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Genome-wide association data on male-pattern baldness

ABSTRACT: The study comprises 1000Genomes imputed data for 581 MPB cases and 416 male controls. Cases are selected for age<40 and Hamilton-Norwood grade V-VII. Control include 270 males >60 years no signs of AGA (Hamilton-Norwood grade I).

PROVIDER: EGAS00001001354 | EGA |

REPOSITORIES: EGA

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ena-DATASET-IHGUB-03-08-2015-14:22:25:952-12 - samples

Project description:1000Genomes imputed data set of 581 cases and 417 controls for male-pattern baldness

| EGAD00001001456 | EGA

Integrated with Proteome-sequencing, bulk RNA-sequencing and Single cell RNA-sequencing to identify potential biomarkers in different grades of intervertebral disc degeneration

Project description:We selected humann intervertebral disc samples to perform proteomics analysis. There were 1 case of grade I , 1 case of grade II, 3 cases of grade Ⅲ and 3 cases of grade Ⅳ according to Pfirrmann classfication. RNA seqencing analysis and single-cell RNA sequencing were integrated with proteomics data to identify the hub genes for intervertebral disc degeneration using bioinformatic method.

2023-05-10 | PXD040593 | Pride

Effect of recombinant IL-33s, particularly IL-3395-270, IL-3399-270,IL-33109-270, and IL-33112-270 in HRMVECs

Project description:To investigate the expression prolfile of genes regulated by IL-3395-270, IL-3399-270, IL-33109-270, and IL-33112-270 in HRMVECs.

2024-07-24 | GSE245784 | GEO

RSPO4 is a potential risk gene of stages III–IV, grade C periodontitis through effects on innate immune response and oral barrier integrity

Project description:Aim R-spondin 4 (RSPO4) is a suggestive risk gene of stage III–IV, grade C periodontitis and upregulated in gingiva of mice resistant to bacteria-induced alveolar bone loss. We aimed to replicate the association, identify and characterize the putative causal variant(s) and molecular effects, and understand the downstream effects of RSPO4 upregulation. Materials and Methods We performed a two-step association study for RSPO4 with imputed genotypes of a German–Dutch (896 stage III–IV, grade C periodontitis cases, 7104 controls) and Spanish sample (441 cases and 1141 controls). We analysed the allelic effects on transcription factor binding sites with reporter gene and antibody electrophoretic mobility shift assays. We used CRISPR/dCas9 activation and RNA sequencing to pinpoint RSPO4 as the target gene and to analyse downstream effects. Results RSPO4 was associated with periodontitis (rs6056178, pmeta = 4.6 × 10−5). rs6056178 contains a GATA-binding motif. The rs6056178 T-allele abolished reporter activity (p = .004) and reduced GATA binding (−14.5%). CRISPRa of the associated region increased RSPO4 expression (25.8 ± 6.5-fold, p = .003). RSPO4 activation showed strongest induction of Gliomedin (439-fold) and Mucin 21 (178-fold) and of the gene set “response to interferon-alpha” (area under the curve [AUC] = 0.8, p < 5 × 10−6). The most repressed gene set was “extracellular matrix interactions” (AUC = 0.8, padj = .00016). Conclusion RSPO4 is a potential periodontitis risk gene and modifies host defence and barrier integrity.

2023-01-09 | GSE222437 | GEO

Brain region and sex specific transcriptome of peripubertal stress induced adult male mice showing escalated aggression and adult female mice with no signs of aggression.

Project description:Purpose: The goal of this study is to uncover the molecular basis of peripubertal stress induced aggressive behaviour and its sex differences focussing on brain region specific transcriptome profiling (RNA-seq) and validation by quantitative reverse transcription polymerase chain reaction (qRT–PCR) Methods: Hypothalamus (Hypo) and Prefrontal cortex (PFC) mRNA profiles of 90-day-old control adult male and female and PPS exposed escalated aggressive adult male (SEagg) mice and non aggressive adult female (SNagg) were sequenced on Illumina HiSeq 2500, in 3 biological replicates.The FASTQ sequencing reads were adapter-trimmed along with a minimum length cut-off of 50 bases using Prinseq-lite. The reads were aligned to mouse genome assembly using TopHat (v.2.0.11) followed by reference-based assembly using Cufflinks (v.2.2.1). Then differentially expressing transcripts were identified using Cuffdiff (v.2.2.1). qRT–PCR validation was performed using SYBR Green assays. Results:Hypo of SEagg males showed 49 differentially expressed genes (DEGs) amongst which 28 were down-regulated, 20 were up-regulated and 1 was expressed in SEagg males but not in control males. PFC of SEagg males showed 87 DEGs amongst which 57 were downregulated, 28 were upregulated and 2 were only expressed in SEagg males but not control males. SNagg females showed 684 DEGs in Hypo and 152 DEGs in PFC when compared to their respective control samples. Conclusions: We provide the first prefrontal cortex and hypothalamus specific transcriptome profiles of peripubertal stress (PPS) exposed, Balb/c adult male mice exhibiting escalated aggression and Balb/c adult female mice showing no signs of aggression.

2022-11-02 | GSE199844 | GEO

MiRNA Expression Analysis of Intraductal Papillary Mucinous Neoplasms (IPMNs) of the Pancreas

Project description:To discover a panel of mi(cro)RNAs that accurately differentiate between high-risk IPMN tissue (from pathologically-confirmed invasive or high-grade IPMN cases) and low-risk IPMN tissue (from pathologically-confirmed low-or moderate-grade IPMN cases).

2015-01-29 | GSE63102 | GEO

Sinorhizobium medicae strain:416

Project description:Sinorhizobium medicae 416 Resequencing

| PRJNA499407 | ENA

Array comparative genomic hybridization analysis of flat epithelial atypia (DIN1a) and lobular intraepithelial neoplasia

Project description:Low grade flat ductal intraepithelial neoplasia (DIN1a, flat epithelial atypia) is one of the earliest morphologically recognizable neoplastic lesions of the breast. Frequently, it occurs in association with lobular intraepithelial neoplasia (LIN). The aim of this study was to elucidate chromosomal aberrations in these early neoplastic breast lesions using array comparative genomic hybridization (CGH) analysis. Laser capture microdissection of 12 archival formalin-fixed, paraffin-embedded specimens harbouring both foci of DIN1a as well as LIN was performed. All analyzed cases of DIN1a and LIN showed chromosomal gains and losses. The aberration encountered most often was loss on 16q in 7 DIN1a (70%) and 10 LIN (91%) cases. Regarding changes in chromosome 1, four DIN1a (40%) and 7 LIN (64%) cases showed a gain on 1q. The results of our study show concurrent chromosomal aberrations of 1q gains and 16q losses in several cases with coexisting LIN and low grade flat DIN. These aberrations are known to be common in low grade invasive ductal carcinomas as well as more advanced (conventional) types of low grade DIN (low grade ductal carcinoma in-situ). Our results raise the possibility of similar molecular-genetic pathways in most of the cases with coexisting LIN and low grade flat DIN.

2010-05-05 | GSE18187 | GEO

Expression data from hybrid male Xenopus sex reversal experiment

Project description:Gene expression was examined in genetic females that were sex-reversed to be phenotypically male compared to normal hybrid males We used microarrays to test expression in the gonad of sex-reversed males (ZW) compared to normal males (ZZ) Keywords: treatment

2007-11-07 | GSE9505 | GEO

Discovery of novel hypermethylated gene loci in prostate cancer using genome wide coverage CpG island microarrays

Project description:In order to identify methylation changes in prostate cancer, we performed a genome-wide analysis of DNA methylation using Agilent human CpG island arrays. We then chose specific genes to validate methylation both in the same cases as were hybridized to the array (using quantitative EpiTYPER analysis) and in an independent series of prostate cancer samples (using MethyLight quantitative methylation specific PCR). We specifically chose low grade (Gleason score 6 cases) and high grade (Gleason score 8 cases) to discover methylated genes/loci that may be involved in the progression to a higher grade of prostate cancer.

2009-03-27 | GSE15298 | GEO

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