Dataset features

Specifications


Application: RNA-seq analysis
Number of samples: 15
Release date: Jun 23 2017
Last update date: Nov 19 2018
Access: Public
Diseases: Cerebellar Diseases, Polyneuropathies, Ventricular Dysfunction, Neurodegenerative Diseases, Mitochondrial Diseases, Renal Insufficiency
Chemicals: Cholesterol
Dataset link Deletions in the ATAD3 gene cluster cause cerebellar developmental defects with mitochondrial DNA abnormalities owing to local cholesterol insufficiency

Experimental Protocol


We designed the experiment to compare the expression profiles of cells carrying deletions in the ATAD3 gene cluster (ATAD3CAS & ATAD3F) with that of a normal control cell line. Because we suspected that cholesterol metabolism would be altered by ATAD3 deficiency we also prepared RNA from the same three cell lines treated with a drug, pravastatin, that inhibits the rate limiting step of cholesterol synthesis, to determine if the drug produced similar effects on gene expression to ATAD3 deficiency. In practice, pravastatin had almost no signficant effects (FDR 0.05) on any of the cells and none related to cholesterol homeostasis, indicating the drug does not act at the level of gene expression. This proved convenient as two RNA samples from ATAD3CAS failed QC, but the ATAD3CAS + pravastatin versus control (with or without pravastatin) provided additional replicates and displayed almost identical differences to ATAD3CAS (no drug) vs Control.

Repositories


GEO

GSE86550

ENA

SRP087536

BioProject

PRJNA342177

Download


Contact


ian holt

Dataset Statistics

info

Citations per year

Dataset publication