A genetic porcine model of cancer
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina HiSeq 2000
ORGANISM(S): Sus scrofa
SUBMITTER: Kyle Schachtschneider
PROVIDER: E-MTAB-3382 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:We sequenced the whole mRNA of six pig (Sus scrofa) fat, liver and muscle tissues, generating a total of 1.3 billion short reads with 90-bp pair-end sequences from 24 samples. Comparing with current genome annotation, we identified 32,361 unigene clusters spanning 51.83 Mb that contained 11,933 (36.87%) annotated genes. More than 60% (20,428) unigene clusters did not match any current equine gene model. We identified 189,973 single nucleotide variations (SNVs) from the aligned sequences against the horse reference. Most SNVs (171,558 SNVs; 90.31%) were novel compared with over 1.1 million equine SNPs from two databases. Some genes have significantly different expression levels under different environment. We define those identical genes which have different expression levels are ‘differentially expressed’ and carried out differentially expressed gene analysis before and after exercise conditions. We discovered, 62 up- and 80 down-regulated genes in the blood and 878 up- and 285 down-regulated genes in the muscle from the 24 samples. Six out of 28 previously exercise-related known genes, HIF1A, ADRB2, PPARD, VEGF, TNC, and BDNF, were highly expressed in the muscle after exercise. We discovered 56 functionally unknown transcription factors that are probably associated with an early regulatory exercise mechanism from 91 differentially expressed transcription factors. We found interesting RNA expression patterns where different alternative splicing forms of the same gene showed reversed expressions before and after exercising. whole mRNA sequencing profiles of six pig (Sus scrofa) fat, liver and muscle tissues
2014-09-01 | E-GEOD-45204 | biostudies-arrayexpress
Project description:Purpose: Next-generation sequencing (NGS) was used to select genes potentially associated with fiber-type distribution and cell size in porcine muscle tissue. Methods: The histological profile of the longissimus lumborum muscle was establish by method involving detection of NADPH dehydrogenase (diaphorase) and immunohistochemically detection of myosin chains. The muscle transcriptome sequencing was performed for 11 pigs using Illumina HiScan SQ in 50 single-end cycles. The quantifying transcript abundances was made using the RSEM supported by STAR aligner. The raw reads were aligned to the Sus scrofa reference genome (assembly Sscrofa10.2). Differentially expressed genes were detected by edgeR, baySeq and DESeq2. The RNA-seq results were validated using by qPCR. Results: The RNA-seq approach allows to identify 397 differentially expressed genes (DEGs) indicated as significant (FDR<0.05) using three software: DESeq2, edgeR and baySeq. Detected genes and pathways deregulated in muscle depend on tissue microstructure were associated with metabolic processes â?? 158 genes; cellular processes â?? 122; biological regulation â?? 62; localization â?? 51 and 35 genes with developmental processes. The detected DEGs were included in such pathways as: PI3K-Akt; FoxO and MAPK signaling pathways, regulation of actin cytoskeleton, lysine degradation and insulin signaling pathway as well as in mTOR and Hippo signaling. Conclusions: This results highlight the mainly metabolic pathways related with glucose metabolism and contraction processes of muscle cells. The comparison of whole gene expression profiles between muscles characterized by different fiber-type distribution showed that processes of growth and proliferation of different fiber types are determined by diverse molecular mechanism, which conditioned the unique histological structure of muscle tissue. The muscle (longissimus lumborum) transcriptome sequencing was performed for 11 pigs using Illumina HiScan SQ in 50 single-end cycles and in five technical repetitions.
2015-12-06 | E-GEOD-75493 | biostudies-arrayexpress
Project description:To optimize the genome annotation, nine tissue and one pool RNA libraries (i.e. heart, liver, spleen, lung, kidney, muscle, fat, ovary, pool.) were constructed using the Illumina mRNA-spleeneq Prep Kit We sequenced nine tissues and one pool using illumina Hiseq 2500 platform
2016-07-05 | E-GEOD-77776 | biostudies-arrayexpress
Project description:Myocardial infarction (MI) is the leading cause for hear failure (HF). Following MI, the non-infarcted region of left ventricle (LV) is critical for maintaining heart function, and disruption of the LV contributes greatly to post-MI HF. Transcriptomic profiling by high-throughput sequencing was performed in a chronic HF pig model, to explore the molecular changes in the post-MI LV related to cardiovascular deterioration. Samples were taken from heart tissue of MI-induced pigs and from control pigs not subjected to MI. Regions of the heart where samples were taken included the site of ischemia (LV ischemia), area bordering ischemia (LV border), area remote to ischemia (LV remote) and the right ventricle (RV).
2021-10-04 | E-MTAB-8856 | biostudies-arrayexpress
Project description:We report gene expression of Treg cells isolated from injured muscle in IL-33 vs PBS treated mice. Male Foxp3-GFP C57BL/6 reporter (2 months old) mice were injured intramuscularly with cardiotoxin/rIL-33 (0.3 ug/muscle). Tregs were sorted directly into Trizol from injured muscle 4 days post-injury. Gene expression profiling of muscle Tregs from IL-33 vs PBS injured mice.
2016-01-12 | E-GEOD-76722 | biostudies-arrayexpress
Project description:Abstract; Background: Gene transfer by electroporation (electro gene transfer) to muscle results in high level long term transgenic expression, showing great promise for treatment of e.g. protein deficiency syndromes. However little is known about the effects of electro gene transfer on muscle fibres. We have therefore investigated transcriptional changes through gene expression profile analyses, as well as morphological changes evaluated by histological analysis. Electro gene transfer was obtained using a combination of a short high voltage pulse (HV, 1000 V/cm, 100 @s) followed by a long low voltage pulse (LV, 100 V/cm, 400 ms); a pulse combination optimised for efficient and safe gene transfer. Muscles were transfected with green fluorescent protein (GFP) and excised at 4 hours, 48 hours or 3 weeks after treatment. Results: Differentially expressed genes were investigated by microarray analysis, and descriptive statistics were performed to evaluate the effects of 1) electroporation, 2) DNA injection, and 3) time after treatment. The biological significance of the results was assessed by gene annotation and supervised cluster analysis. Generally, electroporation caused down-regulation of structural proteins e.g. sarcospan and catalytic en-zymes such as phosphoenolpuryvate carboxykinase. Injection of DNA induced down-regulation of intracellular transport proteins e.g. sentrin. The effects on muscle fibres were transient as the expression profiles 3 weeks after treatment were closely related with the control muscles. Most interestingly, no changes in the expression of proteins involved in inflammatory responses or muscle regeneration was detected, indicating limited muscle damage and regeneration. Histological analysis revealed structural changes with loss of cell integrity and striation pattern in some fibres after DNA+HV+LV treatment, while electroporation alone caused minor loss of striation pattern but preservation of cell integrity. Conclusion: The small and transient changes found in the gene expression profiles are of great importance, as this demonstrates that electro gene transfer is safe with minor effects on the muscle host cells. These findings are essential for introducing the electro gene transfer to muscle for clinical use. Indeed the HV+LV pulse combination used have been optimised to ensure highly efficient and safe electro gene transfer. Experiment Overall Design: The mice did recieve to their tibialis cranialis muscle either No tretment/control (CTRL), Electroporation only (EP), Plasmid injection only (DNA) or Plasmid DNA and in vivo Electro gene transfer (EP+DNA). Experiment Overall Design: Four hrs, 48 hrs and 3 weeks after treatment the mice were euthanized and the expression profile of the treated muscles were analysed. Experiment Overall Design: The following number of mice were included: Experiment Overall Design: CTRL, 3 mice, Experiment Overall Design: EP at 4 hrs, 1 mouse, Experiment Overall Design: EP at 48 hrs, 1 mouse, Experiment Overall Design: EP at 3 weeks, 1 mouse, Experiment Overall Design: DNA at 4 hrs, 1 mouse, Experiment Overall Design: DNA at 48 hrs, 1 mouse, Experiment Overall Design: DNA at 3 weeks, 1 mouse, Experiment Overall Design: EP+DNA at 4 hrs, 2 mice, Experiment Overall Design: EP+DNA at 48 hrs, 1 mouse, Experiment Overall Design: EP+DNA at 3 weeks, 1 mouse. Experiment Overall Design: A total number of mice 13.
2009-04-23 | E-GEOD-6686 | biostudies-arrayexpress
Project description:Endoplasmic reticulum (ER) and oxidative stress are two related phenomena that have important metabolic consequences. As many skeletal muscle diseases are triggered by oxidative stress, we explored the chain of events linking a hyper oxidized ER (which causes ER and oxidative stress) with skeletal muscle dysfunction. Using exon expression arrays we show that the combined genetic modulation of the two master ER redox proteins, selenoprotein N (SEPN1) and endoplasmic oxidoreductin 1 (ERO1), leads to an SEPN1-related myopathic phenotype due to excessive signalling of transforming growth factor (TGF)-beta. One-month-old WT and SEPN1 KO mice were intramuscularly injected with AAV2/1-ERO1a (an adeno-associated virus driving ERO1a) in three sites of the right gastrocnemius muscle and vehicle alone was injected into the contralateral muscle. The animals were sacrificed four-six weeks after injection and total RNA was isolated from muscle tissues using the RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions. Genechip Mouse Gene 2.1 ST arrays (Affymetrix) were used for whole genome gene-expression analysis of duplicated samples derived from WT and SEPN1 KO mice in presence of either ERO1 or PBS.
2016-10-01 | E-MTAB-4933 | biostudies-arrayexpress
Project description:Despite the advanced understanding of disease mechanisms, the current therapeutic regimens fail to cure most patients with acute myeloid leukemia (AML). In the present study, we address the role of protein synthesis control in leukemia function and leukemia propagation. Using a transgenic eIF6 mouse strain that permits inducible and graded regulation of ribosomal subunit joining, we have generated a murine model of MLL-AF9 acute myeloid leukemia where the expression of transgenic eIF6 is doxycycline-inducible. Using this model system, we have performed scRNA-seq expression analysis to study the impact of eIF6 overexpression on leukemia cell function. scRNA-seq was performed using the 10x Chromium Next GEM Single Cell 3ʹ platform. BM cells were harvested from leukemia-engrafted mice that were administered doxycycline for six days and viable GFP+ leukemia cells were sorted into PBS containing 0.05 % BSA following the manusfacturer’s protocol. 5 samples: 2 control and 3 eIF6 overexpression.
2024-10-10 | E-MTAB-13567 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
2013-12-11 | E-GEOD-49018 | biostudies-arrayexpress
Project description:Utilizing glycerol intramuscular injections in M. musculus provide a models of skeletal muscle damage followed by skeletal muscle regeneration. In particular, glycerol-induced muscle injury triggers accute activation of skeletal muscle stem cells, called satellite cells. However, aging dramatically impairs the regenerative capacity of satellite cells. We characterized genome-wide expression profiles of young and old satellite cells in the non-proliferative and activated state, freshly isolated to non-injured or damaged muscles, respectively. Our goal was to uncover new regulatory signaling specific to satellite cells entry into the activation and myogenic program that are affected with age. Satellite cells were isolated in either quiescent / non-proliferative or activated state from uninjured or 3 days after glycerol-induced injury of tibialis anterior, gastrocnemius and quadriceps, respectively. Young (2-4 months old) and old (20-24 months old) wildtype C57BL/6J male were used, with five to six biological replicates per group.
2016-07-04 | E-GEOD-81096 | biostudies-arrayexpress