Project description:The effects exerted by three mixtures of Polychlorinated Biphenyls (PCB), one featuring dioxin-like (DL) and two featuring non dioxin-like (NDL) congeners, on human fetal corpora cavernosa cells representative of a major male endocrine-sensitive organ, have been evaluated by gene expression profiling. PCB congeners concentrations used were derived from human internal exposure data to explore the impact of the adult body burden on a fetal tissue. Cell exposure were performed for 72h mimicking a chronic exposure. Experiment conditions: control, three treatments with PCB-Mix1, PCB-Mix2 or PCB-Mix3. Biological replicates: 3 control replicates, 3 replicates per treatment. Technical replica: 2 (dye swap) per biological replica. Direct comparison design (control vs treated samples) in 12/16 arrays (biological replicates 1 and 2); Loop design in 4/16 arrays (biological replicate 3).
Project description:Gene expression from primary neuronal, astrocytic, oligodendrocytic and microglial cultures, as well as from RNA mixtures thereof. Keywords: Primary cell cultures Primary neuronal, astrocytic, oligodendrocytic and microglial cultures (4 biological replicates of each), as well as RNA mixtures thereof (5 different mixing proportions, 2 independent replicates of each mixing proportion).
Project description:We report a deconvolution and identification strategy of scRNA-seq datasets using mixed PMBCs data. After sequencing the data were processed with the de-goulash pipeline and analyzed with aim to identify and aquire biogeogrpahical ancestry of the involved individuals. The study includes samples of biological mixtures and in silico mixtures.
Project description:Biotechnology-derived therapeutics manufacturing is highly regulated to assure product quality, safety and efficacy. Process conditions are closely monitored as they can influence product characteristics. Culture of mammalian cells at different scales is a vital part of biomanufacturing. Currently, scale up of bioreactors is largely done based on engineering parameters such as oxygen transfer and mixing characteristics. There is a lack of genomic translational studies in mammalian cell culture scale-up that can help delineate measurable cellular attributes for improved process understanding. These could be used for quantifying physiological response of cells due to changes in bioreactor environment. In this study, we identified 18 process-sensitive sentinel genes using microarray statistical analysis, which we further verified by qRT-PCR. These were differentially expressed transcripts between a typical 5 liter bench-scale bubble-aerated and impeller-agitated bioreactor and novel 35 mL high-throughput minibioreactors. Using expression changes and biochemical-pathway guidance of these sentinel genes, we were able to tune engineering parameters such that the improved scale-down resulted in both process parameter and sentinel gene profile convergence between the two systems, further solidifying the functionality evidence of these sentinel genes. This study serves as a starting point for developing qRT-PCR assays as comparability metrics that could be performed near-at-line during the cell culture process itself leading to enhanced process control. Additional broad applications of sentinel genes could be to validate different manufacturing facilities for the same product, and allow better process definition by fingerprinting the manufacturing process for more rapid biogenerics and vaccine approvals. We ran consecutive bioreactor (5L and HTCB) runs, each with an independent vial thaw, to achieve multiple biological replicates per time-point. Bioreactors were sampled approximately every 12 hours for RNA extraction. For the 5L bioreactors, microarray samples were run for day 1 (n=2), day 2 (n=2), day 3 (n=3), and day 3.5 (n=3). Here 2 or 3 of the three biological replicates run for each time-point were included in the analysis, based on >70% genes found. For the High-Throughput Controlled Minibioreactors (HTCB), microarray samples were run for day 1 (n=3), day 2 (n=3), day 3 (n=3), day 4 (n=2), and day 4.5 (n=2). Here 2 to 4 of the 4 biological replicate runs were included in the analysis, based on >70% genes found. We define early exponential as day 1, peak exponential as day 2 and day 3 and late stationary as day 3.5.
Project description:Human pluripotent stem cells (hPSCs) have an unlimited capacity to self-renewal and generate any somatic cell types in the human body, offer a promising cell resource for disease modeling and transplantation. However, the systematic mechanism leading the conversion of hPSCs into lineage specification, which is the earliest cellular event during human embryonic development, is elusive. Here, combining a lineage-specific reporter with inducible CRISPR/Cas9 system, we conducted a genome-scale screening in hESCs for overall drawing the track of cell fate decision. We defined eight functional modules containing embryonic development, mRNA processing, metabolism process, epigenetic regulation, cell cycle and others, that participate in full to the lineage commitment.
Project description:The objective of the study was to utilize DNA methylation to quantify human leukocyte subsets in human blood. This file contains data from an Illumina custom VeraCode GGMA microarray for human leukocyte subtypes (purified from whole blood samples via magnetic activated cell sorting (MACS) and purity confirmed by flourescence activated cell sorting (FACS)) as well as for complex mixtures of DNA from those samples, and for human whole blood samples.
Project description:The effects exerted by three mixtures of Polychlorinated Biphenyls (PCB), one featuring dioxin-like (DL) and two featuring non dioxin-like (NDL) congeners, on human fetal corpora cavernosa cells representative of a major male endocrine-sensitive organ, have been evaluated by gene expression profiling. PCB congeners concentrations used were derived from human internal exposure data to explore the impact of the adult body burden on a fetal tissue. Cell exposure were performed for 72h mimicking a chronic exposure.