Project description:Comparison of the transcriptome profiles of a widely commercialized maize MON810 variety and its non-GM near-isogenic counterpart subjected to low N fertilization farming practices
Project description:The Amish and Hutterites are U.S. farming populations with remarkably similar lifestyles. However, the Amish follow traditional farming practices, while the Hutterites employ modern farming techniques, and also show striking differences in asthma prevalence. Little is known about immune responses underlying these differences. To address this, we obtained genome-wide gene expression data in peripheral blood leukocytes from Amish and Hutterite schoolchildren.
2016-08-05 | GSE85007 | GEO
Project description:Mulching practices manipulate microbial community diversity
Project description:Quinoa is widely recognized for its exceptional nutritional properties, particularly its complete protein content. This study, for the first time, investigates the effects of processing methods (boiling and extrusion) and farming conditions (conventional and organic) on the quinoa’s proteomic profile. Following a label-free shotgun proteomics approach, a total of 1,796 proteins were identified and quantified across all quinoa samples. Regarding processing, both boiling and extrusion produced protein extracts with lower total protein content, with the number of identified proteins decreasing from 1,695 in raw quinoa to 957 in processed quinoa. Boiling led to a reduction in protein diversity and expression, while extrusion, which involves high temperatures and pressures, specifically decreased the abundance of high molecular mass proteins. Concerning cultivation practices, organic farming was associated with a broader protein diversity, especially proteins related to translation (28% vs. 5%), while conventional farming showed a higher abundance of catalytic and enzymatic proteins (67% vs. 46%). These findings highlight the distinct proteomic changes induced by different processing methods and farming conditions, offering valuable insights to manage quinoa’s nutritional, bioactive, and functional properties across various production practices.
Project description:The Amish and Hutterites are U.S. farming populations with remarkably similar lifestyles. However, the Amish follow traditional farming practices, while the Hutterites employ modern farming techniques, and also show striking differences in asthma prevalence. Little is known about immune responses underlying these differences. To address this, we obtained genome-wide gene expression data in peripheral blood leukocytes from Amish and Hutterite schoolchildren. The study includes data from whole blood samples from age- and sex-matched Amish and Hutterite schoolchildren. Written consent was obtained from the parents and written assent was obtained from the children. One mL of whole blood was drawn into a TruCulture tube containing media alone, and incubated upright on a dry heat block at 37°C for 30 hours. Cells were isolated and total RNA was extracted using Qiagen AllPrep DNA/RNA Mini Kits. RNA concentration was assayed with a Nanodrop ND-100 Sepectrophotometer; RNA quality was assessed with an Agilent 2100 Bioanalyzer. Samples underwent cDNA synthesis and were then hybridized on the Illumina HumanHT-12 v4 Expression BeadChip arrays at the Functional Genomics Core at the University of Chicago.
Project description:We developed an automated high-throughput Smart-seq3 (HT Smart-seq3) workflow via robotic implementation and established best practices to consistently achieve high cell capture efficiency and data quality. In comparison with the 10X platform, HT Smart-seq3 analysis of primary CD4+ T-cells demonstrated superior sensitivity in gene detection and similar capability to capture major cellular heterogeneity upon sufficient scaling up. Notably, through T-cell receptor (TCR) reconstruction, HT Smart-seq3 identified more productive pairs of alpha and beta chains without additional primer design, enabling more comprehensive profiling of TCRs. Collectively, HT Smart-seq3 provides a cost-effective and scalable method for characterization of single-cell transcriptomes and immune repertoires.
Project description:We developed an automated high-throughput Smart-seq3 (HT Smart-seq3) workflow via robotic implementation and established best practices to consistently achieve high cell capture efficiency and data quality. In comparison with the 10X platform, HT Smart-seq3 analysis of primary CD4+ T-cells demonstrated superior sensitivity in gene detection and similar capability to capture major cellular heterogeneity upon sufficient scaling up. Notably, through T-cell receptor (TCR) reconstruction, HT Smart-seq3 identified more productive pairs of alpha and beta chains without additional primer design, enabling more comprehensive profiling of TCRs. Collectively, HT Smart-seq3 provides a cost-effective and scalable method for characterization of single-cell transcriptomes and immune repertoires.
Project description:We developed an automated high-throughput Smart-seq3 (HT Smart-seq3) workflow via robotic implementation and established best practices to consistently achieve high cell capture efficiency and data quality. In comparison with the 10X platform, HT Smart-seq3 analysis of primary CD4+ T-cells demonstrated superior sensitivity in gene detection and similar capability to capture major cellular heterogeneity upon sufficient scaling up. Notably, through T-cell receptor (TCR) reconstruction, HT Smart-seq3 identified more productive pairs of alpha and beta chains without additional primer design, enabling more comprehensive profiling of TCRs. Collectively, HT Smart-seq3 provides a cost-effective and scalable method for characterization of single-cell transcriptomes and immune repertoires.