Results 101 to 110 of about 10,065,126 (260)

Reconstructing the chondro-osteoblastic lineage by single cell RNA-seq

, 2016
Reconstructing the chondro-osteoblastic lineage by single cell RNA-seq Kwok Yeung Tsang1, Xiangyu Li2, Jin Gu2, Danny Chan1, Michael Q. Zhang2,3, Kathryn SE Cheah1 1School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of ...
Tsang, KY, Gu, J, Li, X, Chan, D, Zhang, MQ, Cheah, KSE   +5 more
core  

Single-cell long-read targeted sequencing reveals transcriptional variation in ovarian cancer

Nature Communications
Single-cell RNA sequencing predominantly employs short-read sequencing to characterize cell types, states and dynamics; however, it is inadequate for comprehensive characterization of RNA isoforms. Long-read sequencing technologies enable single-cell RNA
Ashley Byrne, Daniel Le, Kostianna Sereti, Hari Menon, Samir Vaidya, Neha Patel, Jessica Lund, Ana Xavier-Magalhães, Minyi Shi, Yuxin Liang, Timothy Sterne-Weiler, Zora Modrusan, William Stephenson   +12 more
doaj   +1 more source

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

Dual native G‐quadruplex folding is associated with chromatin looping at the MYC locus

FEBS Open Bio, EarlyView.
BG4‐detectable G‐quadruplex (G4) in HaCaT and NHEK keratinocytes identified folded and unfolded G4s enriched at promoters/TSSs and active enhancers, whereas unfolded G4s also overlapped weak/poised enhancers. At MYC–PVT1, 3C‐qPCR detected enhancer–promoter looping only when G4s were simultaneously folded at both regulatory elements under native ...
Dieila Giomo de Lima, Gustavo Narvaes Guimarães, Emilyane de Oliveira Santana Amaral, Bianca Caroline Figueiredo Bianco, Manuel Jara‐Espejo, Sérgio Roberto Peres Line, Ana Paula de Souza, Aline Cristiane Planello   +7 more
wiley   +1 more source

Cell and gene data for testicular single-cell RNA-Seq

, 2018
Tables containing additional information on genes and cell obtained from single-cell RNA-Seq analysis of mouse testis data. SuppTableCells.xlsx contains the 10X Barcode as identifier, the replicate ID, position in the t-SNE plot, UMI and gene count per ...
Andreas Winterpacht (5099627), Elisabeth Bosch (1647505), Soeren Lukassen (5089880), Arif B. Ekici (146432)   +3 more
core   +1 more source

Bioinformatics perspectives on transcriptomics: A comprehensive review of bulk and single‐cell RNA sequencing analyses

Quantitative Biology
The transcriptome, the complete set of RNA molecules within a cell, plays a critical role in regulating physiological processes. The advent of RNA sequencing (RNA‐seq) facilitated by Next Generation Sequencing (NGS) technologies, has revolutionized ...
Jorge A. Tzec‐Interián, Daianna González‐Padilla, Elsa B. Góngora‐Castillo   +2 more
doaj   +1 more source

GelMA‐based 3D spheroids recapitulate transcriptomic and functional hallmarks of myeloid sarcoma

FEBS Open Bio, EarlyView.
GelMA 5% hydrogels support the formation of myeloid leukemia spheroids that recapitulate MS‐specific features, including G1 arrest, apoptosis, and ECM‐driven transcriptomic reprogramming. The 3D model mimicked soft‐tissue‐like stiffness and oxygen conditions, and transcriptomic convergence with primary MS samples confirmed its utility as a preclinical ...
Nicolas Germain, Elise Buret, Le Hoang Thanh Nguyen, Marion Cocheteux, Nicolas Touya, Mélanie Dhayer, Romain Dubois, Frank Lafont, Sebastien Janel, Patrice Maboudou, Steve Lancel, Philippe Marchetti   +11 more
wiley   +1 more source

Condition-Associated Pattern Extraction and Recovery From Multi-Condition Single-Cell RNA-seq Data With CAPER. [PDF]

Adv Sci (Weinh)
Decoupling biological signals from unwanted variation in multi‑condition single‑cell RNA sequencing data remains challenging. CAPER disentangles condition‑associated biological effects from sample heterogeneity through matrix factorization, producing interpretable latent factors and a batch‑corrected expression matrix.
Li Y, Ning J, Wang A, Shi M, Chen Y, Liu G, Sun S.   +6 more
europepmc   +2 more sources

Using cell‐free RNA to identify B‐ and T‐cell clonality for diagnosis and monitoring of B‐ and T‐cell neoplasms

FEBS Open Bio, EarlyView.
Using peripheral blood for determining B‐cell or T‐cell clonality is more reliable when we use cell‐free RNA (cfRNA) because cells release blood significantly more RNA than DNA. Next‐generation sequencing (NGS) of cfRNA allows us to evaluate fragment cfRNA and evaluate clonality reliably without the need for prior determination of the specific dominant
Adam Albitar, Sally Agersborg, Ahmed Charifa, Pooja Phull, Noa Biran, David Vesole, Harsh Parmar, Andrew Pecora, Andrew Ip, Andre Goy, David Siegel, Maher Albitar   +11 more
wiley   +1 more source

Linearly Amplified Single-Stranded RNA-Derived Transcriptome Sequencing (LAST-seq)

Bio-Protocol
Single-cell RNA sequencing (scRNA-seq) stands as a cutting-edge technology widely used in biological and biomedical research. Existing scRNA-seq methods rely on reverse transcription (RT) and second-strand synthesis (SSS) to convert RNA to cDNA before ...
Jun Lyu, Chongyi Chen
doaj   +1 more source