| 2037102 | ecrin-mdr-crc
Project description:Purpose: The goals of this study are to compare next generation sequencing-derived brain cortex transcriptome profiling (RNA-seq) to study the role of neutral sphingomyelinase 2 (smpd3) in brain aging. Methods: Brain cortex mRNA profiles of 10 month old (fro/+) and smpd3 total knockout (fro/fro) mice were generated by deep sequencing, in duplicate, using Illumina NovaSeq 6000. (https://en.novogene.com) Results:A total of 1462 transcripts differed between genotypes, with 891 transcripts increased and 571 transcripts decreased. Conclusions: Transcriptome differences link decreased oxidative stress and astrocyte activation in brain cortex to nSMase2 deficiency, while synaptic signaling transcripts increased in ways consistent with increased cognitive function previously demonstrated in nSMase2-deficient mice.
2022-04-27 | GSE179045 | GEO
Project description:Alkaline sphingomyelinase (alk-SMase) hydrolyses sphingomyelin (SM) to ceramide in the gut. To evaluate the physiological importance of the enzyme, we generated alk-SMase knockout (KO) mice by the Cre-recombinase-Locus of X-over P1(Cre-LoxP) system and studied SM digestion. Both wild-type (WT) and KO mice were fed ³H-palmitic acid labeled SM together with milk SM by gavage. The lipids in intestinal content, intestinal tissues, serum, and liver were analyzed by TLC. In KO mice, nondigested ³H-SM in the intestinal content increased by 6-fold and the formation of ³H-ceramide decreased markedly, resulting in 98% reduction of ³H-ceramide/³H-SM ratio 1 h after gavage. The absorbed ³H-palmitic acid portion was decreased by 95%. After 3 h, a small increase in ³H-ceramide was identified in distal intestine in KO mice. In feces, ³H-SM was increased by 243% and ceramide decreased by 74% in the KO mice. The KO mice also showed significantly decreased radioactivity in liver and serum. Furthermore, alkaline phosphatase activity in the mucosa was reduced by 50% and histological comparison of two female littermates preliminarily suggested mucosal hypertrophy in KO mice. This study provides definite proof for crucial roles of alk-SMase in SM digestion and points to possible roles in regulating mucosal growth and alkaline phosphatase function.
| S-EPMC3284167 | biostudies-literature
Project description:Lotus japonicus is a model legume broadly used to study transcriptome regulation under different stress conditions and microorganism interaction. Understanding how this model plant respond gainst alkaline stress will certainly help to develop more tolerant cultivars in economically important Lotus species as well as in other legumes. In order to uncover the most important response mechanisms activated during alkaline stress, we explored by microarray analysis the transcriptome regulation occurring in the phenotypically contrasting ecotypes MG-20 and Gifu B-129 of L. japonicus after 21 days of alkaline stress.
2014-03-25 | E-MTAB-2418 | biostudies-arrayexpress
Project description:To investigate the rapid adaptation mechanism of Bacillus thuringiensis in an alkaline environment, we have employed whole genome microarray expression profiling as a discovery platform to identify the difference of gene expression between normal condition and alkaline condition.
2024-06-24 | GSE270261 | GEO
Project description:Alkaline sphingomyelinase (alk-SMase) is expressed in the intestine and human liver. It may inhibit colonic tumorigenesis, and loss of function mutations have been identified in human colon cancer. The present study investigates its expression in human liver cancer. In HepG2 liver cancer cells, RT-PCR identified three transcripts with 1.4, 1.2 and 0.4 kb, respectively. The 1.4 kb form is the wild-type cDNA with five translated exons, the 1.2 kb product lacks exon 4 and the 0.4 kb form is a combination of exons 1 and 5. Genomic sequence showed that these aberrant transcripts were products of alternative splicing. Transient expression of the 1.2 kb form showed no alk-SMase activity. In HepG2 cells, the alk-SMase activity is low in monolayer condition and increased with cell polarisation. Coexistence of 1.4 and 1.2 kb forms was also identified in one hepatoma biopsy. GenBank search identified a cDNA clone from human liver tumour, which codes a protein containing full length of alk-SMase plus a 73-amino-acid tag at the N terminus. The aberrant form was translated by an alternative starting codon upstream of the wild-type mRNA. Expression study showed that linking the tag markedly reduced the enzyme activity. We also analysed human liver biopsy samples and found relatively low alk-SMase activity in diseases with increased risk of liver tumorigenesis. In conclusion, expression of alk-SMase is changed in hepatic tumorigenesis, resulting in loss or marked reduction of the enzyme function.
| S-EPMC2360232 | biostudies-literature