Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling of melanized domamine neurons isolated from male and female patients with Parkinson disease to investigate gender differences

ABSTRACT: We used 500 melanized dopamine neurons isolated from post-mortem human substantia nigra pars compacta of each sample with laser capture microdissection. Total RNA was extracted with Arcturus PicoPure RNA extraction kit and amplified two times with Arcturus RiboAmp RNA amplification kit. the samples were then sent to the Partners Center for Genetics and Genomics (HPCGG.org) for labeling, hybridization and scanning according to standard Affymetrix protocols. Samples from a total of 16 human brains, 8 PDs (4 male and 4 female) and 8 controls (4 male and 4 female) were studied. These were selected from available material after screening total RNA extracted from a small region of the SN for integrity of 18S and 28S species using an Agilent bioanalyzer. We also matched the cases for age and post mortem interval (PMI) (PD Female age, 75 ± 4.4, PMI, 20.5 ± 2.5; PD Male age 77 ± 6.3, PMI 13.85 ± 1.7; Con Female age 68 ± 3.3, PMI 21.8 ± 0.8; Con Male age 70.2 ± 6.3, PMI 18.11 ± 3.6). Vital Statistics of the cases used in this study. PD= Parkinson disease, C= Control, F=Female, M=Male: Case Age Sex PMI Cel file Pdf1 81 F 17 459F cf1 61 f <24 515H Pdf2 84 F 24.08 515K cf2 n/a f >48 515I Pdf3 69 F <24 515J cf3 74 f 23.00 459D Pdf4 66 F <24 515F cf4 69 f 20.70 459A pdm1 68 m 17.16 515E Cm1 67 m 22.33 459C pdm2 67 m 14.5 515D Cm2 63 m 21.50 459B pdm3 94 m 9.25 515G Cm3 62 m 21.20 515L pdm4 78 m 14.50 515B Cm4 89 m 7.42 515C

ORGANISM(S): Homo sapiens

SUBMITTER: Ippolita Cantuti-Castelvetri

PROVIDER: E-MEXP-1416 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Publications

Effects of gender on nigral gene expression and parkinson disease.

Cantuti-Castelvetri Ippolita I Keller-McGandy Christine C Bouzou Bérengère B Asteris Georgios G Clark Timothy W TW Frosch Matthew P MP Standaert David G DG

Neurobiology of disease 20070303 3

To identify gene expression patterns in human dopamine (DA) neurons in the substantia nigra pars compacta (SNc) of male and female control and Parkinson disease (PD) patients, we harvested DA neurons from frozen SNc from 16 subjects (4 male PDs, 4 female PDs, 4 male and 4 female controls) using Laser Capture microdissection and microarrays. We assessed for enrichment of functional categories with a hypergeometric distribution. The data were validated with QPCR. We observed that gender has a perv ...[more]

PMID: 17412603

Similar Datasets

Project description:Recent developments in liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS)-based proteomics have drastically increased analytical depth and sample throughput, establishing a robust tool for comprehensive system-wide analyses. Such analyses are instrumental in studying the pathophysiology of diseases. One crucial source of material for this is post-mortem individuals. However, there is a significant gap in our understanding of the multi-organ temporal impacts of body decomposition on the proteome. This deficiency compromises result validity due to challenges in controlling the post-mortem interval (PMI). To address this, we reanalyzed published data to compare the effect of the PMI on the proteome alterations to the disease effects. Additionally, we conducted a clinically relevant time-course experiment using isogenic mice and applied LC-MS/MS in data-independent acquisition (DIA) mode to systematically study the proteome alterations post-mortem. Our experiment uncovered dramatic organ-specific protein regulation post-mortem, with only certain aspects attributable to protein autolysis suggesting active post-mortem protein regulation. Notably, the liver and spleen exhibited substantial proteome changes within hours of PMI, while the heart showed comparatively modest changes even after 96 hours. Subcellular fractionation of the heart led to an unexpected surge in the number of proteins exhibiting abundance differences early in PMI. We conducted a compressive analysis of semi-tryptic peptides for the first time, revealing distinct consensus motifs for different organs, indicating organ-specific protease activity. In conclusion, when designing LC-MS/MS-based studies, meticulous consideration of sample collection is crucial as PMI effects may outweigh disease effects. It is preferred that both experimental and control samples are taken in the operation room, especially for studies including subcellular fractionation or trans-organ comparison. In single-organ studies, the planning should involve careful control of the PMI, preferably by sample matching.

Dataset Information

Transcription profiling of melanized domamine neurons isolated from male and female patients with Parkinson disease to investigate gender differences

Publications

Effects of gender on nigral gene expression and parkinson disease.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets