Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Proteomic Analysis of Skin Punch Biopsies from a Parkinson's Disease Patient Cohort: A PPMI Pilot Study

ABSTRACT: A human skin proteome MS spectral library, generated from tissue punch biopsies of the C8 paravertebral region in Parkinson's disease patients. This data and associated protocol (https://www.protocols.io/view/proteomics-sample-preparation-of-human-skin-punch-14egn9e46l5d/v1) were generated as part of a pilot study in collaboration with the Michael J. Fox Foundation. The biospecimens were obtained from the Parkinson’s Progression Marker Initiative (PPMI) (RRID:SCR_006431). For up-to-date information on the study, visit www.ppmi-info.org.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Skin

DISEASE(S): Parkinson's Disease

SUBMITTER: Matthew Jaconelli

LAB HEAD: Prof. Dario

PROVIDER: PXD060089 | Pride | 2025-01-23

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	20240713_MJ_Skin_F1.raw	Raw
	20240713_MJ_Skin_F10.raw	Raw
	20240713_MJ_Skin_F11.raw	Raw
	20240713_MJ_Skin_F12.raw	Raw
	20240713_MJ_Skin_F13.raw	Raw

Items per page:

1 - 5 of 100

Similar Datasets

AGO2 Plasma exRNA Profiles

Project description:The Michael J. Fox Foundation (MJFF) collected AGO2 exRNA samples for distribution to interested individuals.

2018-12-22 | GSE124269 | GEO

Platelet mRNA in response to antiplatelet therapy exposure

Project description:The purpose of this study was to identify changes in platelet mRNA that result from exposure to antiplatelet therapy. A total of 84 healthy volunteers were recruited into a longitudinal study of various antiplatelet exposures with 58 completing all study visits. This was a 5 visit study where each visit was separated by ~ 4 weeks. At each Visit purified platelets using a CD45 negative selection protocol was performed in addition to platelet function testing using light transmittance aggregometry (ADP, EPI, and Collagen) and PFA100 (Col/EPI). After the baseline visit (V1), participants were randomized to receive 81mg/day or 325mg/day aspirin x 4 weeks followed by Visit 2. Participants then crossed over to the alternative dose of aspirin for 4 weeks followed by Visit 3. Between Visits 3 and 4 participants washed out their aspirin for 4 weeks. The final exposure was ticagrelor 90mg twice daily x 4 weeks until Visit 5.

2022-03-14 | GSE158765 | GEO

miRNA Expression in Firefighters’ Skin and Blood

Project description:Firefighters are routinely exposed to polycyclic aromatic hydrocarbons (PAHs) during fire suppression activities, molecular biomarkers reflecting such exposure remain underexplored. Thus, we explored an integrated exposure assessment framework linking PAH contamination on turnout gear and skin to changes in microRNA (miRNA) expression in skin and blood biospecimens.

2025-08-01 | GSE296706 | GEO

Modular repertoire analyses identify dynamic type I and type II interferon transcriptional signatures in adult SLE patients

Project description:Gene expression profiling (compared to healthy controls) to identify patients with active SLE disease and patients with quiescent disease 157 “SLE” and 20 “Healthy controls of SLE were followed up for up to 3 years. Clinical assessment, current treatment, laboratory results and SLEDAI score were collected at each visit (V1, V2...). SLE patients are compared to control groups.

2014-04-01 | E-GEOD-49454 | biostudies-arrayexpress

Bulk-cell RNA-seq analysis of early cutaneous wound healing in mouse

Project description:To study early-onset gene expression changes in cutaneous wound healing, 3 mm wounds were induced into the back skin of female wildtype C57BL/6 mice using a biopsy punch. Mice were sacrificed 2h, 6h or 24h post wound induction (PWI) and 1 - 1.5 mm of skin lining the wound edge was isolated and sequenced. The skin from the initial punch biopsy (0h PWI) was preserved and taken as a control sample to identify differentially expressed genes.

2018-07-31 | E-MTAB-6686 | biostudies-arrayexpress

Differences in cell subsets between sun-exposed and unexposed skin: preliminary single-cell sequencing and biological analysis from a single case

Project description:The microcosmic and specific changes of human photoaging skin without chronologic aging is still unclear and rare-ly analyzed. We aimed to assess biological processes of the cell-subgroups alteration and mechanisms of skin pho-toaging using single cell sequencing and biological analysis were used between sun-exposed forearm skin and un-exposed buttock skin in same individual via skin punch biopsy.

2024-08-28 | GSE275491 | GEO

Human Alopecia Areata Skin Biopsy Samples

Project description:Gene expression profiling of scalp skin biopsies from patients with alopecia areata or normal healthy controls Scalp skin punch biopsies were taken from the indicated patients and stored in PAXgene tissue containers for shipping to a central location, where the samples were processed

2017-02-09 | GSE68801 | GEO

Scalable Acid-Aided Lysis of Skin Samples Improves Proteome Coverage

Project description:In this study, we present a robust and scalable sample preparation protocol based on chemical lysis with trifluoroacetic acid (TFA), adapted from the SPEED method and optimized for human skin samples. The protocol simplifies tissue lysis while selectively leaving ECM scaffolds largely insoluble. As a result, abundant collagens and structural proteins are effectively depleted from the soluble fraction, improving the dynamic range of detectable proteins and increasing sensitivity for less abundant species. Using TFA lysis followed by solid-phase-enhanced sample preparation (SP3), we identified up to 6,200 protein groups from full-thickness human skin punch biopsies. Notably, the protocol enables high-depth proteomic analysis from 2 mm punch biopsies, which are less invasive and more suitable for longitudinal or large-cohort studies. Tape strip samples—commonly used in dermatological research for minimally invasive epidermal sampling—were also compatible with this protocol, yielding up to 2,300 protein groups, representing a two- to threefold increase compared to previously reported studies.

2025-08-21 | PXD066029 | Pride

Allergen Challenge for Evoked Phenotypes in Asthma (the ACE Study)

Project description:This protocol outlines a single-site mechanistic study aiming to investigate long RNAs differentially expressed in the airway epithelium of asthma patients both at baseline and in response to segmental airway allergen challenges. Over approximately 14 days, the study spanned three visits: Visit 1: Comprehensive characterization of participants, encompassing lung function testing, methacholine challenge testing, and allergen skin prick testing. Visit 2: Participants underwent bronchoscopy wherein three procedures were performed a. Epithelial brushings were performed in a segmental airway (baseline sample) b. Diluent (inactive control) was instilled into another segmental airway c. A small dose of allergen was administered into a third segmental airway using standardized cat or dust mite allergen extracts. Visit 3 (24 hours or 7 days post Visit 2): Another bronchoscopy was carried out to collect epithelial brushings in the diluent challenged and allergen challenged segments The collected epithelial brush samples underwent analysis for mRNA expression in the epithelial brushings. The study successfully incorporated a total of 23 subjects, which included 18 asthmatics (with stable or well-controlled conditions), 2 allergic non-asthmatics, and 3 non-allergic non-asthmatics.

2024-03-08 | GSE250241 | GEO

circRNA expression in cutaneous squamous cell carcinoma (cSCC)

Project description:Punch biopsies from patients with cSCC (n=3) and non-lesional skin (n=3) were included in the study. Microarray based circRNA expression profiles were acquired using Arraystar circRNA Arrays V. 2.0 screening for 13.617 distinct human circRNA candidates. We identified circRNAs differentially expressed in cSCC compared to non-lesional skin (control).

2016-06-18 | GSE74758 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data