(Press-News.org) (Boston)—CITE-seq (cellular indexing of transcriptomes and epitopes) is an RNA sequencing-based method that simultaneously quantifies cell surface protein and transcriptomic data within a single cell readout. The ability to study cells concurrently offers unprecedented insights into new cell types, disease states or other conditions.
While CITE-seq solves the problem of detecting a limited number of proteins while using single-cell sequencing in an unbiased way, one of its limitations is the high levels of background noise that can hinder analysis.
To rectify this problem, researchers from Boston University Chobanian & Avedisian School of Medicine and Collage of Arts and Sciences have developed a novel tool which can identify and remove unwanted background noise that comes from various sources.
“We created DecontPro, a statistical model that decontaminates two sources of contamination that were observed empirically in CITE-seq data,” explains corresponding author Joshua Campbell, PhD, associate professor of medicine at the School. “It can be used as an important quality assessment tool that will aid in the downstream analysis and help researchers to better understand the molecular cause of disease,” he said.
The researchers examined several publicly available datasets that profiled different types of tissue with CITE-seq and found a novel type of artifact, which they called a “spongelet.” The spongelets contributed a large amount of background noise in several datasets. The researchers found that DecontPro can estimate and remove different sources of background noise, including contamination from spongelets, from ambient material that may be present in the cell suspension, or from non-specific binding of antibodies.
Masanao Yajima, PhD, professor of the practice in the department of mathematics and statistics states, “DecontPro is a Bayesian hierarchical model. We carefully constructed it so that it can tease apart the signals from noise in single-cell datasets without being overly aggressive.”
These findings appear online in the journal Nucleic Acids Research.
Funding was provided by a grant from the Chan Zuckerberg Initiative.
BU researchers develop new method to help with analysis of single cell data
ELSE PRESS RELEASES FROM THIS DATE:
Azerbaijan women behind global average for thalassemia screening and genetic counselling | BGI Insight
5.2% of the global population carry hemoglobin abnormalities, resulting in 300,000 to 400,000 children born with severe hemoglobinopathies annually. Thalassemia, a hereditary hemoglobinopathy, occurs in 4.4 out of every 10,000 live births, and is prevalent in Mediterranean coastal areas, Africa, the Middle East, Southeast Asia, and southern China. To facilitate greater understanding of thalassemia, a hereditary hemoglobinopathy, BGI Genomics today released its State of Thalassemia Awareness Report. This report assesses the level of knowledge and attitudes related to the associated health risks, thalassemia carrier ...
Alliance and WEF sign agreement for Food Action Alliance
The Alliance Bioversity International and CIAT signed an agreement with the World Economic Forum that enables the Alliance to manage initiatives under the Food Action Alliance, a movement led by the World Economic Forum for transforming sustainable food systems. The Alliance would establish and manage initiatives in Latin America, the Caribbean, and other regions under the Food Action Alliance to boost the transformation of food systems, facilitating and scaling up multi-stakeholder flagship initiatives in specific countries mostly with multi-national companies such as Bayer, Microsoft, PepsiCo, AB InBev; among others. The Food Action Alliance will continue to grow initiatives ...
USDA introduces a multi-year plan to strengthen U.S. genebank management of plant germplasm
WASHINGTON, November 17, 2023 – The U.S. Department of Agriculture (USDA) released today the National Strategic Germplasm and Cultivar Collection Assessment and Utilization Plan in support of the Agricultural Research Service (ARS) U.S. National Plant Germplasm System’s (NPGS) mission. The USDA-ARS NPGS is confident that implementing this plan will address current operational and research challenges. The collection is vital for maintaining the nation’s food supply by providing breeders and researchers the germplasm they need to furnish U. S. consumers with abundant, ...
Unravelling the secrets of neurodegenerative diseases, one protein at a time
Proteins misfolding and clumping together, a process known as aggregation, is a key feature seen in several neurological conditions, including Alzheimer's and Parkinson's diseases. These disorders involve the formation of small, potentially harmful structures called oligomers, which could serve as valuable indicators for early diagnosis. They are incredibly small, however, and much rarer than the healthy non-aggregated proteins. This makes it hard to detect and measure them accurately. In collaboration with UCB Biopharma, researchers from the University of Edinburgh’s ...
A world's first in validating a UNFCCC report by a cost-efficient and transparent method to measure CO2 emission estimates using GOSAT
Researchers in Japan and Mongolia have carried out the world's first instance of incorporating satellite-based CO2 emission estimates into a GHG emission report as the verification on the Second Biennial Update Report (BUR2) of Mongolia submitted to the UNFCCC on 15 November 2023, resulting in high accuracy match with actual reported values, reports a new study published online in Scientific Reports in 2023. Countries have reported their CO2 emissions to the UNFCCC, primarily from human activities and a significant contributor to climate change. ...
New cooling mechanism set to revolutionize conventional environmentally harmful refrigeration technologies
Approximately one-fifth of the world's electric energy is dedicated to refrigeration, and the International Energy Agency anticipates a twofold increase in the number of air conditioning units by 2040. Despite a century of advancements, existing refrigeration systems, relying on vapour compression, have hit their thermodynamic threshold. These systems not only emit greenhouse gases, contributing to environmental issues, but also produce significant noise. Prioritizing the development of energy-efficient and eco-friendly systems is thus paramount to address global warming ...
When growth becomes a weakness
Growth is a fundamental biological process and a prerequisite for living organisms to develop and reproduce. The processes of cell growth (i.e. the production of new biomass) and of cell division must be coordinated with each other. In multicellular organisms such as humans, the growth of cells must also be coordinated with their environment so that cells are present in the right number and size to form functional tissue or organs. Cell growth is therefore strictly regulated and takes place only when certain growth signals are present. But cancer cells are different. They grow unchecked, they divide ...
HKU Engineering ‘Super Steel’ team develops new ultra stainless steel for hydrogen production
A research project led by Professor Mingxin Huang at the Department of Mechanical Engineering of the University of Hong Kong (HKU) has made a brand-new breakthrough over conventional stainless steel and the development of stainless steel for hydrogen (SS-H2). This marks another major achievement by Professor Huang’s team in its ‘Super Steel’ Project, following the development of the anti-COVID-19 stainless steel in 2021, and ultra-strong and ultra-tough Super Steel in 2017 and 2020 respectively. The new steel developed by the team exhibits high corrosion ...
AI supporting creative Industries
NYC Media Lab (NYCML) and Bertelsmann unveiled the latest cohort joining the AI & the Creative Industries Challenge, a nine-week program in which teams explore new ways to use artificial intelligence (AI) to create digital content and reach new audiences for three Bertelsmann companies: Fremantle, Penguin Random House, and BMG. The teams are tasked with addressing how AI will impact these important creative industries. This ongoing partnership, NYCML’s third project with Bertelsmann, will continue to build on new business frontiers enabled by technology. The four selected teams, from around the globe, come from various multidisciplinary ...
Porous platinum matrix shows promise as a new actuator material
Actuators are common machine components that convert energy into movement, like the muscles in the human body, vibrators in mobile phones or electric motors. Ideal actuator materials need good electrochemical properties to repeatedly conduct electrical currents made of flowing electrons. In addition, actuator materials require excellent mechanical properties to withstand the physical stress associated with continual movement. Nanoporous platinum (np-Pt), a platinum matrix containing tiny pores to increase energy conduction, was recently created in large quantities and in a cost-efficient manner, making np-Pt an ideal and more practical actuator material. A ...