Ontology highlight
ABSTRACT:
PROVIDER: PRJNA470779 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Sex chromosomal abnormalities areare associated with multiple defects. In this study, we retrospectively analyzed the single nucleotide polymorphism (SNP) arrays of 186 early embryos with sex chromosomal abnormalities. using single nucleotide polymorphism (SNP) array. Among them, 52 cases of Turner syndrome, 21 cases of triple X syndrome, 35 cases of Klinefelter syndrome and 14 cases of XYY syndrome were detected. Moreover, 27 cases of mosaic sex chromosomal abnormalities were determined. Sex chromosomal deletions and duplications were found in 37 cases. Overall, our results presented a detailed manifestation of sex chromosomal abnormalities.
2022-07-29 | GSE208389 | GEO
Project description:The Salicaceae family is of growing interest in the study of dioecy in plants because the sex determination region (SDR) has been shown to be highly dynamic, with differing locations and heterogametic systems across taxa. Previous studies investigating the mechanisms regulating sex in the genus Salix have been limited to genome resequencing and differential expression, which are mostly descriptive in nature, and functional validation of candidate sex determination genes has not been conducted. Here we use functional analysis to test a suite of previously identified candidate genes involved in sex determination and sex dimorphism in the bioenergy shrub willow Salix purpurea. Six candidate master regulator genes for sex determination were overexpressed in Arabidopsis, followed by floral proteome analysis. Eleven transcription factors with predicted roles in mediating sex dimorphism downstream of the SDR were tested using DAP-Seq in both male and female S. purpurea DNA. The results of this study provide further evidence to support models for the roles of ARR17 and GATA15 as master regulator genes of sex determination in S. purpurea, contributing to a regulatory system that is notably different from that of the related genus Populus. Two transcription factors, an AP2/ERF family gene and a homeodomain-like transcription factor, have evidence supporting roles in downstream regulation of sex dimorphism.
2023-02-01 | MSV000091180 | MassIVE
Project description:Esophageal squamous cell carcinoma (ESCC) is an aggressive tumor with poor prognosis. Understanding molecular changes in ESCC should improve identification of risk factors in molecular subtypes and provide potential targets for early detection and therapy. To better characterize molecular changes in ESCC, we followed up a previous cDNA array study with additional discovery and confirmatory studies in new ESCC cases using alternative methods. We profiled global gene expression (Affymetrix U133A/B chip) for discovery and confirmation, and validated selected dysregulated genes with additional RNA (qRT-PCR, N=51) or protein studies (immunohistochemistry [IHC] of tumor tissue microarray [TMA], N=275).We also found genes associated with survival. The dysregulated genes should aid in identifying risk factors in ESCC, as well as potential targets for early detection, and outcome prediction and therapy.
2010-09-01 | GSE23400 | GEO
Project description:Analysis of the effects of the rs4919510C>G SNP on miRNA-608 target gene expression. The hypothesis tested in the present study was that the rs4919510C>G SNP may influence the expression of miRNA-608 target genes. Results provide important information of the effects of the rs4919510C>G SNP on miRNA-608 target genes, including immunity and defense genes, DNA repair genes, cell growth-related genes, tumor invasion and metastasis-related genes, cancer stem cell-related genes, and cell death-related genes.
2013-05-15 | GSE46372 | GEO
Project description:Aphelocoma coerulescens SNP discovery
| PRJNA245756 | ENA
Project description:Gasterosteus aculeatus SNP discovery
| PRJNA235365 | ENA
Project description:Purpose: Accurate identification of sex-biased genes requires precise measurement of gene expression levels in gonads. This study is designed to provide such data for various Drosophila species to enhance studies of sex-biased gene expression and evolution across the genus. Methods: Virgin flies were collected and aged 6-10 days before dissecting 2-3 replicates of testes or ovaries. Total RNA was extracted using the Arcturus® PicoPure® kit . Illumina® TruSeq® RNA library kits were used to poly-A+ select and reverse-transcribe mRNA, shear cDNA into ~120 bp fragments, and produce libraries for 1x50 bp sequencing on an Illumina GAIIx or HiSeq2000. Illumina®’s Real Time Analysis v1.13 module processed images, called bases, and provided base qualities. Reads were mapped to the current reference genomes using Bowtie v2.1.0 (Langmead and Salzberg, 2012, Nat Meth) with default settings. Differentially expressed genes were detected using Cufflinks v 2.1.0 (Trapnell et al., 2010, Nat Biotech; default settings) or edgeR (Robinson et al., 2010, Bioinformatics; full-quantile GC-content normalization and full-quantile between-sample normalization). Genes were called differentially expressed at a Benjamini-Hochberg false discovery rate of 0.01. Results: Thousands of male- and female-biased genes were detected for each species using both DE detection methods. These results provide a significant improvement in sensitivity of sex-biased gene detection relative to using whole-body RNA-sequencing data. These data provide a foundation for accurate identification of sex-biased genes throughout the Drosophila genus.
2013-11-04 | GSE52058 | GEO
Project description:It is becoming clear that copy number polymorphism in the human genome is a significant form of genetic variation. We have developed a new method that uses SNP genotype data from parent-offspring trios and applied it to HapMap to conduct high-resolution detection of deletion polymorphism. Of the delections uncovered, approximately 100 have been experimentally validated using comparative genome hybridization on these tiling-resolution oligonucleotide microarrays. We identified a total of 586 distinct regions that harbor deletion polymorphisms in one or more of the parent-offspring trios. This new method will permit future identification of deletion polymorphisms from high density SNP data derived from parent-offspring trios or other family relationships. Keywords: comparative genomic hybridisation
2005-11-17 | GSE3474 | GEO
Project description:Screening for gene copy-number alterations (CNAs) has improved by applying genome-wide microarrays, where SNP arrays also allow analysis of loss of heterozygozity (LOH). We here analyzed 10 chronic lymphocytic leukemia (CLL) samples using four different high-resolution platforms: BAC arrays (32K), oligonucleotide arrays (185K, Agilent), and two SNP arrays (250K, Affymetrix and 317K, Illumina). Cross-platform comparison revealed 29 concordantly detected CNAs, including known recurrent alterations, which confirmed that all platforms are powerful tools when screening for large aberrations. However, detection of 32 additional regions present in 2-3 platforms illustrated a discrepancy in detection of small CNAs, which often involved reported copy-number variations. LOH analysis revealed concordance of mainly large regions, but showed numerous, small nonoverlapping regions and LOH escaping detection. Evaluation of baseline variation and copy-number ratio response showed the best performance for the Agilent platform and confirmed the robustness of BAC arrays. Accordingly, these platforms demonstrated a higher degree of platform-specific CNAs. The SNP arrays displayed higher technical variation, although this was compensated by high density of elements. Affymetrix detected a higher degree of CNAs compared to Illumina, while the latter showed a lower noise level and higher detection rate in the LOH analysis. Large-scale studies of genomic aberrations are now feasible, but new tools for LOH analysis are requested.
2008-12-10 | GSE13557 | GEO
Project description:The aim of the study was to enhance colorectal cancer prognostication by integrating single nucleotide polymorphism (SNP) and gene expression (GE) microarrays for genomic and transcriptional alteration detection; genes with concurrent gains and losses were used to develop a prognostic signature.
2022-03-15 | GSE197802 | GEO