Optimized Workflow for Whole Genome and Transcriptome Next-Generation Sequencing of Single Cells or Limited Nucleic Acid Samples.

Whole genome and whole transcriptome sequencing require orders of magnitude more of starting nucleic acid than what is found in single cells or other extremely limited samples. High fidelity amplification of this minute amount of nucleic acids is essential to overcome the limitations caused by the low input, degradation and contamination, and to ensure a sufficient amount of DNA for preparation of high complex and high quality next-generation sequencing (NGS) libraries. Recent technical advances in multiple displacement amplification (MDA) enable studies of rare cell types, heterogeneity of body fluids, tissues, environmental samples, and organisms that cannot be cultured. Several strategies for amplification of limiting amounts of nucleic acid have been described, with PCR being popular. However, PCR-based methods result in high error rates, lower library complexity, and lower coverage uniformity. In this article, a HiFi MDA is used to accurately amplify the limited material and to allow library preparation starting from high input, while reducing PCR cycling to achieve sufficient library yields. This article describes a complete workflow from cells and small quantities of DNA or RNA to NGS libraries for Illumina sequencing instruments. © 2023 QIAGEN GmbH. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Whole genome amplification from single cells Support Protocol 1: PicoGreen™ quantification of MDA amplified DNA Support Protocol 2: Purification of amplified DNA after MDA Basic Protocol 2: Whole transcriptome amplification from single cells Alternate Protocol: Whole transcriptome amplification from purified RNA Basic Protocol 3: Enrichment of complete small genomes using target-specific primers in MDA Basic Protocol 4: Complete viral RNA amplification using target-specific primers in MDA Basic Protocol 5: Enzymatic fragmentation and adapter ligation of MDA amplified material Basic Protocol 6: Normalization of library concentration using magnetic beads.

Molecular Analysis of Fetal and Adult Primary Human Liver Sinusoidal Endothelial Cells: A Comparison to Other Endothelial Cells.

In humans, Factor VIII (F8) deficiency leads to hemophilia A and F8 is largely synthesized and secreted by the liver sinusoidal endothelial cells (LSECs). However, the specificity and characteristics of these cells in comparison to other endothelial cells is not well known. In this study, we performed genome wide expression and CpG methylation profiling of fetal and adult human primary LSECs together with other fetal primary endothelial cells from lung (micro-vascular and arterial), and heart (micro-vascular). Our results reveal expression and methylation markers distinguishing LSECs at both fetal and adult stages. Differential gene expression of fetal LSECs in comparison to other fetal endothelial cells pointed to several differentially regulated pathways and biofunctions in fetal LSECs. We used targeted bisulfite resequencing to confirm selected top differentially methylated regions. We further designed an assay where we used the selected methylation markers to test the degree of similarity of in-house iPS generated vascular endothelial cells to primary LSECs; a higher similarity was found to fetal than to adult LSECs. In this study, we provide a detailed molecular profile of LSECs and a guide to testing the effectiveness of production of in vitro differentiated LSECs.

Single-Cell Genome and Transcriptome Sequencing Library Construction Using Combination of MDA and Nextera Library Prep Method.

Single-cell analysis gives insights into the heterogeneity of neighboring cells within tissues or within cell populations and is increasing in importance in life science and medicine. Genome and transcriptome sequencing require orders of magnitude of more starting material than what is found in an individual cell. Handling such small quantities means that degradation, sample loss, and contamination can have a pronounced effect on sequence quality and robustness. Recent technical advances in amplification have helped mitigate these challenges. Single-cell sequencing addresses studies of rare cell types, heterogeneous samples, phenotypes associated with mosaicism or variability, and microbes that cannot be cultured. Single-cell sequencing can enable the discovery of clonal mutations, cryptic cell types, or transcriptional features that would be diluted or averaged out in bulk tissue. This unit describes the entire workflow from cells to next-generation sequencing (NGS), including cell lysis, MDA-based whole-genome and whole-transcriptome amplification, and NGS library preparation. © 2016 by John Wiley & Sons, Inc.

Organized Silica Films Generated by Evaporation-Induced Self-Assembly as Hosts for Iron Oxide Nanoparticles.

In this work, we prepared oriented mesoporous thin films of silica on various solid substrates using the pluronic block copolymer P123 as a template. We attempted to insert guest iron oxide (FexOy) nanoparticles into these films by two different methods: (a) by co-precipitation-where iron precursors are introduced in the synthesis sol before deposition of the silica film-and subsequent oxide production during the film calcination step; (b) by preparing and calcining the silica films first then impregnating them with the iron precursor, obtaining the iron oxide nanoparticles by a second calcination step. We have examined the structural effects of the guest nanoparticles on the silica film structures using grazing incidence X-ray scattering (GISAXS), high-resolution transmission electron spectroscopy (HRTEM), spectroscopic ellipsometry, X-ray photoelectron spectroscopy (XPS), and Raman microscopy. Formation of nanoparticles by co-precipitation may induce substantial changes in the film structure leading, in our adopted process, to the appearance of lamellar ordering in the calcination stage. On the contrary, impregnation-based approaches perturb the film structures much more weakly, but are also less efficient in filling the pores with nanoparticles.

Dendritic polyglycerols with oligoamine shells show low toxicity and high siRNA transfection efficiency in vitro.

RNA interference provides great opportunities for treating diseases from genetic disorders, infection, and cancer. The successful application of small interference RNA (siRNA) in cells with high transfection efficiency and low cytotoxicity is, however, a major challenge in gene-mediated therapy. Several pH-responsive core shell architectures have been designed that contain a nitrogen shell motif and a polyglycerol core, which has been prepared by a two-step protocol involving the activation of primary and secondary hydroxyl groups by phenyl chloroformate and amine substitution. Each polymer was analyzed by particle size and ζ potential measurements, whereas the respective polyplex formation was determined by ethidium bromide displacement assay, atomic force microscopy (AFM), and surface charge analysis. The in vitro gene silencing properties of the different polymers were evaluated by using a human epithelial carcinoma cell (HeLaS3) line with different proteins (Lamin, CDC2, MAPK2). Polyplexes yielded similar knockdown efficiencies as HiPerFect controls, with comparably low cytotoxicity. Therefore, these efficient and highly biocompatible dendritic polyamines are promising candidates for siRNA delivery in vivo.

Synthesis of linear polyamines with different amine spacings and their ability to form dsDNA/siRNA complexes suitable for transfection.

In this paper we report on the synthesis of diversified linear polyamine architectures with different chain lengths and compositions and their interaction with phosphate groups of DNA/siRNA. The polyplex formation between model nucleotide (dsDNA) and these linear polyamines has been determined at different nitrogen to phosphorus (N/P) ratios using small-angle neutron scattering (SANS) and atomic force microscopy (AFM) techniques. AFM images showed that while linear poly(ethylene imine) (PEI)/DNA complex results in bigger spherical aggregates, poly(propylene imine)s forms torroid and cigar shaped structures upon complexation with DNA. The poly(butylene imine)s (LPBI)s form compact and soluble DNA complexes with a radii range of R(g) = 15-30 nm. Among the studied linear polyamines, the LPBIs did show the best transfection efficiency.

siRNA stabilization prolongs gene knockdown in primary T lymphocytes.

RNA interference (RNAi)-mediated knockdown of target gene expression represents a powerful approach for functional genomics and therapeutic applications. However, for T lymphocytes, central regulators of immunity and immunopathologies, the application of RNAi has been limited due to the lack of efficient small interfering RNA (siRNA) delivery protocols, and an inherent inefficiency of the RNAi machinery itself. Here, we use nucleofection, an optimized electroporation approach, to deliver siRNA into primary T lymphocytes with high efficiency and negligible impairment of cell function. We identify siRNA stability within the cells as the critical parameter for efficient RNAi in primary T cells. While generally short-lived and immediately lost upon T-cell activation when conventional siRNA is used, target gene knockdown becomes insensitive to cell activation and can persist for up to 2 wk in non-dividing cells with siRNA stabilized by chemical modifications. Targeting CD4 and the transcription factor GATA-3, we show that the use of stabilized siRNA is imperative for functional gene analysis during T lymphocyte activation and differentiation in vitro as well as in vivo.

Tumor progression and serum anti-HuD antibody concentration in patients with paraneoplastic neurological syndromes.

The aim of this study was to investigate whether there are clues for a correlation between tumor progression and serum anti-Hu antibody concentration in patients with anti-Hu-associated paraneoplastic neurological syndromes (PNS). 19 patients with anti-Hu-associated PNS were assigned to three groups according to the course of tumor progression. Group 1 corresponds to patients with rapid tumor progression [n = 5; mean survival in months/standard deviation (SD); 24/10]; in group 2 patients with a favorable tumor prognosis were included (n = 7; mean/SD 79/25, 6 patients still alive); group 3 consisted of patients in whom tumor progression could not be assessed (n = 7; mean/SD 23/20). The anti-Hu antibody concentrations in sera were measured in a recombinant HuD-ELISA. In sera from patients of group 1 the anti-Hu antibody concentration was modest (mean OD 0.56, SD 0.08) whereas a significantly higher anti-Hu antibody concentration was detected in sera from patients with a favorable tumor prognosis (group 2, mean OD 1.86, SD 0.34). These results hint at a negative correlation between tumor progression and the anti-Hu antibody concentration in sera from patients with PNS. These findings confirm and extend previous reports of more indolent tumor growth in patients with an anti-Hu immune response.