Project description:Genome wide DNA methylation and hydroxymethylation profiling of 6 isolated single cell clones and the parental (SUM149-PT) cell line. The Illumina Infinium Human MethylationEPIC Beadchip was used to obtain DNA methylation and hydroxymethylation profiles across approximately 850,000 CpGs in 6 isolated single cell clones that represent the phenotypes of the epithelial-to-mesenchymal spectrum along with the parental (SUM149-PT) cell line. Isolated single cell clones represent varying phenotypes of the epithelial-to-mesenchymal transition. Detailed isolation and characterization methods can be found in Brown et al, 2021. https://doi.org/10.1101/2021.03.17.434993
Project description:This SuperSeries is composed of the SubSeries listed below. The main processed data are organized in the following two Figshare links: Seurat objects: https://doi.org/10.6084/m9.figshare.23290004 ReDeeM-V output: https://doi.org/10.6084/m9.figshare.24418966.v1
Project description:This SuperSeries is composed of the SubSeries listed below. Publication: D Janecki, R Sen, N Szóstak, A Kajdasz, M Kordys, K Plawgo, D Pandakov, A Philips, Z Warkocki (2024): LINE-1 mRNA 3’ end dynamics shape its biology and retrotransposition potential. Nucleic Acids Research. https://doi.org/10.1093/nar/gkad1251
Project description:Raw sequencing data used in the paper \"A biological-computational cell lineage discovery platform based on duplex MIPs\" (doi: https://doi.org/10.1101/191296) involving single cells from the YUCLAT melanoma patient and DU145 cell line which cultured in standart condition as recommend. The single cells were prepared by CellCellector for DU145 and FACS for YUCLAT, amplified by RepliG WGA kit . Targeting sequencing library is cronstructed with duplex Molecular Inversion Probes wtih the protocol as described in the paper. Illumina NextSeq is used to sequence these libraries.
Project description:Human telomerase reverse transcriptase (hTERT)-Immortalized cell line (T-HF) with or without DOX-induced KD of SSPR1 and SPT6 were infected with wild-type simplex virus 1 (HSV-1) strain F or with ICP22-null mutant at a multiplicity of infection (MOI) of 10. Omni-ATAC-seq libraries were prepared starting with 50,000 cells per condition following the protocol described by Corces, M., Trevino, A., Hamilton, E. et al. An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat Methods 14, 959–962 (2017). https://doi.org/10.1038/nmeth.4396
Project description:Human retinal organoids have been invaluable in vitro models of retinal development and disease. To investigate whether cell states and gene expression changes observed in human fetal cone development are accurately replicated in organoids, we produced H9 hESC-derived retinal organoids using two published methods (Kuwahara et al. 2015, Nat Comm 6, 6286, https://doi.org/10.1038/ncomms7286; Zhong et al. 2014, Nat Comm 5, 4047, https://doi.org/10.1038/ncomms5047). We then FACS-enriched cone and rod precursors and retinal progenitor cells every two weeks from 55-140 DIC, as well as at 225 DIC, and performed deep, full-length scRNA-seq chemistry. These data were used to identify maturation differences related to the organoid production method, identify aberrant cell populations or gene expression timing relative to human fetal retina, and define cone and rod photoreceptor trajectories in the retinal organoid setting.
Project description:Here we applied a novel approach to isolate nuclei from complex plant tissues (https://doi.org/10.1371/journal.pone.0251149), to dissect the transcriptome profiling of the hybrid poplar (Populus tremula × alba) vegetative shoot apex at single-cell resolution.
Project description:Identification of proteins in Candida albicans biofilm-derived extracellular vesicles. Raw data underlying data published in https://doi.org/10.3390/jof9111078.
Project description:Human telomerase reverse transcriptase (hTERT)-Immortalized cell line (T-HF) inducibly expressing ICP22 or ICP27 (doxycycline-induced) were analysed for downstream open chromation region (dOCR) formation. ICP22 or ICP27 expression was induced for 24 h prior to other treatments or harvest, respectively. ICP22 expressing cells were additionally treated with KCl (200 mM) for 2 h prior to harvest. OMNI-ATACseq libraries were prepared with 50000 cells/sample as described by Corces, M., Trevino, A., Hamilton, E. et al. An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat Methods 14, 959–962 (2017). https://doi.org/10.1038/nmeth.4396
Project description:E10.5 whole brain were isolated from WT and Piezo1-KO mice (C57BL/6J strain backgound) described in Ranade et al 2014. https://doi.org/10.1073/pnas.1409233111
