Next generation sequencing in ZS rats
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ABSTRACT:
ORGANISM(S): Rattus norvegicus
SUBMITTER: Hai Lin
PROVIDER: E-GEOD-44375 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Purpose of the study: the goal of this study was to use Next-generation sequencing to investigate the gene expression profile of skeletal muscle from mice exposed to chemotherapy (Folfiri) for up to 5 weeks. Methods: Standard methods were used for polyA mRNA-seq library construction, EZBead preparation and Next-Gen sequencing, based on Life Technologies SOLiD5000xl system. Briefly, one microgram total RNA per sample was applied for library preparation. PolyA mRNA was first captured using the standard protocol of Dynabeads® mRNA DIRECT⢠Micro Kit (Life Technologies, #61021). Following the enrichment of polyA mRNA, the cDNA library was prepared and barcoded per sample using the standard protocol of SOLiD Total RNA-seq Kit (Life Technologies, #4445374). Each barcoded library was quantified by Bioanalyzer High Sensitivity DNA chip (Agilent, #5067-4626) and pooled in equal molarity. EZBead preparation, bead library amplification, and bead enrichment were then conducted using Life Technologies EZ Bead⢠E80 System (Life technologies, #4453095). Approximately four hundred forty million library-enriched beads per lane were deposited onto a SOLiD5500xl FlowChip (6 lanes/chip). Finally sequencing by ligation was carried out using standard single-read, 5â-3â strand-specific sequencing procedure (75b-read) on SOLiD5500xl Sequencer. The resulting 75 bp solid reads were mapped to Mus musculus mm9 reference genome using in-house mapping pipelines that utilizes bfast-0.7.0a [67]. In brief, using our RNA-seq pipeline, low quality reads and reads mapped to rRNA/tRNAs were first discarded. The remaining reads were mapped to reference genome mm9 and a splice-junction library, respectively; the genomic and splice-junction library mapping were merged at the end. The gene based expression levels were calculated using bamutils from NGSUtils based on the RefSeq gene annotation of mm9. Differential expression of genes across different treatments was determined with edgeR Results: Gene expression profiling, performed by means of RNA-Sequencing analysis, identified a limited number of genes that were significantly modulated (False Discovery Rate < 0.05) following Folfiri administration. Interestingly, the pathway analysis showed marked down-regulation of the regulators of mitochondrial metabolism Ucp1, Cidea1 and Acot2, as well as the marker of muscle cell proliferation/pluripotency Fhl3 . Further, we found increased expression of regulators of lipid metabolism and transport (such as Fabp1, Apoa1, Apob, Apoa2, Alb, Prkcz and Scd2) as well as acute phase response proteins (such as Alb, Fga and Fgb), and members of the PPAR signaling and markers of the Energy metabolism (such as Dnah5) were reported . Conclusions: Our study represents the first gene expression profiling of muscle from mice exposed to chemotherapy. The findings from our study identified several signaling pathways that were modulated following chemotherapy administration. These results will contribute to identify new modulators of muscle wasting associated with Folfiri administration, that might also represent putative new targets of interventions. Next-generation sequencing of RNA extracted from quadriceps muscle of CD2F1 male mice exposed to either Folfiri (a combination of 5-FU, Leucovorin and CPT-11) or vehicle alone (n=4) for up to 5 weeks.
2016-05-18 | E-GEOD-80473 | biostudies-arrayexpress
Project description:RNAPII is responsible for transcription of protein-coding genes and short, regulatory RNAs. In Saccharomyces cerevisiae, termination of RNAPII-transcribed RNAs ≤1000 bases requires the NNS complex (comprised of Nrd1, Nab3, and Sen1) processing by the exosome, and the nuclear specific catalytic subunit, Rrp6. It has been shown that Rrp6 interacts directly with Nrd1, but whether or not Rrp6 is required for NNS-dependent termination is unclear. Loss of Rrp6 function may result in extension (or inhibition of termination) of NNS-dependent transcripts, or Rrp6 may only function after the fact to carry out RNA 3’ end processing. Here, we performed in-depth differential expression analyses and compare RNA-sequencing data of transcript length and abundance in cells lacking RRP6 to previously published sequencing data measuring the length of RNAs in Nrd1-depleted cells. We find many transcripts that were defined as unterminated upon loss of Nrd1 activity are of similar length in rrp6Δ, and expression levels of downstream genes are significantly decreased. This suggests a similar transcription interference mechanism occurs in cells lacking either Nrd1 or Rrp6, supporting the hypothesis that Rrp6 activity is required for proper NNS termination in vivo. Four biological replicates each for deletion mutant (RRP6) and reference cells (WT)
2015-04-14 | E-GEOD-57155 | biostudies-arrayexpress
Project description:Next generation sequencing in a rat model of diabetic nephropathy was employed to study in depth the pathogenic alterations involved in progressive diabetic kidney damage. We employed the obese, diabetic ZS rat, a model that develops renal failure and fibrosis, the hallmarks of human disease. We then used RNA-seq to examine in a comprehensive manner the combined effects of renal cells and infiltrating inflammatory cells acting as a pathophysiological unit.
2014-02-06 | GSE44375 | GEO
Project description:Embryonic stem cells are maintained in a self-renewing and pluripotent state by multiple regulatory pathways. Pluripotent-specific transcriptional networks are sequentially reactivated as somatic cells reprogram to achieve pluripotency. How epigenetic regulators modulate this process and contribute to somatic cell reprogramming is not clear. Here we perform a functional RNAi screen to identify the earliest epigenetic regulators required for reprogramming. We identify components of the SAGA histone acetyltransferase complex, in particular Gcn5, as critical regulators of reprogramming initiation. Furthermore, we show in mouse pluripotent stem cells that Gcn5 strongly associates with Myc and that upon initiation of somatic reprogramming, Gcn5 and Myc form a positive feed forward loop that activates a distinct alternative splicing network and the early acquisition of pluripotency-associated splicing events. These studies expose a Myc-SAGA pathway that drives expression of an essential alternative splicing regulatory network during somatic cell reprogramming. Examination of expression level changes at D0 and D2 MEFs
2015-04-15 | E-GEOD-67715 | biostudies-arrayexpress
Project description:Small molecule inhibitors of mitochondrial electron transport chain (ETC) hold significant promise in the field of mitochondrial research and aging biology. In this study, we studied two molecules: mycothiazole (MTZ) - isolated from the marine sponge P. mycofijiensis and its semisynthetic acetylated derivative 8-O-acetylmycothiazole (8-OAc) as efficient alternatives for their high efficiency to inhibit ETC complex I function. Similar to rotenone, a widely used complex I inhibitor, these two compounds showed anticancer activity and strikingly demonstrate a lack of toxicity to non-cancer cells, a highly beneficial feature in the development of anti-cancer therapeutics. Furthermore, experiments with these small molecules in vivo utilizing C.elegans demonstrate their additional utilization to aging studies. We observed that both molecules have the ability to induce a mitochondria-specific unfolded protein response (UPRMT) pathway, which extends lifespan of worms when applied in their adult stage. Interestingly, we also found that these two molecules employ different pathways to extend lifespan in worms, where MTZ utilize the transcription factors, ATFS-1 and HSF-1, which are involved in the UPRMT and heat shock response (HSR) pathways, respectively. In opposition,8-OAc only required HSF-1 and not ATFS-1. This observation elucidates an important insight into the functional roles of various protein subunits of ETC complexes and their regulatory mechanisms associated with aging.
2024-01-01 | E-MTAB-13546 | biostudies-arrayexpress
Project description:The purpose of the study was to determine the potential role of ATF4 in gene regulation by brain derived neurotrophic factor (BDNF). To achieve this, we compared gene regulation by BDNF in cultured rat hippocampal neurons with or without prior ATF4 knockdown with shRNA. We surveyed cultures after 0,2,4,8 and 16 hrs of exposure to BDNF.
2017-09-09 | E-MTAB-6046 | biostudies-arrayexpress
Project description:In diabetes, the kidney contributes to the development of diabetic hyperglycemia by increasing glucose reabsorption from the primary urine and by upregulating gluconeogenesis in the proximal tubule. However, these two processes are also controlled by the circadian clock, a mechanism that synchronizes a large number of specific renal functions with environmental daily cycles. Here, we investigated the (patho)physiological role of intrinsic renal tubule circadian clocks in the diabetic kidney. We demonstrate that diabetic mice devoid of the circadian transcriptional regulator BMAL1 in the renal tubule exhibit additional enhancement of renal gluconeogenesis, exacerbated hyperglycemia, increased glucosuria, polyuria and renal hypertrophy. Collectively, our results suggest that diabetic hyperglycemia can be worsened by dysfunction or misalignment of intrinsic renal circadian clocks.
2022-05-27 | GSE178319 | GEO
Project description:OVE26 mouse was chosen to study the progressive changes in renal gene expression because it displays the most advanced albuminuria mouse models that assembles advanced human diabetic nephropathy. OVE26 mice induce inflammatory gene expression changes consistent with advanced renal disease, associated with severe albuminuria and not reported in any other diabetic models. They provide the first opportunity in a model of diabetic nephropathy to assess the effect of induction of inflammatory proteins that have been implicated in renal injury. Microarray expression was performed on whole kidney from control and diabetic mice at 2, 4 and 8 months of age and validated by rtPCR, in situ hybridization or immunohistochemistry.
2010-04-06 | E-GEOD-20636 | biostudies-arrayexpress
Project description:Mechanical stress is a measure of internal resistance exhibited by a body or material when external forces, such as compression, tension, bending, etc. are applied. The study of mechanical stress on health and aging is a continuously growing field, as major changes to the extracellular matrix and cell-to-cell adhesions can result in dramatic changes to tissue stiffness during aging and diseased conditions. For example, during normal aging, many tissues including the ovaries, skin, blood vessels, and heart exhibit increased stiffness, which can result in a significant reduction in function of that organ. As such, numerous model systems have recently emerged to study the impact of mechanical and physical stress on cell and tissue health, including cell-culture conditions with matrigels and other surfaces that alter substrate stiffness and ex vivo tissue models that can apply stress directly to organs like muscle or tendons. Here, we sought to develop a novel method in an in vivo, model organism setting to study the impact of mechanical stress on aging, by increasing substrate stiffness in solid agar medium of C. elegans. To our surprise, we found shockingly limited impact of growth of C. elegans on stiffer substrates, including limited effects on cellular health, gene expression, organismal health, stress resilience, and longevity. Overall, our studies reveal that altering substrate stiffness of growth medium for C. elegans have only mild impact on animal health and longevity; however, these impacts were not nominal and open up important considerations for C. elegans biologists in standardizing agar medium choice for experimental assays.
2024-04-05 | E-MTAB-13938 | biostudies-arrayexpress
Project description:Diabetic nephropathy (DN) is the leading cause of chronic kidney disease and end-stage renal disease. Emerging evidence suggests that complement activation is involved in the pathogenesis of DN. The aim of this study was to investigate the pathogenic role of C3a and C3a receptor (C3aR) in DN. The expression of C3aR was examined in the renal specimen of DN patients. Using a C3aR gene knockout mice (C3aR-/-), we evaluated kidney injury in diabetic mice. The mouse gene expression microarray was performed to further explore the pathogenic role of C3aR. Then the underlying mechanism was investigated in vitro with macrophage treated with C3a. Compared with normal controls, the renal expression of C3aR was significantly increased in DN patients. C3aR-/- diabetic mice developed less severe diabetic renal damage compared with WT diabetic mice, exhibiting significantly lower level of albuminuria and milder renal pathological injury. Microarray profiling uncovered significantly suppressed inflammatory responses and T cell adaptive immunity in C3aR-/- diabetic mice compared with WT diabetic mice and this result was further verified by immunohistochemical staining of renal CD4+, CD8+ T cells and macrophages infiltration. In vitro study demonstrated C3a can enhance macrophages secreted cytokines which could induce inflammatory responses and differentiation of T cell lineage. In conclusion, C3aR deficiency could attenuate diabetic renal damage through suppressing inflammatory responses and T cell adaptive immunity, possibly by influencing macrophages secreted cytokines. Thus, C3aR may be a promising therapeutic target for DN.
2020-04-10 | GSE133597 | GEO