Results 51 to 60 of about 10,065,126 (260)

Circular RNA expression landscapes in myelodysplastic neoplasms: Associations with mutational signatures and disease progression

Molecular Oncology, EarlyView.
In this explorative study, the abundance of circular RNA molecules in bone marrow stem cells was found to be elevated in patients with high‐risk myelodysplastic neoplasms, and to be associated with an increased risk of progression to acute myeloid leukemia.
Eileen Wedge, Morten Tulstrup, Gabriele Todisco, Pedro Moura, Christophe Côme, Jakob Werner Hansen, Jakob Schmidt Jespersen, Balthasar Schlotmann, Maria Creignou, Mette Dahl, Claudia Schöllkopf, Klas Raaschou‐Jensen, Krister Wennerberg, Bo Porse, Joachim Weischenfeldt, Eva Hellström‐Lindberg, Lasse Sommer Kristensen, Kirsten Grønbæk   +17 more
wiley   +1 more source

Differential expression analysis for sequence count data [PDF]

, 2010
*Motivation:* High-throughput nucleotide sequencing provides quantitative readouts in assays for RNA expression (RNA-Seq), protein-DNA binding (ChIP-Seq) or cell counting (barcode sequencing).
Simon Anders, Wolfgang Huber, Klawonn, Frank   +2 more
core   +1 more source

Single-cell total-RNA profiling unveils regulatory hubs of transcription factors

Nature Communications
Recent development of RNA velocity uses master equations to establish the kinetics of the life cycle of RNAs from unspliced RNA to spliced RNA (i.e., mature RNA) to degradation. To feed this kinetic analysis, simultaneous measurement of unspliced RNA and
Yichi Niu, Jiayi Luo, Chenghang Zong
doaj   +1 more source

KDM7A and KDM1A inhibition suppresses tumour promoting pathways in prostate cancer

Molecular Oncology, EarlyView.
Treatment resistance is a major challenge for patients with advanced prostate cancer. This study examined an alternative approach to target the major prostate cancer‐promoting pathway by targeting epigenetic factors, whose levels are higher in tumours.
Jennie N Jeyapalan, Veronika M Metzler, Simone de Brot, Corinne L Woodcock, Anna E Harris, Jennifer Lothion‐Roy, Emeli M Nilsson, Atara Ntekim, Michael S Toss, Jenny L Persson, Francesca Khani, Brian D Robinson, Lorraine J Gudas, Emad Rakha, David M Heery, Catrin S Rutland, Nigel P Mongan   +16 more
wiley   +1 more source

scGSECA:identification of altered biological processes in single-cell RNA-sequencing data by discretization of expression profiles

, 2023
Bimodality of the distribution of expression levels has been observed in bulk RNA-seq. Two possible explanations underpin this kind of partitioning and refer to opposite paradigmatic models.
Salvatore Oliviero, Michele Caselle, Matteo Cereda, Andrea Lauria, Serena Peirone, Francesca Priante, Sarah Perrone   +6 more
core   +2 more sources

scRepli-RamDA-seq: a multi-omics technology enabling the analysis of gene expression dynamics during S-phase

Nature Communications
Single-cell sequencing has advanced our understanding of cell-type diversity and heterogeneity. However, existing single-cell multi-omics methods lack the ability to monitor gene expression dynamics during S-phase progression.
Rawin Poonperm, Taiki Yoneda, Taito Imada, Saori Takahashi, Takako Ichinose, Hisashi Miura, Tetsutaro Hayashi, Mariko Kuse, Mika Yoshimura, Koji Nagao, Chikashi Obuse, Itoshi Nikaido, Ichiro Hiratani, Shin-ichiro Takebayashi   +13 more
doaj   +1 more source

Bulk brain tissue cell-type deconvolution with bias correction for single-nuclei RNA sequencing data using DeTREM

BMC Bioinformatics, 2023
Background Quantifying cell-type abundance in bulk tissue RNA-sequencing enables researchers to better understand complex systems. Newer deconvolution methodologies, such as MuSiC, use cell-type signatures derived from single-cell RNA-sequencing (scRNA ...
Nicholas K. O’Neill, Thor D. Stein, Junming Hu, Habbiburr Rehman, Joshua D. Campbell, Masanao Yajima, Xiaoling Zhang, Lindsay A. Farrer   +7 more
doaj   +1 more source

Developmental programmes drive cellular plasticity, disease progression and therapy resistance in lung adenocarcinoma

Molecular Oncology, EarlyView.
This study shows that lung adenocarcinomas exploit developmental branching morphogenesis to acquire a therapy resistant basal‐like tumour cell state. This process was found to be regulated by combined TP53 loss‐of‐function and type‐I interferon signalling, identifying a novel axis for biomarker and therapeutic target discovery.
Kamila J Bienkowska, Stephany Gallardo, Nur S. Zainal, Leena Arora, Matthew Ellis, Maria‐Antoinette Lopez, Judith Austine, Sai Pittla, Serena J Chee, Aiman Alzetani, Emily C Shaw, Christian H Ottensmeier, Gareth J Thomas, Christopher J Hanley   +13 more
wiley   +1 more source

Time-resolved single-cell RNA-seq using metabolic RNA labelling [PDF]

, 2022
Single-cell RNA sequencing offers snapshots of whole transcriptomes but obscures the temporal RNA dynamics. Here we present single-cell metabolically labeled new RNA tagging sequencing (scNT-seq), a method for massively parallel analysis of newly ...
Lusser, Alexandra, Hennig, Thomas, Prusty, Bhupesh K; https://orcid.org/, Kirschenbaum, Daniel; https://orcid.org/, Erhard, Florian; https://orcid.org/, Toussaint, Christophe; https://orcid.org/, Friedel, Caroline C; https://orcid.org/, Amit, Ido, Saliba, Antoine-Emmanuel, Dölken, Lars; https://orcid.org/, Abadie, Kathleen, Miska, Eric A; https://orcid.org/, Micura, Ronald   +12 more
core   +1 more source

Deep Batch Integration and Denoise of Single‐Cell RNA‐Seq Data

Advanced Science
Numerous single‐cell transcriptomic datasets from identical tissues or cell lines are generated from different laboratories or single‐cell RNA sequencing (scRNA‐seq) protocols.
Lu Qin, Guangya Zhang, Shaoqiang Zhang, Yong Chen   +3 more
doaj   +1 more source