Genomics

Dataset Information

42

Fiber and NMJ / synaptic gene expression comparisons in rat extraocular muscle (EOM) and tibialis anterior (TA) muscle.


ABSTRACT: Purpose: To examine and characterize the expression profile of genes expressed at the neuromuscular junctions (NMJs) of extraocular muscles (EOMs) in comparison to the NMJs of tibialis anterior muscle (TA). Methods: Adult rat rectus EOMs and TAs were dissected, flash-frozen, serially sectioned and stained for acetylcholinesterase to identify NMJs. Approximately 6000 NMJs for EOM (EOMsyn) and 6000 NMJs for TA (TAsyn) and equal amounts of NMJ-free fiber regions (EOMfib, TAfib) and underlying myonuclei were captured using laser capture microdissection (LCM). RNA was isolated, processed and used for microarray-based expression profiling. Profiles were generated for genes differentially expressed at synaptic and non-synaptic regions of TA (TAsyn vs TAfib) and EOM (EOMsyn vs EOMfib) using a false discovery rate (FDR) of 5% as well as an “interaction list” revealing the most significantly differentially expressed genes at an FDR of 1%. We validated the profiles by real-time quantitative reverse transcription-polymerase chain reaction (qPCR). Results: The regional transcriptomes associated with NMJ of EOMs and TAs were identified. We found 275 genes that were preferentially expressed in EOMsyn and 230 known transcripts that were preferentially expressed in TAsyn; 288 of the transcripts were common to both synapses; these included well-known, evolutionarily conserved, synaptic markers (e.g. nicotinic Acetylcholine receptor (ACHR) alpha and epsilon subunits, nestin) as well as a large number of novel genes. Conclusion: Transcriptome level differences exist between EOM synaptic regions and TA synaptic regions. Our definition of the synaptic transcriptome provides insight into the mechanism of formation and functioning of the unique synapses of EOM and their differential involvement in diseases noted in the EOM allotype. Overall design: Tissue preparation: A total of 4 rats were killed by CO2 inhalation. The bony orbit was removed from the skull and opened at the lamina cribrosa. The globe with the four recti EOMs still attached was carefully dissected from the bony orbit. The eyeball with muscles was placed on cryomolds, covered with OCT tissue embedding medium (Tissue-Tek: Sakura Finetek, Tokyo, Japan) and flash-frozen in isopentane, cooled in liquid nitrogen and stored at -80 °C. The tibialis anterior (TA) muscles of all rats were dissected and frozen in the same way. The EOM’s and TA’s were then cut transversely into 10 μm sections using a Microm HM 500 cryostat (Zeiss, Oberkochen, Germany), mounted on PEN (poly-ethylene-naphthalene) Membrane Slides (Arcturus) and refrozen immediately. Unfixed sections were stored at -80°C until needed. Section staining: Sections for LCM were stained for acetylcholinesterase based on the method of Karnowsky and Roots to visualize NMJ. Palm microdissection: The PALM MicroBeam System was used for microdissection and for catapulting isolated tissue into a microfuge cap containing 80 μl RLT-Lysis Buffer (Quiagen). Approximately 1000 NMJ and equal amount of non-synaptic regions were collected for each muscle.

INSTRUMENT(S): [Rat230_2] Affymetrix Rat Genome 230 2.0 Array

ORGANISM(S): Rattus norvegicus  

SUBMITTER: Murat T Budak  

PROVIDER: GSE15737 | GEO |

SECONDARY ACCESSION(S): PRJNA116627

REPOSITORIES: GEO

Dataset's files

Source:
Action DRS
GSE15737_RAW.tar Raw
filelist.txt Txt
Items per page:
1 - 2 of 2

Similar Datasets

2010-04-28 | E-GEOD-15737 | ArrayExpress
2010-01-01 | S-EPMC2941174 | BioStudies
2012-01-01 | S-EPMC3462430 | BioStudies
2013-01-01 | S-EPMC3582511 | BioStudies
2011-01-01 | S-EPMC3223174 | BioStudies
2019-12-12 | GSE92400 | GEO
2003-01-01 | S-EPMC6742194 | BioStudies
2020-01-01 | S-EPMC7495279 | BioStudies
2013-01-01 | S-EPMC3568149 | BioStudies
2019-01-01 | S-EPMC6482306 | BioStudies