Muscle Transcriptomic Circuits Linked to Periarticular Physiology in End-Stage Osteoarthritis.
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE205431 | GEO | 2022/12/28
REPOSITORIES: GEO
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Project description:To test the hypothesis that different muscles may express variable amounts of different isoforms of muscle genes, we applied a custom-designed exon microarray containing probes for 57 muscle-specific genes to assay the transcriptional profiles in sets of human adult, lower limb skeletal muscles. Muscle biopsies from 15 individuals were selected for analysis dissected from 21 anatomically different muscles collected from eight men and seven women, ranging from 61 to 91 years The muscle tissue samples collected included samples from 11 different thigh muscles––vastus medialis, vastus lateralis, vastus intermedialis, sartorius, gracilis, semimembranosus, semitendinosus, biceps femoris, adductor magnus, adductor longus, and rectus femoris––and 10 lower leg muscles––flexor digitorum longus, extensor digitorum longus, tibialis posterior, tibialis anterior, peroneus longus/brevis, extensor hallucis longus, gastrocnemius lateralis, gastrocnemius medialis, flexor hallucis longus, and soleus. Approximately five to seven muscle pieces were collected from each individual muscle sampled. The muscle sample pieces obtained for histological analysis measured roughly 10 mm x 5 mm, and the pieces for RNA isolation 5 mm x 5 mm. The samples were obtained directly from the proximal vital parts of the amputated limbs and processed immediately following their removal to avoid tissue degradation.To test the hypothesis that different muscles may express variable amounts of different isoforms of muscle genes, we applied a custom-designed Agilent exon microarray containing probes for 57 muscle-specific genes to assay the transcriptional profiles in sets of human adult, lower limb skeletal muscles
2015-06-17 | E-GEOD-69938 | biostudies-arrayexpress
Project description:We generated a large transcriptome atlas of human skeletal muscles by collecting biopsies from 6 different muscles to determine molecular signatures that may be distinct between leg muscles. The biopsies were collected from gracilis (GR), semitendinosus (ST), vastus lateralis (VL), vastus medialis (VM), rectus femoris (RF), and gastrocnemius lateralis (GL) muscles. We also investigated molecular differences within the muscle by including two biopsies from the middle and distal sides of the semitendinosus muscle (STM and STD, respectively). In total, 128 samples from 20 individuals (aged 25 ± 3.6 yr) were analyzed.
| EGAD00001008657 | EGA
Project description:We generated a large transcriptome atlas of human skeletal muscles by collecting biopsies from 6 different muscles to determine molecular signatures that may be distinct between leg muscles. The biopsies were collected from gracilis (GR), semitendinosus (ST), vastus lateralis (VL), vastus medialis (VM), rectus femoris (RF), and gastrocnemius lateralis (GL) muscles. We also investigated molecular differences within the muscle by including two biopsies from the middle and distal sides of the semitendinosus muscle (STM and STD, respectively). In total, 128 samples from 20 individuals (aged 25 ± 3.6 yr) were analyzed.
| EGAS00001005904 | EGA
Project description:Purpose The effects of the commonly utilized intraoperative tourniquet on gene expression within the skeletal muscle cells are barely examined. Our group already showed that tourniquet application results in higher proteolytic activity within vastus medialis cells (KSSTA 2016), without influence on the amount and function of mitochondria (EJOT 2016). The purpose of the present study was to examine the gene expression within the skeletal muscle cells after tourniquet-induced ischemia and to identify differential expressed genes (DEGs). Methods As part of a randomized, controlled, monocentric trial (Clinical-Trials.gov NCT02475603) we included 20 patients scheduled to undergo primary total knee arthroplasty (TKA). The patients received a written consent and were randomly assigned to Group A (TKA with tourniquet) (n=10) and Group B (TKA without tourniquet) (n=10). Muscle biopsies of (5×5×5 mm) were obtained from the vastus medialis immediately after performing the surgical approach and exactly 60 min later. After preparation of a muscle homogenate, RNA extraction was performed (RNeasy Plus Universal Mini Kit Qiagen) and RNA integrity (RIN) was determined (Agilent 2100 Bioanalyzer,RNA 6000 Pico Kit). Gene expression profiling was performed methodological validated (GeneChip™ Human Transcriptome Array 2.0;Affymetrix). Statistical analysis include the number of significant DEGs with p-value < 0,05, number of DEGs with relative difference >25% and pathway analysis (SPSS-Version 24; SAS JMP10 Genomics, Version 6). The power analysis considered an effect size of 0,4 and a statistical power > 0,8, sample size n=10 for each group. The protocol was approved by our Institutional Ethics Committee (File reference 2012-334N-MA). Results and conclusion Numerous genes were differencially expressed during tourniquet induced ischemia. Further investigations and statistical analysis are ongoning.
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Project description:Analysis of tissues of DBA/2 mice fed a standard breeding diet (SBD) and high fat diet (HFD) revealed tissue specific roles in inflammation and disease, and altered communication between tissues. The tissues surveyed incuded adipose tissues (brown, inguinal, mesenteric, retro-peritoneal, subcutaneious and gonadal), muscle and liver. After the 6 weeks feeding period with different diets, individual blood and tissues were collected from 12 weeks old mice for the determination of serum factors, gene expression analyses and the determination of fatty acid profiles. Mice were individually fasted for two hours prior to dissection that was carried out between 1 PM and 3 PM on three successive days. After the fasting period, blood was withdrawn from the retroorbital plexus of each mouse through a heparin-coated hematocrit tube into a 1.5 ml tube and placed on room temperature until all samples were centrifuged at 600 x g for 10-15 min to obtain serum for the analysis of lipids, glucose, insulin and leptin. Subsequently, animals were sacrificed by cervical dislocation. After bleeding, the subcutaneous fat pads (mainly inguinal fat pads), the gluteal fat pads (between legs left and right to the after), the quadriceps (musculus rectus femulus, m. vastus intermedius, m. vastus lateralis, m. vastus medialis), the gonadal fat pads (surrounding gonads), the retroperitoneal fat pads (below the kidney), the liver, the mesenteric fat pad (hanging at the intestine), and the brown adipose tissues (surrounded by white adipose tissue) were carefully dissected in the given order and immediately collected in RNAlater (Ambion, Austin, TX). The sampling protocol lasted no longer than 15 min per animal.
2010-04-13 | E-GEOD-15822 | biostudies-arrayexpress
Project description:To define the skeletal muscle adaptations induced by exercise performed at high altitude hypoxia, we investigated if the gene expression profile of Vastus lateralis muscle was affected by 5000 m-above-sl-expedition. Two-condition experiment, Vastus lateralis muscle biopsy post-expedition vs Vastus lateralis muscle biopsy pre-expedition. Five volunteers/climbers. Biological replicates: 1 pre-expedition sample, 1 post-expedition sample.
2010-11-27 | E-GEOD-25618 | biostudies-arrayexpress
Project description:entex skeletal muscle gatsrocnemius medialis For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
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Project description:RNA from skeletal muscle of mice over-expressing selectively in the skeletal muscle the gene FRG1, a candidate of facioscapulohumeral muscular dystrophy, was compared to RNA from skeletal muscle of WT mice. Total RNA obtained from isolated vastus lateralis muscles of 4 weeks old females WT mice and vastus lateralis muscles of 4 weeks old mice over-expressing FRG1, FSHD region gene 1.
2013-09-04 | E-GEOD-28575 | biostudies-arrayexpress
Project description:We assessed vastus lateralis muscle gene expression levels of 12 women with the metabolic syndrome before and after a 6 month exercise training program RNA was isolated from a vastus lateralis muscle biopsy of 6 women with the metabolic syndrome before and after a 6 month guided endurance exercise training program
2013-11-05 | E-GEOD-43760 | biostudies-arrayexpress