Similar Datasets
Project description:we performed whole heart proteomic analyses in both WT and NDUFS4 heart-specific cKO mice (n = 5 mice/group).
2023-06-01 | PXD036399 | Pride
Project description:Purpose: Purpose: we used next generation sequencing to analyze gene expression profiles of pancreatic tissues from wild-type (WT) and miR-21-/- (miR-21 KO) mice treated with saline(control) or caerulein. The goals of this study are to compare the different gene expression profiles of pancreatic tissue between WT and miR-21 KO mice treated with caerulein. Methods: Female WT and miR-21 KO mice were administered 8-hourly intraperitoneal injection of 50μg/kg caerulein. Mice were sacrificed at 24 hours after the first caerulein injection and total RNA was extracted. mRNArna profiles were generated by deep sequencing WT treated with saline in single, WT treated with caerulein in duplicate, miR-21KO treated with caerulein in duplicate, using High-seq 2000 Illumina sequencing platform. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays Results: After quality filtering of raw sequencing data, we obtained 32,797,327 (69.9%) out of 46,941,672 tags from WT mice treated with saline, 42,587,312 (87.1%) out of 48,919,213 tags from WT mice treated with caerulein, and 57,139,408 (85.1%) out of 67,111,415 tags from miR-21 KO mice treated with caerulein. We then mapped these tags to the mouse genome. We identified 1457 differential expressed genes (DEGs) between WT mice treated with caerulein and with saline, and 152 genes between WT mice and miR-21 KO mice treated with caerulein with a fold change more than 2.0 (up-regulation) or less than 0.5 (down-regulation). Altered expression of 16 genes was confirmed with qRT-PCR. Conclusions: Our study represents the first detailed analysis of pancreatic transcriptomes generated by RNA-seq technology. By using RNA-seq based transcriptome analysis, we identified 6 miR-21 target genes and 10 downregulated genes involved in pancreatic injury. Specifically, up-regulation of Pias3 and down-regulation of Hmgb1 when miR-21 was ablated coincided with reduced pancreatitis severity. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex pancreatic functions.
2017-11-07 | GSE106550 | GEO
Project description:Purpose: The purpose of this study was to compare the hepatic transcriptome in the control group and severe acute pancreatitis, in order to identify metabolic gene changes during pancreatitis. Methods: 6-week Balb/c mice were subjected to control (Saline*12) and SAP (caerulein *12), and mice liver tissues were harvested at 24 hours for RNA preparation (n=6 each group). Results: Among 18257 mapped genes, 3639 differentially expressed genes were identified by RNA-seq, including 1714 genes induced in SAP compare to Control and 1892 genes down regulated in SAP compare to Control. The genes up regulated were mainly related to immune response and ER stress, while genes that down regulated were associated with fatty acids oxidation and oxidative phosphorylation. Conclusions: Our study revealed that in SAP, genes associated with immune response are upregulated in liver, fatty acid oxidation related genes are downregulated in liver. Our data revealed the crosstalk between pancreas and liver, illustrated the change of liver metabolism in SAP.
2022-04-06 | GSE183158 | GEO
Project description:Pancreatic ductal adenocarcinoma (PDA) is the devastating disease in urgent need to identify new strategies for diagnosing and treating. Chronic pancreatitis is a risk factor for PDA in humans. Nardilysin (Nrdc, NRDC), a zinc peptidase of the M16 family has been shown to promote cancer cell growth in vitro. Here, we report that pancreatic deletion of Nrdc dramatically accelerates formation of pancreatic intraepithelial neoplasia (PanIN) and invasive PDA in the presence of oncogenic Kras. Nrdc was expressed in the nucleus of pancreatic acinar cells and pancreatic deletion of Nrdc was dispensable for pancreatic development in mice, but led to spontaneous chronic pancreatitis concomitant with acinar-to-ductal conversion, fibrotic change, infiltrated inflammatory cells, increased apoptosis, and atrophic pancreas in adult mice. Ex vivo acinar cell explants culture experiments showed that acinar-to-ductal conversion was not induced through a cell autonomous mechanism and that expression of several chemokines, including Cxcl10, was markedly up-regulated in Nrdc-null pancreatic acinar cells. Microarray analysis revealed that pathways implicated in pancreatitis and tumorigenesis, including chemotaxis, NF-κB and Erk1/2 signaling, were up-regulated in Nrdc-cKO pancreata compared with WT controls. Finally, immunostaining for NRDC revealed absence of NRDC expression in a subset of human PanINs and PDAs. These data demonstrate a previously unappreciated tumor suppressive function of Nrdc in the pancreas through suppressing chronic pancreatitis with acinar-to-ductal conversion in mice.
2017-05-31 | GSE99438 | GEO
Project description:Purpose: The purpose of this study was to compare the hepatic transcriptome in the control group, acute pancreatitis, and severe acute pancreatitis, in order to identify metabolic gene changes during pancreatitis. Methods: 6-week Balb/c mice were subjected to AP (caerulein), SAP (caerulein and LPS) and control (saline), and mice liver tissues were harvested at 24 hours for RNA preparation (n=8 each group). Results: Among 11952 mapped genes, 8977 differentially expressed genes were identified by RNA-seq, including 351 genes induced in AP compare to Control and 5249 genes down regulated in SAP compare to AP. The genes up regulated were mainly related to fatty acid oxidation and ketone body synthesis especially Cpt2 and Acadvl, while genes that down regulated were associated with energy metabolism and inflammation. The overlap of two gene sets were 96 genes that involved in fatty acid metabolism. Conclusions: Our study revealed that in AP, genes associated with ketone body synthesis are upregulated in liver, in SAP, fatty acid oxidation related genes are downregulated in liver. Our data revealed the crosstalk between pancreas and liver, illustrated the difference of metabolism in AP and SAP.
2022-04-06 | GSE151927 | GEO
Project description:Analysis of germinal center B cells derived from WT and SAP-deficient mice revealed that SAP-deficient mice have reduced Myc signature
2019-12-28 | GSE142640 | GEO
Project description:Purpose: To fully realize the potential molecular mechanism that S100A14 deficiency enhances esophageal carcinogenesis Methods: Total RNA of esophageal tumors in 4NQO WT and 4NQO S100A 14 CKO group mice was extracted with TRIzol Reagent. RNA libraries were constructed using an Illumina TruSeq RNA Sample Preparation kit according to the manufacturer’s protocol. A total of 150 base paired-end reads were sequenced using the Novaseq 6000 S4 platform. The read alignment was conducted using TopHat 2.0.13, and relative transcript abundances and differentially expressed genes were determined using the DESeq R package. Results: We identified 14,157 transcripts in esophageal tumors of 4NQO WT and 4NQO S100A14 CKO group mice. Approximately 8% of the transcripts showed differential expression between the esophageal tumors of 4NQO WT and 4NQO S100A 14 CKO group mice, with a fold change ≥1.0 and p value <0.05. Conclusions: Our study represents the first analysis of esophageal tumors derived from S100A14 CKO mice with biologic replicates, generated by RNA-seq.
2022-07-07 | GSE200772 | GEO
Project description:Purpose: We compared the transcriptomes of mouse CD4 T cells lacking the vhl gene ( vhlfl/fl cd4 cre= vhl cKO) with WT controls from the lungs of mice 8 weeks after aerosol infection with Mycobacterium tuberculosis. Results: Using an optimized data analysis workflow, between 40-55 million sequence reads per sample to the mouse genome (build mm10) and identified 14700 transcripts in the CD4 T cells of WT and mutant mice after performing HISAT2 alignements to the mm10 reference. Conclusion: The transcriptome of WT anf vhl cKO was compared. Groups did cluster differentially with regards to their transcript abundance. The WT group has enriched DNA synthesis/ proliferation pathways whereas the Vhl cKO was enriched in hypoxia pathways. Transcripts assocaited with T cell differentiation were increased in WT group while T cell inhibitory molecules was elevated in the transcriptome of vhl cKO CD4 T cells.
2022-06-01 | GSE190909 | GEO
Project description:Severe acute pancreatitis (SAP) is the most serious type of pancreatitis with high morbidity and mortality. The underlying mechanism behind SAP pathogenesis is complex and remains elusive. In the present study, next-generation RNA sequencing was utilized to identify circRNA transcripts in the pancreatic tissues from three SAP mice and three matched normal tissues. Our results discovered that 56 circRNAs were differently expressed in SAP compared with normal control. Our findings may provide novel insights for pathophysiological mechanism of SAP and offer novel targets for SAP.
2020-02-19 | GSE139173 | GEO
Project description:Mice knocked-out or wild type for the NAPE PLD gene specifically in adipose tissue, were recruited for this expression profiling experiment. Each group of mice (WT versus cKO) were fed with a control diet or a high fat diet. Then mice were sacrificed and adipose tissue samples form the subcutaneous adipose tissue were processed for RNA extraction. Total RNA of each sample was then pooled with those of the same group and treatment for microarray hybridization.
2015-03-06 | GSE56852 | GEO