Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

45 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Huntington's disease biomarker progression profile identified by transcriptome sequencing in peripheral blood

ABSTRACT: In this study we investigated the suitability of blood to identify HD transcriptomic biomarkers, validated the outcome in an independent cohort and derived a first empiric panel of biomarkers capable of predicting HD motor scores. Finally we examined whether patient gene expression profiles could provide information about HD affected biological pathways. Examination of differentially expressed genes in peripheral whole blood using linear modelling of gene expression data (3 DGE) against UHDRS total motor scores of Huntington's Disease mutation carriers and controls.

ORGANISM(S): Homo sapiens

SUBMITTER: Anastasios Mastrokolias

PROVIDER: E-GEOD-51799 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Huntington's disease biomarker progression profile identified by transcriptome sequencing in peripheral blood.

Mastrokolias Anastasios A Ariyurek Yavuz Y Goeman Jelle J JJ van Duijn Erik E Roos Raymund A C RA van der Mast Roos C RC van Ommen GertJan B GB den Dunnen Johan T JT 't Hoen Peter A C PA van Roon-Mom Willeke M C WM

European journal of human genetics : EJHG 20150128 10

With several therapeutic approaches in development for Huntington's disease, there is a need for easily accessible biomarkers to monitor disease progression and therapy response. We performed next-generation sequencing-based transcriptome analysis of total RNA from peripheral blood of 91 mutation carriers (27 presymptomatic and, 64 symptomatic) and 33 controls. Transcriptome analysis by DeepSAGE identified 167 genes significantly associated with clinical total motor score in Huntington's disease ...[more]

PMID: 25626709

Similar Datasets

Transcription profiling by array of Sordaria macrospora wild type strain undergoing sexual development and the mutant strains dSmtA-1 and dSmtA-2

Project description:Cross-species hybridizations of Sordaria macrospora targets on Neurospora crassa microarrays were performed with targets derived from the S. macrospora wild type undergoing sexual development (wt.sex) and the mutant strains dSmtA-1 and dSmtA-2. For each strain, two independent experiments were carried out with a dye switch in the second experiment. The following slide/target/dye combinations were done: slide N16-86: Cy3-target: wt.sex (1), Cy5-target: dSmtA-1 (1) slide N16-87: Cy3-target: dSmtA-1 (2), Cy5-target: dSmtA-2(2) slide N16-88: Cy3-target: dSmtA-2 (1), Cy5-target: wt.sex (2)

2010-04-29 | E-MEXP-2600 | biostudies-arrayexpress

RNA-Seq of Streptomyces venezuelae grown overnight (14 hrs) with Mitomycin-C against untreated controls.

Project description:Mitomycin C is a DNA crosslinking agent. This experiment was carried out to determine the effect of Mitomycin C on genome wide transcription in Streptomyces venezuelae NRRL B65442.

2022-07-06 | E-MTAB-11556 | biostudies-arrayexpress

RNA-Seq of Streptomyces venezuelae to compare global gene expression between the wild-type and BldB deletion strains after 10, 14 and 22 hours of growth.

Project description:BldB is a regulatory protein in Streptomyces and most species have a number of paralogs in their genomes. Deletion of BldB leads to a developmental deficiency and the colonies fail to produce aerial mycelium. In this experiment global gene expression was compared between the WT and BldB deletion strain of Streptomyces venezuelae NRRL B65442 after 10, 14 and 22 hours of growth in liquid cultures.

2023-04-14 | E-MTAB-12832 | biostudies-arrayexpress

RNA-Seq of Streptomyces venezuelae NRRL B65442 to compare global gene expression between the wild-type and bldB deletion strain and, wild-type and bldB plus whiJ9 double mutant after 14 hours growth in liquid medium.

Project description:Expression of iosA is greatly activated in the bldB deletion strain. whiJ9 is divergently transcribed from iosA and the double mutant (whiJ9 + bldB) was made to determine if WhiJ mediates the activation of iosA in the absence of BldB.

2023-04-14 | E-MTAB-12836 | biostudies-arrayexpress

RNA-Seq of Pseudomonas fluorescens SBW25 with and without the plasmid pQBR103 and with the rsmQ deleted from pQBR103 to determine the effect of the plasmid on global gene transcription.

Project description:Plasmids can affect expression of genes on the host chromosome. This experiment was carried out to determine the effect of the presence of the plasmid pQBR103 (with and without the rsmQ gene on it) on global gene expression in Pseudomonas fluorescens SBW25.

2022-12-15 | E-MTAB-11868 | biostudies-arrayexpress

Transcription profiling and cross species hybridization of Sordaria macrosopora samples undergoing sexual development (wt.sex), wild type growing vegetatively (wt.veg), and mutant strains pro1, pro41, and pro1/41 on Neurospora crassa arrays

Project description:Cross-species hybridizations of Sordaria macrospora targets on Neurospora crassa microarrays were performed with targets derived from the S. macrospora wild type undergoing sexual development (wt.sex), the wild type growing vegetatively (wt.veg), and the mutant strains pro1, pro41, and pro1/41 (pro1.41). For each strain or growth condition, two independent experiments were carried out with a dye switch in the second experiment. The following slide/target/dye combinations were done: slide N12-105: Cy3-target: wt.veg (1), Cy5-target: pro1.41 (2) slide N12-106: Cy3-target: wt.sex (1), Cy5-target: wt.veg(2) slide N12-108: Cy3-target: pro1 (1), Cy5-target: wt.sex(2) slide N12-109: Cy3-target: pro41(1), Cy5-target: pro1 (2) slide N12-110: Cy3-target: pro1.41(1), Cy5-target: pro41 (2)

2007-05-09 | E-MEXP-915 | biostudies-arrayexpress

Genome-wide expression kinetics of children with Type 1 diabetes (T1D) -associated autoantibodies or progression towards clinical T1D, compared to healthy matched controls .

Project description:To unravel genes and molecular pathways involved in the pathogenesis of type 1 diabetes (T1D), we performed genome-wide gene expression profiling of prospective venous blood samples from children developing T1D-associated autoantibodies or progressing towards clinical diagnosis. 357 peripheral blood RNA samples from 10 autoantibody-positive children (Case) and their matched controls (Control) or alternatively 18 prediabetic children (T1DCase) and their matched controls (T1DControl) were analyzed with Affymetrix U219 gene array, in order to study the gene expression changes occuring during the pathogenesis of Type 1 diabetes (T1D). Each case child (positive for T1D-specific autoantibodies) was matched with a persistently autoantibody-negative control child, with the same HLA-DQB1 risk category, gender, and place and date of birth. Seroconversion is determined as the first detection of T1D-specific autoantibody/autoantibodies (ICA titre >4 JDFU, IAA >3.47 RU, GADA >5.4 RU, IA-2A >0.43 RU, ZnT8A >0.61 RU). Two control children were selected for T1D cases 3, 5, 13 and 17. Case5 & T1DCase15 and Case7 & T1DCase3 share the same matched control. Sample T1DControl7_4 was excluded from the final analysis as an outlier, resulting in 356 total Samples listed below.

2014-02-20 | E-GEOD-43488 | biostudies-arrayexpress

Total RNAseq of human healthy control inferior turbinate and glucocorticoid-treated, NSAID-exacerbated respiratory disease (N-ERD) nasal polyp nasal brushings

2020-06-30 | E-MTAB-7962 | biostudies-arrayexpress

mRNAseq of human sputum macrophages and alveolar-like monocyte-derived macrophages of healthy controls and NSAID-exacerbated respiratory disease (N-ERD) patients

Project description:NSAID-exacerbated respiratory disease (N-ERD) represents a particularly severe endotype of chronic rhinosinusitis with nasal polyps (CRSwNP), which affects around 10-16% of CRSwNP patients. N-ERD is characterized by severe and refractory nasal polyposis, bronchial asthma and intolerance to non-steroidal anti-inflammatory drugs (NSAIDs), including aspirin. Today, the pathogenesis of N-ERD remains incompletely understood and curative treatments are lacking. Macrophages are important source and target cells of arachidonic acid metabolites during type 2 inflammation, that have been neglected in N-ERD pathogenesis despite their presence in the nasal mucosa of N-ERD patients. Using a global transcriptomic approach, we identified systemic and local changes in macrophages between N-ERD patients and healthy controls. We isolated macrophages from induced sputum (sMac) and compared them to 7-days in vitro-differentiated, alveolar-like monocyte-derived macrophages (aMDM). Cells were lysed in RLT buffer with 1% beta-mercaptoethanol and stored at -80°C until RNA isolation and RNAseq. Since sMac yield of healthy controls was low, we pooled RNA of three donors (= sample S1) but excluded the data from subsequent analyses. Thus Analysis 1 shows the intra-group comparison of N-ERD sMac vs. N-ERD aMDM. In a second analysis (Analysis 2), we compared N-ERD aMDM vs. healthy control aMDM for transcriptome differences present in monocyte (blood)-derived cells.

2020-06-30 | E-MTAB-7965 | biostudies-arrayexpress

Transcriptome sequencing reveals aberrant alternative splicing in Huntington's disease

Project description:Huntingtonâs disease (HD) is an autosomal dominant neurodegenerative disorder caused by a CAG expansion in the gene encoding Huntingtin (HTT). Transcriptome dysregulation is a major feature of HD pathogenesis, as revealed by a large body of work on gene expression profiling of tissues from human HD patients and mouse models. These studies were primarily focused on transcriptional changes affecting steady-state overall gene expression levels using microarray based approaches. A major missing component however has been the study of transcriptome changes at the post-transcriptional level, such as alternative splicing. Alternative splicing is a critical mechanism for expanding regulatory and functional diversity from a limited number of genes, and is particularly complex in the mammalian brain. Here we carried out a deep RNA-seq analysis of 7 human HD brains and 7 controls to systematically discover aberrant alternative splicing events and characterize potential associated splicing factors in HD. We identified 593 differential alternative splicing events between HD and control brains. Using an expanded panel of 54 brain tissues from patients and controls, we also identified 9 splicing factors exhibiting significantly altered expression levels in HD patient brains. Moreover, follow-up molecular analyses of one splicing factor PTBP1 revealed its impact on disease-associated splicing patterns in HD. Collectively, our data provide genomic evidence for widespread splicing dysregulation in HD brains, and suggest the role of aberrant alternative splicing in the pathogenesis of HD RNA-seq analysis of the BA4 motor cortex of 7 control and 7 Huntington's disease patients. 1.5 ug of total RNA was used for RNA-seq library preparation using the TruSeqâ¢ Stranded mRNA LT Sample Prep Kit (Illumina). 100x2 bp paired-end RNA-seq reads were generated on a HiSeq 2000 sequencer.

2016-06-14 | E-GEOD-79666 | biostudies-arrayexpress

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