Results 111 to 120 of about 38,805 (217)

sNucConv: A bulk RNA-seq deconvolution method trained on single-nucleus RNA-seq data to estimate cell-type composition of human adipose tissues

iScience
Summary: Deconvolution algorithms mostly rely on single-cell RNA-sequencing (scRNA-seq) data applied onto bulk RNA-sequencing (bulk RNA-seq) to estimate tissues’ cell-type composition, with performance accuracy validated on deposited databases.
Gil Sorek, Yulia Haim, Vered Chalifa-Caspi, Or Lazarescu, Maya Ziv-Agam, Tobias Hagemann, Pamela Arielle Nono Nankam, Matthias Blüher, Idit F. Liberty, Oleg Dukhno, Ivan Kukeev, Esti Yeger-Lotem, Assaf Rudich, Liron Levin   +13 more
doaj   +1 more source

Peripheral Neutrophil Activation and Extracellular Trap Formation in Amyotrophic Lateral Sclerosis

Annals of Clinical and Translational Neurology, EarlyView.
Markers of neutrophil activation are increased in plasma during ALS, and markers of NET formation associate with ALS survival. ABSTRACT Objectives Peripheral neutrophil levels in amyotrophic lateral sclerosis (ALS) inversely correlate with survival, suggesting a role for neutrophils in disease progression.
Lillia A. Baird, Haley McQuown, Jihyun Park, Samuel J. Teener, Ian F. Webber‐Davis, Andrew D. Carter, Dae‐Gyu Jang, Eva L. Feldman, Stephen A. Goutman, Benjamin J. Murdock   +9 more
wiley   +1 more source

Increasing usable reads in RNA-seq protocols

iScience
Summary: Bulk and single-cell RNA-seq are powerful tools for transcriptomic analysis, providing insights into molecular and cellular phenotypes. Costs constrain the biological insights obtainable within a given budget, and as sequencing prices decline ...
Felix Pförtner, Eva Briem, Wolfgang Enard, Daniel Richter   +3 more
doaj   +1 more source

Integrated PANoptosis Profiling Identifies Immunosuppressive Subtypes and a Prognostic Signature With Functional Validation of MLKL in Glioblastoma

Annals of Clinical and Translational Neurology, EarlyView.
ABSTRACT Objective The prognosis of glioblastoma (GBM) remains highly unfavorable, largely due to high tumor heterogeneity and an immunosuppressive microenvironment. However, the functional role of PANoptosis in this context is poorly understood. Methods Patients were stratified via K‐means clustering. A risk score model was constructed using prognosis‐
Langfei Tian, Minghui Zhao, Yuanbo Hu, Kaiyue Wang, Haiguang Liu, Zetong Bai, Kebin Zheng   +6 more
wiley   +1 more source

Comparison of gene fusion detection algorithms reveals frequently overlooked driver fusions in hematologic malignancies

npj Precision Oncology
Accurate detection of driver gene fusions is essential for the diagnosis, treatment, and prognostic prediction of hematologic malignancies. Despite increasing reliance on RNA sequencing (RNA-seq) for fusion detection, its algorithms have not been ...
Zen Tamura, Yuki Saito, Yasunori Kogure, Yuji Oshikawa-Kumade, Suguru Fukuhara, Sumito Shingaki, Hirokazu Kariyazono, Yoshiya Kikukawa, Yuta Ito, Kota Mizuno, Yuichi Shiraishi, Kotoe Katayama, Seiya Imoto, Koji Izutsu, Koichi Murakami, Junji Koya, Keisuke Kataoka   +16 more
doaj   +1 more source

Intracerebral Hemorrhage Induces Monocyte TNF Signaling in Patients That Is Suppressed by BAF312

Annals of Clinical and Translational Neurology, EarlyView.
ABSTRACT Objective Intracerebral hemorrhage (ICH) causes high morbidity and mortality, with neurotoxic inflammation driven by infiltrating monocytes. This study is an in‐depth longitudinal examination of the immune response during the first week of ICH in the presence and absence of the immunomodulatory drug BAF312 (Siponimod).
Jonathan Howard DeLong, Sebastian Díaz‐Pérez, Kevin Navin Sheth, Jang‐Ho Cha, C. J. Malanga, Patricia G. M. Wagner, Nicole Pezous, Aurelie Hanin, Kyle B. Walsh, H. E. Hinson, Lauren Hachmann Sansing   +10 more
wiley   +1 more source

Swelling‐Programmed Topographical Guidance for Dynamic Spheroid Self‐Assembly via a Mechanochemical Hydrogel Niche

Advanced Functional Materials, EarlyView.
A swelling‐programmed micropatterned hydrogel guides adherent cells through a controlled transition from cell–matrix anchoring to cadherin‐mediated cell–cell compaction, enabling rapid assembly of high‐viability spheroids with defined size and morphology.
Han Gyeol Nam, Seon Yeong Chae, Young Woo Kwon, Hye Jin Heo, Hye Rin Lee, Ji Hyeok Lee, Dong‐Wook Han, Yun Hak Kim, Suck Won Hong   +8 more
wiley   +1 more source

Tuning Mechanoreceptor Signaling Enhances the Adjuvant Effect of Biomaterial Vaccines

Advanced Functional Materials, EarlyView.
Matrix stiffness serves as an independent immunological signal in biomaterial vaccines. Stiffer microporous hydrogel vaccines enhance dendritic cell maturation and migration to draining lymph nodes, promote T follicular helper cell expansion through Yap/Taz signaling, and increase antigen‐specific antibody production.
Lily Shang, Daniel P. Mayer, Prabhat K. Purbey, Yingzi Liu, Kindra Kelly‐Scumpia, Clara Kang, Natalie Tsubamoto, Dhriti Bolangadi, Iqra Arshad, Charisse Ng, Maksim V. Plikus, Dino Di Carlo, Jason S. Weinstein, Philip O. Scumpia   +13 more
wiley   +1 more source

Introduction to RNA-seq

, 2015
RNA-seq is a useful sequencing-based technology for identifying a snapshot of the transcriptional output from the cell. It has been used to estimate gene expression levels and estimate the impact of different treatments on gene expression. A new generation of methods, based upon RNA-seq is gaining exciting insights into RNA:RNA interactions, RNA ...
openaire   +1 more source

Hierarchical Collagen Nanofiber Gels Recapitulate a Physiologically Relevant Tumor Stromal Microenvironment

Advanced Healthcare Materials, EarlyView.
The collagen nanofiber (CNF) gel supports cancer cell culture, exhibiting cell morphology and cancer‐related protein expression similar to Matrigel. It offers a higher collagen concentration than commercial gels. Additionally, the CNF gel allows replication of the high elasticity of in vivo cancer tissue by controlling collagen fiber sizes, ranging ...
Naoko Sasaki, Tomoyuki Suezawa, Shiro Kitano, Ryohei Katayama, Michiya Matsusaki   +4 more
wiley   +1 more source