Investigation of the genetic basis of the rare syndrome Post-Transfusion Purpura (PTP)
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PROVIDER: EGAS00001000053 | EGA |
REPOSITORIES: EGA
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Project description:CHOPS syndrome is caused by germline gain-of-function mutations of AFF4. Cornelia de Lange syndrome is caused by germline mutations of cohesin loading factors or cohesin complex genes such as NIPBL, SMC1A, SMC3 and HDAC8. There are many overlapping clinical features exist between CHOPS syndrome and Cornelia de Lange syndrome. To identified commonly dysregulated genes in CHOPS syndrome and Cornelia de Lange syndrome, we perfomred side-by-side transcriptome comparison between CHOPS syndrome and Cornelia de Lange syndrome.
2015-01-27 | GSE64034 | GEO
Project description:CHOPS syndrome is caused by germline gain-of-function mutations of AFF4. Cornelia de Lange syndrome is caused by germline mutations of cohesin loading factors or cohesin complex genes such as NIPBL, SMC1A, SMC3 and HDAC8. There are many overlapping clinical features exist between CHOPS syndrome and Cornelia de Lange syndrome. To identified commonly dysregulated genes in CHOPS syndrome and Cornelia de Lange syndrome, we perfomred side-by-side transcriptome comparison between CHOPS syndrome and Cornelia de Lange syndrome. In this transcriptome analysis, patient derived skin fibroblasts from two CHOPS syndrome probands, two Cornelia de Lange syndrome probands, and four age-gender-ethnicity matched healthy control subjects were used.The samples used for Human Gene 2.0 arrays are two CHOPs syndrome samples (CDL160 and CDL444), two Cornelia de Lange syndrome samples (CdL006: 7 year-old Caucasian female NIPBL 742_743delCT ;L248TfsX6 and CdL015: 10 year-old Caucasian male NIPBL 2969delG;G990DfsX2), and four age gender matched control samples (GM01652, GM01864, GM02036 and GM03348).
2015-01-27 | E-GEOD-64034 | biostudies-arrayexpress
Project description:In this study, we sought to extend knowledge of lymphocyte development by studying patients with classical Omenn syndrome or T-B- SCID. to gain further insight into pathomechanism, we undertook single cell studies of cryopreserved peripheral blood mononuclear cells from patients with Omenn syndrome associated with either the NUDCD3 variant (3 patients/3 samples), or pathogenic defects of RAG1 (6 patients/6 samples) or RAG2 (2 patients/2samples), and healthy controls (2 samples) for comparison.
2024-06-06 | E-MTAB-12283 | biostudies-arrayexpress
Project description:Cryopreservation is a key method for long-term storage of biological specimens. The development of optimal cryopreservation condition will reduce the damage from the storage as least as possible. The effect of the cryopreservation condition we used on peripheral blood mononuclear cells (PBMCs) has been previously evaluated with microarray analysis. The emerging single-cell RNA sequencing (scRNA-seq) technology enable deeper exploring cellular heterogeneity and function. In the current study, we further optimized the cryopreservation procedure using FACS analysis, and the method were further evaluated by ScRNA-Seq for two different length of storage time: six months and 12 months in comparison to fresh cells. We identified major immune cell types from both fresh and recovered cryopreserved PBMCs, including monocytes, dendritic cells (DCs), natural Killer (NK) cells, CD4+ T cells, CD8+ T cells, and B cells. The cell viability of all identified immune cell types was relatively stable during the initial 6-month of cryopreservation, while showed10 ~ 40 % decline after cryopreserved for 12 months for different cell types. Furthermore, transcriptome profile of cryopreserved samples did not show obvious perturbation during whole 12 months testing time, although a few key genes involved in stress response or apoptosis, exhibited significant change, especially in monocytes, DC and NK cells. Our results validate that the optimized cryopreservation is a reliable procedure for maintaining these major immune cell types in PBMCs, also highlight the importance of careful assessment of individual sample as variation could be introduced by cryopreservation.
2025-08-07 | GSE304704 | GEO
Project description:Pes anserine syndrome is a cause of inferomedial knee pain. It occurs in patients with diabetes mellitus, osteoarthritis, rheumatoid arthritis and in overweight patients. It is a challenge to identify the causes of knee pain following knee replacement surgery. We present a case report of pes anserine syndrome in a 79-year-old female who had undergone knee arthroplasty 13 years prior. She was pain free until one year ago when her knee pain resurfaced without any symptoms of infection or history of trauma. She was successfully treated with a combination of stretching exercise and steroid local steroid injection. We want to highlight that such common condition as pes anserine syndrome, could occur in total knee arthroplasty, and should be considered as one of the possible diagnosis.
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Project description:Molecular basis for autosomal-dominant renal Fanconi syndrome caused by HNF4A
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Project description:A specific missense mutation in the DNA binding domain of HNF4A, R85W, causes Fanconi renotubular syndrome (FRTS). To confirm results found in Drosophila, a direct reprogramming approach was applied. Induced renal epithelial tubular cells (iRECs) were generated using transcription factors Hnf1b, Pax8 and either HNF4A WT or HNF4A R85W. RNA Seq analysis of reprogrammed cells shows mitochondrial dysfunction caused by the R85W mutation.
2019-12-16 | GSE139674 | GEO
Project description:Cryopreserved synovial fluid mononuclear cells from three patients with seropositive rheumatoid arthritis were thawed and stained for surface antibodies, then fixed and stained for intracellular granzyme K and granzyme B. CD8 T cells with the following expression patterns were then isolated by FACS.
2022-05-08 | GSE202365 | GEO
Project description:Light intensity and spectral quality are two important factors that affect the cryopreservation success of plant germplasm. In a previous study, we found that LEDs with 90% red and 10% blue (RB) light have a positive effect on potato (Solanum tuberosum L.) shoot tip recovery during post-cryopreservation regeneration. In the present study, transcriptome profiles of non-cryopreserved (-) and cryopreserved (+) potato shoot tips exposed to RB, cool white fluorescent tubes (CW) and full darkness (D) were compared. Results indicated that light spectrum significantly affects transcript numbers in post-cryopreserved samples resulting in 3,284 differentially expressed genes of recovering shoot tips exposed to CW, RB and D. Gene ontology (GO) enrichment analysis revealed that several stress-related terms were more abundant in CW+, whereas morphogenesis-related processes were activated under RB+. Overall, cryopreservation had an extensive effect on gene expression, as 12,017 genes were differentially expressed in non-cryopreserved and cryopreserved shoot tips. Among all cryopreserved samples, enriched GO terms included various defense and stress responses to biotic stimuli and oxidative stress, whereas suppressed responses were mainly related to organ morphogenesis. The present study emphasizes that the optimization of light spectral properties to decrease light-related stress may greatly benefit the cryopreservation efficiency of plant germplasm.
2025-08-19 | GSE262492 | GEO
Project description:BackgroundHypoplastic right heart syndrome (HRHS) is a rare congenital defect characterized by underdevelopment of the right heart structures commonly accompanied by an atrial septal defect. Familial HRHS reports suggest genetic factor involvement. We examined the role of copy number variants (CNVs) in HRHS.MethodsWe genotyped 32 HRHS cases identified from all New York State live births (1998-2005) using Illumina HumanOmni2.5 microarrays. CNVs were called with PennCNV and prioritized if they were ≥20 Kb, contained ≥10 SNPs and had minimal overlap with CNVs from in-house controls, the Database of Genomic Variants, HapMap3, and Childrens Hospital of Philadelphia database.ResultsWe identified 28 CNVs in 17 cases; several encompassed genes important for right heart development. One case had a 2p16-2p23 duplication spanning LBH, a limb and heart development transcription factor. Lbh mis-expression results in right ventricular hypoplasia and pulmonary valve defects. This duplication also encompassed SOS1, a factor associated with pulmonary valve stenosis in Noonan syndrome. Sos1-/- mice display thin and poorly trabeculated ventricles. In another case, we identified a 1.5 Mb deletion associated with Williams-Beuren syndrome, a disorder that includes valvular malformations. A third case had a 24 Kb deletion upstream of the TGFβ ligand ITGB8. Embryos genetically null for Itgb8, and its intracellular interactant Band 4.1B, display lethal cardiac phenotypes.ConclusionTo our knowledge, this is the first study of CNVs in HRHS. We identified several rare CNVs that overlap genes related to right ventricular wall and valve development, suggesting that genetics plays a role in HRHS and providing clues for further investigation. Birth Defects Research 109:16-26, 2017. © 2016 Wiley Periodicals, Inc.
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