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RNAseq Analysis Investigates Transcriptional Similarities and Differences Between Cryopreserved Parental and Engineered iPSC Derived Macrophages

ABSTRACT: RNAseq Analysis Investigates Transcriptional Similarities and Differences Between Cryopreserved Parental and Engineered iPSC Derived Macrophages

PROVIDER: PRJNA718884 | ENA |

REPOSITORIES: ENA

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RNAseq Analysis Investigates Transcriptional Similarities and Differences Between Cryopreserved Parental and Engineered iPSC Derived Macrophages

Project description:RNA-seq analysis was used to investigate the transcriptional profile to reflect the changes in the parental vs engineered iPSC-derived macrophages. The RNA seq analysis provided an insight to uncover underlying mechanisms that might be triggered by perturbations in SNCA, Progranulin, and MeCP2 genes in iPSC derived macrophages. RNA seq data revealed an upregulation of 431 genes and concomitant downregulation of 276 in SNCA A53T Macrophages, an upregulation of 549 genes and concomitant downregulation of 356 in GRN R493X macrophages, an upregulation of 466 genes and concomitant downregulation of 406 genes in MeCP2HM macrophages when compared to the parental unengineered macrophages. These genes affected pathways regulating cell metabolism, exocytosis, transport, degranulation, immune activation, vascular circulation and neural differentiation and provided a comprehensive analysis of all cellular pathways perturbed by genetic engineering in SNCA, Progranulin, and MeCP2 genes.

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Transcription profiling of human neuro-invasive pancreatic tumors engineered in-vitro compared to less invasive parental cells

Project description:Perineural invasion (PNI) is considered to be a specific path for the spread of pancreatic cancer cells and PNI is thought to be one of the important factors that determine local recurrence after resection. In addition PNI has been implicated in the pain syndrome that affects the majority of pancreatic ductal adenocarcinoma (PDAC) patients. Here we aimed to investigate the transcriptional differences between neuro-invasive tumors engineered in-vitro compared to less invasive parental cells. Two colour differential hybridisations were performed with human universal reference total RNA (Clontech, #636538).

2009-04-01 | E-TABM-400 | biostudies-arrayexpress

Anti-apoptotic regulation contributes successful nuclear reprogramming using cryopreserved oocytes

Project description:The cryopreservation has a negative effect on the quality of oocytes and may be closely associated with increased levels of reactive oxygen species (ROS) and apoptotic events. The purpose of the present study was to evaluate the detrimental effects on the developmental competence of somatic cell nuclear transferred (SCNT)- mouse embryos using vitrified (cryopreserved) oocytes and to evaluate the recovery effects of melatonin on cryo-damage in cloned embryos. Development of SCNT embryos using cryopreserved oocyte cytoplasm (SCNT-CROC) was inferior to those using fresh cytoplasm (SCNT-FOC). Using RNA-sequencing analysis, we found upregulation of 8 pro-apoptotic-related genes (Cyct, Dapk2, Dffb, Gadd45g, Hint2, Mien1, P2rx7, and Pmaip) in the SCNT-CROC group. Furthermore, the addition of melatonin, an agent that reduces apoptosis and ROS production, enhanced blastocyst formation rates in the SCNT-CROP group when compared with the melatonin-untreated group. Additionally, melatonin-treatment increased the derivation efficiency of pluripotent stem cells from cloned embryos using cryopreserved oocyte.

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RockDove Parental Care

Project description:RockDove Parental Care

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Project description:Excess/residual urea is a pervasion problem in wine and Sake fermentation. We sought to reduce residual urea levels (to reduce ethyl carbamate leves) by engineering the Sake yeast strain K7 to constitutively express either the urea amidolyase (Dur1,2) or urea importer (Dur3). We sought to then compare the gene expression profiles of the metabolically engineered yeast strains to the parental strain during fermentation. Engineered strains would hopefully have gene expression profiles that were minimally different from the parental strain.

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Mitochondrial DNA sequencing of iPSC, parental cells, and iPSC derived cardiomyocytes

Project description:The aim of this work was to analyze to which extent mitochondrial DNA (mtDNA) variants in human induced pluripotent stem cells (iPSC) originate from their parental cells or from de novo mutagenesis, and whether dynamics in variant heteroplasmy levels during prolonged expansion culture of iPSC are caused by inter- or intra-cellular selection or genetic drift. Hence, mtDNA of 26 early passage iPSC clones from, in total, 10 donors and the corresponding parental cell populations (here endothelial cells) were sequenced. Furthermore, 7 iPSC clones were expanded up to passage 50 and the change in variant heteroplasmy levels was monitored. Lastly, the effect of differentiation on the variant heteroplasmy levels was investigated during directed cardiomyocyte differentiation of 4 iPSC clones.

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Expression of M-CSF from cryopreserved teeth-derived human periodontal ligament cells with different freezing protocols

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Single Cell Transcriptome Conservation in Cryopreserved Cells and Tissues

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Gene expression profiling of human fresh and cryopreserved sperm

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cryopreserved CD34 positive human umbilical cord blood cells

Project description:Human umbilical cord blood cells (UCB) is an important alternative resource for the hematopoietic stem cells in treatment of leukemia and other non-malignant diseases. The failure of hematopoiesis reconstruction by the UCB is known to be associated with several clinicopathological features of host patients. There are very few reports available, however, seeking for the association with the quality of umbilical cord blood cells (UCB) themselves. Here we try to address the quality of UCBs by transfusion to the lethally irradiated immunocompromized mice. The cryopreserved CD34+ UCBs cells from twelve different single human donors were transplanted to the irradiated NOD/shi-scid Jic mice. In parallel, total RNAs of the UCBs were subjected to the gene expression profiling with oligonucleotide microarrays. The UCBs from three donors failed to establish the engraftment in the host mice whereas other 9 UCBs succeeded to various extents. Oligonucleotide microarray analysis indicated that 71 genes, including HOXB4 and ETS2, were specifically overexpressed and 23 genes were suppressed more than 2 fold in the successful UCBs comparing with the failed ones (p<0.005, Student’s t-test). Functional annotation analyses revealed that the genes mediated cell growth and cell cycle regulations were enriched in successful UCBs comparing with the failed ones. Our results suggest that the hematopoiesis reconstitution ability may vary among the cryopreserved UCBs and the quality can be distinguished with certain sets of gene expression.

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