2214db0b-98f8-4cb8-9ac3-6def3a146ff6 - samples
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ABSTRACT:
PROVIDER: EGAD00001008645 | EGA |
REPOSITORIES: EGA
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Project description:We report a 14-year-old boy with mosaic 45,X/48,XYYY karyotype presenting with subtle dysmorphic features and height deficiency, requiring growth hormone therapy. Single-cell RNA sequencing revealed widespread differences in genotype distribution between 45,X and 48,XYYY immune cells, with concordant results at DNA level. Deregulation of predominantly autosomal genes was observed, including TCL1A overexpression in 45,X B-lymphocytes and other known genes associated with hematological malignancies, prompting long-term personalized hemato-oncological surveillance in the reported patient.
| EGAS00001005697 | EGA
Project description:The widely variable phenotypic spectrum and the different symptom severity in men with Klinefelter syndrome (KS) suggest a role for epigenetic mediators. Therefore, the aim of this study was to evaluate the possible involvement of miRNAs in the clinical manifestations of KS. To accomplish this, we performed a transcriptome analysis in peripheral blood mononuclear cells (PBMCs) of 10 non-mosaic KS patients , 10 aged-matched healthy male and 10 aged-matched healthy female controls with normal karyotype. After RNA extraction from PBMC and the preparation of small RNA libraries, the samples were sequenced using next generation high-throughput sequencing technology. Expression profiling analysis revealed a significant differential expression of 2 miRNAs in KS compared to male controls. In particular, MIR3648 resulted significantly (p<0.0001) down-regulated by -19.084- fold, while MIR3687was non-expressed at all (p<0.0001) in KS patients. These results were confirmed by qRT-PCR. The functional analysis of the two transcripts showed that they seem to play a role in breast cancer, hemopoietic abnormalities, immune defects and adipocyte differentiation and fat cell maturation. Therefore, we speculate that both miRNAs may play a role in the immune and metabolic disorders and in the risk of breast cancer development in men with KS.
2017-12-02 | E-MTAB-6107 | biostudies-arrayexpress
Project description:Purpose: Recombinant human erythropoietin administration studies involving “omics” approaches have demonstrated a gene-expression signature that could aid detection of blood doping. However, current anti-doping testing does not involve blood collection into tubes with RNA preservative. This study investigated if whole blood in short-term storage could be used for transcriptomic analysis despite lacking RNA preservation. Methods: Whole blood samples were collected from fourteen male healthy individuals. Short-term storage: whole blood collected into K2EDTA tubes and subjected to short-term (i.e., at 4°C) storage for 6 hours, 12 hours, 24 hours and 48 hours. After storage, blood from K2EDTA tubes were transferred into Tempus™ Blood tubes, and then extracted using Tempus™ Spin RNA Isolation Kit (Life Technologies, Carlsbad, CA, USA). Samples from four subjects of each time point that presented higher RIN value (≥7) were selected for RNA_Seq analysis. Results: The experiment provided RNA quality and purity for gene expression analysis. Considering 6-hours storage as a reference group, the number of differentially expressed genes were 19, 45 and 70 in comparison to 12, 24 and 48-hours, respectively (which means 0.37, 0.88 and 1.37% of mapped genes). Of the 19 differentially expressed genes in the comparison 6 vs. 12-hours, 9 overlapped with the 45 in the comparison 12 vs. 24-hours. Furthermore, 40 of those 45 overlapped with the 70 differentially expressed in the comparison 6 vs. 48-hours. None of the transcripts described in previous studies (Durussel et al. 2016; Wang, Durussel, et al. 2017) were differently expressed. Conclusion: RNA quantity, purity and integrity was not significantly compromised from short-term storage in blood storage tubes lacking RNA stabilisation, indicating that transcriptomic/omics analysis could be conducted using anti-doping samples collected without RNA preservation.
2021-09-03 | GSE183132 | GEO
Project description:Reovirus propagates with high efficiency in KRAS mutated colorectal cancer (CRC). About 45-50% of CRC patients possess KRAS mutation. Oncolytic reovirus treatment in combination with chemotherapy was tested in patient samples possessing KRAS mutated metastatic CRC. This is the raw data from the peripheral mononuclear cell (PBMC) samples at 4 timepoints (pre treatment, 48 hours, day 8, and day 15).
2021-05-01 | GSE173636 | GEO
Project description:To study the effect of GLI3 knockout in brain organoids, we collected scRNA-seq data from 45 day old brain organoids with GLI3 KO
2022-08-19 | E-MTAB-11997 | biostudies-arrayexpress
Project description:Systemic Lupus Erythematosus (SLE) is a systemic autoimmune disease that displays a significant gender difference in terms of incidence and severity. However, the underlying mechanisms accounting for sexual dimorphism remain unclear. To reveal the heterogeneity in the pathogenesis of SLE between male and female patients. PBMC were collected from 15 patients with SLE (7 males, 8 females) and 15 age-matched healthy controls (7 males, 8 females) for proteomic analysis. Enrichment analysis of proteomic data revealed that type I interferon signaling and neutrophil activation networks mapped to both male and female SLE, while male SLE has a higher level of neutrophil activation compared with female SLE. Our findings define gender heterogeneity in the pathogenesis of SLE and may facilitate the development of gender-specific treatments.
2022-08-12 | PXD033144 | Pride
Project description:Somatic genetic copy number analysis of bone marrow from a male patient with refractory cytopenia with multilineage dysplasia and ringed sideroblasts and an abnormal karyotype, 45,XY,der(5)t(5;14)(q14;?q24),dic(17;20)(p13;q12),dic(17;20)(p11.2;q12),-18,+22[6]/45,XY,der(5)t(5;14)(q14;?q24),dic(17;20)(20pter->20p11.2::17p1?1.2->17p1?3::20q12->20q10::20q10->20q12::17p11.2->17qter),dic(17;20)(p11.2;q11.2),-18,+22[cp2]/46,XY,der(5)t(5;14)(q14;?q24),der(17)(20pter->20p13::20q11.2->20q11.2::17p13->17qter),der(17)(20pter->20p11.2::20q11.2->20q11.2::17p13->17qter),-18, 20,+22,+r[9] (Case 6, MacKinnon et al 2007, Genes Chr Cancer 46:27-36)
2010-01-09 | E-MEXP-2275 | biostudies-arrayexpress
Project description:Objective This study presents a rare case of father-to-offspring mosaic transmission of a supernumerary marker chromosome (SMC) and, through integration of literature analysis and computational modeling, proposes a novel embryonic selection-based regulatory mechanism. Methods Karyotyping and SNP-array were performed on amniotic fluid, cord blood, and parental samples. A systematic review identified 35 additional mosaic SMC transmission cases. Four computational frameworks—agent-based simulation, logistic regression, Bayesian inference, and Markov chain modeling—were used to test the hypothesis of selective regulation during early embryogenesis. Results The father carried a mosaic SMC at 11p11 (57%), transmitted to the fetus (38% in amniotic fluid, 45% in cord blood), with both individuals phenotypically normal and no pathogenic CNVs detected. Literature analysis showed consistent patterns of equal or reduced mosaicism in offspring. Modeling revealed that mild selection pressures could replicate observed retention patterns, supporting a non-random, developmentally regulated mechanism. Conclusion The combined clinical, literature-based, and computational evidence supports a model in which early embryos selectively eliminate SMC+ cells to maintain mosaicism at non-pathogenic levels. This proposed “Shepherd Mechanism” may underlie intergenerational mosaic regulation and provides a theoretical foundation for improved prenatal counseling in mosaic cases.
2025-12-10 | GSE302224 | GEO
Project description:scRNA-seq of male mouse aorta collected over the light-dark cycle
2022-09-13 | GSE206583 | GEO
Project description:BACKGROUND: Pre-implantation genetic screening (PGS) has been used in an attempt to determine embryonic aneuploidy. Techniques that use new molecular methods to determine the karyotype of an embryo are expanding the scope of PGS. METHODS: We introduce a new method for PGS, termed “Parental Support” (PS), which leverages microarray measurements from parental DNA to “clean” single cell microarray measurements on embryonic cells and explicitly computes confidence in each copy number call. The method distinguishes mitotic and meiotic copy errors, and determines parental source of aneuploidy. RESULTS: Validation with 459 single cells of known karyotype indicated that per-cell false positive and false negative rates are roughly equivalent to the “gold standard” metaphase karyotype. The majority of the cells were run in parallel with a clinical commercial PGS service. Computed confidences were conservative and roughly concordant with accuracy. To examine ploidy in human embryos, the method was then applied to 26 disaggregated cryopreserved cleavage stage embryos, for a total of 134 single blastomeres. Only 23.1% of the embryos were euploid, though 46.2% of embryos were mosaic euploid. Mosaicism affected 57.7% of the embryos. Counts of mitotic and meiotic errors were roughly equivalent. Maternal meiotic trisomy predominated over paternal trisomy, and maternal meiotic trisomies were negatively predictive of mosaic euploid embryos. CONCLUSIONS: We have performed a major preclinical validation of a new method for PGS and found that the technology performs approximately as well as a metaphase karyotype. We also directly measured the mechanism of aneuploidy in cleavage stage human embryos and found high rates and distinct patterns of mitotic and meiotic aneuploidy.
2009-12-04 | GSE19247 | GEO