... interests The authors declare no competing or financial interests. 24 8 2023 9 7 2024 © 2024. Published by The Company of Biologists Ltd 2024 https://www.biologists.com/user-licence-1-1/ Summary: Combinatorial multi-omics analyses using ATAC-seq, single-cell RNA-seq...

.... Arabidopsis thaliana Proteomics Early embryogenesis RNA-seq Shenzhen Municipal Science and Technology Innovation Council 20200925153547003 State Key Laboratory of Agrobiotechnology Chinese University of Hong Kong http://dx.doi.org/10.13039/501100004853 8300052...

... encompasses many major morphological events, including segmentation, body regionalization, gut morphogenesis and limb development. In addition, we use short- and long-read RNA-seq to generate an improved Parhyale genome annotation, enabling deeper classification of identified regulatory elements. We discover...

... development. Selfing Isogenic Forward genetics Tail bud Noto Mesogenin Mutant RNA-seq University of Basrah http://dx.doi.org/10.13039/100012026 National Institute of Child Health and Human Development http://dx.doi.org/10.13039/100000071 R15HD060017 References...

... of California. The Universität Basel provided core funding (to A.Z. and R.Z.). Deposited in PMC for immediate release. Data availability All ChIP-seq, ATAC-seq and RNA-seq datasets have been deposited in GEO under the accession number GSE114257 . The peer review history is available online...

... regulation is target and co-factor dependent, contingent on the milieu of factors that are present at different stages of development. To determine the role of Taf15 in early Xenopus development, we used RNA-sequencing (RNA-seq) from single embryos depleted of M- and Z-Taf15, using reagents that targeted...

... analyze the transcriptome of discrete but continuously differentiating germline cysts. We first isolated single cysts at each recognizable stage from wild-type testes, which were subsequently applied for RNA-seq analyses. Our data delineate a high-resolution transcriptome atlas in the entire male GSC...

... in different regions of the central nervous system. Whether astrocyte diversity is attributable to developmental processes and bears functional consequences, especially in humans, is unknown. RNA-seq of human pluripotent stem cell-derived regional astrocytes revealed distinct transcript profiles, suggesting...

... designed to phenocopy Fgf3/Fgf10 double mutants were achieved by feeding pregnant females DOX-chow (200 mg/kg, Custom Animal Diets, LLC) ad libitum for the indicated time periods (E5.5-E10.5, E5.5-E11.5 or E6.5-E11.5). All subsequent inductions to generate samples for paintfilling, RNA-Seq, ISH...

... RNA with 4-thiouracil in a specific cell type in vivo followed by detection through an RNA-seq-based method that specifically distinguishes the thiolated uridine by base conversion. This method has successfully identified the cell type-specific transcriptome in three different tissues: endothelial...

... Amniotes Early embryo RNA-seq Signaling pathways National Research Foundation of Korea 10.13039/501100003725 2015R1A3A2033826 Avian species have been used as valuable research models for virology, cancer, immunology, developmental biology and biotechnology ( Streit et al., 2000...

.... Depending on the samples compared, selection results were affected mostly by technical factors (library construction protocol, RNA-seq coverage, read distribution) where such properties differed between studies and datasets. To reduce these effects, when data from multiple studies were treated in a single...

... for proper PGC specification and development has not been characterized in Xenopus . To begin to understand the gene network required for proper PGC development, we recently completed RNA-sequencing (RNA-seq) analysis of both animal and vegetal pole tips isolated from stage VI oocytes ( Owens et al...

...Mike Adam; Andrew S. Potter; S. Steven Potter Single-cell RNA-seq is a powerful technique. Nevertheless, there are important limitations, including the technical challenges of breaking down an organ or tissue into a single-cell suspension. Invariably, this has required enzymatic incubation at 37°C...

... of heart development, during which many congenital heart disease malformations likely arise, we conducted an RNA-seq timecourse in zebrafish from 30 hpf to 72 hpf and identified 5861 genes with altered expression. We clustered the genes by temporal expression pattern, identified transcription factor...

... as they are clustered at the midline, resembling other midline structures important for maintaining the bilateral organization of the neural tube. Adhesion Cell movement Midline Pituitary Chick RNA-seq Sp8 Placodes are discrete thickenings of the cranial ectoderm localized in the proximity...

... strains, we performed an RNA-seq screen, identifying tip- and stalk-enriched gene sets in the developing collecting duct system. Detailed in situ hybridization studies of tip-enriched predictions identified UBT-enriched gene sets conserved between the mouse and human kidney. Comparative spatial analysis...

... in the genome is poorly understood. Here we identified the transcriptomes of Xenopus foregut and hindgut progenitors, which are conserved with mammals. Using RNA-seq and ChIP-seq we show that BMP/Smad1 regulates dorsal-ventral gene expression in both the endoderm and mesoderm, whereas Wnt/β-catenin acts...

.../ Summary: RNA-sequencing analysis identifies 90 novel mRNAs that are enriched at the vegetal pole of Xenopus laevis oocytes, and reveals novel roles for some of these mRNAs in primordial germ cell development. Xenopus RNA-seq PGCs Localized RNAs Gene pathways Scaffold For many...

... sequencing has been used to study developmental and stem cell biology, providing insights into cell type diversity and developmental dynamics. RNA-Seq Computational biology Gene regulatory networks Pseudotime Single cell Stem cells To characterize the diversity of cell types...