The alteration of intestinal mucosal α-synuclein expression and mucosal microbiota in Parkinson's disease/Experiment 3

EditHistoryDelete

Flag for review

Your review change was submittedDuplicate this ExperimentAdd a new Signature

Reviewed Marked as Reviewed by Svetlana up on 2024-7-3

Curated date: 2024/03/13

Curator: Scholastica

Revision editor(s): Scholastica

Subjects

Location of subjects

China

Host species Species from which microbiome was sampled. Contact us to have more species added.

Homo sapiens

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology

Mucosa of sigmoid colon Mucosa of organ of sigmoid colon,Mucous membrane of sigmoid colon,Organ mucosa of sigmoid colon,Sigmoid colon mucosa,Sigmoid colon mucosa of organ,Sigmoid colon mucous membrane,Sigmoid colon organ mucosa,Mucosa of sigmoid colon,mucosa of sigmoid colon

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology

Parkinson's disease IDIOPATHIC PARKINSON DIS,Idiopathic Parkinson Disease,Idiopathic Parkinson's Disease,IDIOPATHIC PARKINSONS DIS,Idiopathic PD,LEWY BODY PARKINSON DIS,Lewy Body Parkinson Disease,Lewy Body Parkinson's Disease,Paralysis agitans,paralysis agitans,PARKINSON DIS,PARKINSON DIS IDIOPATHIC,Parkinson disease,Parkinson Disease, Idiopathic,Parkinson syndrome,Parkinson's,Parkinson's disease,Parkinson's disease (disorder),Parkinson's disease NOS,Parkinson's disease NOS (disorder),Parkinson's Disease, Idiopathic,Parkinson's Disease, Lewy Body,Parkinson's syndrome,Parkinsonian disorder,Parkinsonism, Primary,Parkinsons,PARKINSONS DIS,PARKINSONS DIS IDIOPATHIC,PARKINSONS DIS LEWY BODY,Parkinsons disease,Primary Parkinsonism,parkinson's disease

Group 0 name Corresponds to the control (unexposed) group for case-control studies

Duodenal mucosa

Group 1 name Corresponds to the case (exposed) group for case-control studies

Sigmoid mucosa

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

Samples from the sigmoid mucosa of Parkinson's disease (PD) patients

Group 0 sample size Number of subjects in the control (unexposed) group

19

Group 1 sample size Number of subjects in the case (exposed) group

19

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)

None

Lab analysis

Sequencing type

16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene

V4

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance

Illumina

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).

relative abundances

Statistical test

Kruskall-Wallis

Significance threshold p-value or FDR threshold used for differential abundance testing (if any)

0.05

MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?

No

LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool

4

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness

increased

Simpson Estimator of species richness and species evenness: more weight on species evenness

increased