Locke2006_CircadianClock_tanh - PLM_10, version 1, SIMPLIFIED
Ontology highlight
ABSTRACT:
SUBMITTER: BioData SynthSys
PROVIDER: 474 | FAIRDOMHub | 2019-01-22
REPOSITORIES: FAIRDOMHub
Similar Datasets
Project description:Miscanthus sacchariflorus WGA version 2
| PRJEB41362 | ENA
Project description:Miscanthus sacchariflorus WGA version 2
| PRJEB41359 | ENA
Project description:Chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) and its ultra-high resolution cousin ChIP-exo are methods that identify where proteins bind along any genome in vivo. ChIP-exo achieves near-base pair resolution by creating exonuclease stop sites just 5’ to where formaldehyde-induced protein-DNA cross-links occur. Whereas construction of ChIP genomic libraries is straightforward and widely adopted for ChIP-seq, ChIP-exo is technically more involved which has resulted in limited adoption. Here we describe multiple ChIP-exo protocols, each with use-specific advantages and limitations. The new versions are greatly simplified through removal of multiple enzymatic steps. This is achieved in part through the use of Tn5 tagmentation and/or single-stranded DNA ligation. The result is greater library yields, lower processing time, and lower cost. A similar streamlined approach was developed for ChIP-seq, called ChIP-seq 1-step, where library construction is achieved in one-step.
2018-08-17 | GSE110681 | GEO
Project description:Comparison of published protocol (Abud et al. Neuron 2016) to simplified method of microglial differentiation which does not require hypoxia or FACS. We show each method produced highly similar microglia.
2018-12-05 | GSE117829 | GEO
Project description:Chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) and its ultra-high resolution cousin ChIP-exo are methods that identify where proteins bind along any genome in vivo. ChIP-exo achieves near-base pair resolution by creating exonuclease stop sites just 5’ to where formaldehyde-induced protein-DNA cross-links occur. Whereas construction of ChIP genomic libraries is straightforward and widely adopted for ChIP-seq, ChIP-exo is technically more involved which has resulted in limited adoption. Here we describe multiple ChIP-exo protocols, each with use-specific advantages and limitations. The new versions are greatly simplified through removal of multiple enzymatic steps. This is achieved in part through the use of Tn5 tagmentation and/or single-stranded DNA ligation. The result is greater library yields, lower processing time, and lower cost. A similar streamlined approach was developed for ChIP-seq, called ChIP-seq 1-step, where library construction is achieved in one-step.
2018-08-17 | GSE114606 | GEO
Project description:Generating primordial germ cells (PGCs) from human pluripotent stem cells (hPSCs) advances studies of human reproduction and development of infertility treatments, but currently entails complex 3D aggregates. Here we develop a simplified, monolayer method to differentiate hPSCs into PGCs within 3.5 days, with higher efficiencies and improved consistency across multiple hPSC lines. We used our simplified differentiation platform and single-cell RNA-sequencing to uncover new insights into PGC specification. Transient WNT activation for 12 hours followed by WNT inhibition specified PGCs; by contrast, sustained WNT instead induced primitive streak. Thus, somatic (primitive streak) and PGCs are related—yet distinct—lineages segregated by temporally-dynamic signaling. Pluripotency factors are continuously expressed during the transition from pluripotency to posterior epiblast to PGCs, thus bridging pluripotent and germline states. Finally, hPSC-derived PGCs can be easily purified by virtue of their CXCR4+PDGFRA-GARP- surface-marker profile and single-cell RNA-sequencing reveals that they harbor strong transcriptional similarities with fetal PGCs. We report single-cell RNA-sequencing data of in vitro differentiated hPSCs (H9) cells into human Primordial germ cell-like cells (PGCLCs), profiled at different time-points of differentiation - Day 0 (H9), D0.5, D3.5 (sorted) and D3.5 unsorted population and a negative control of hPSCs differentiated into definitive endoderm (DE) (using the protocol described in (Loh et al., 2014, Cell Stem Cell 14, 237-252)). The data comprises of 5 single-cell RNA-sequencing libraries (H9, D0.5, D3.5S, D3.5U and DE) generated using 10xChromium Single cell RNA-expression platform and 10xGenomics Chromium version 2 chemistry with a targeted capture of ~6000 cells each. Single cell libraries were sequenced on Illumina HiSeq4000 platform as paired-end 150bp reads.
2023-08-09 | GSE157475 | GEO
Project description:Generating primordial germ cells (PGCs) from human pluripotent stem cells (hPSCs) advances studies of human reproduction and development of infertility treatments, but currently entails complex 3D aggregates. Here we develop a simplified, monolayer method to differentiate hPSCs into PGCs within 3.5 days, with higher efficiencies and improved consistency across multiple hPSC lines. We used our simplified differentiation platform, bulk RNA-seq and single-cell RNA-sequencing to uncover new insights into PGC specification. Transient WNT activation for 12 hours followed by WNT inhibition specified PGCs; by contrast, sustained WNT instead induced primitive streak. Thus, somatic (primitive streak) and PGCs are related—yet distinct—lineages segregated by temporally-dynamic signaling. Pluripotency factors are continuously expressed during the transition from pluripotency to posterior epiblast to PGCs, thus bridging pluripotent and germline states. Finally, hPSC-derived PGCs can be easily purified by virtue of their CXCR4+PDGFRA-GARP- surface-marker profile and single-cell RNA-sequencing reveals that they harbor strong transcriptional similarities with fetal PGCs. We report single-cell RNA-sequencing data of in vitro differentiated hPSCs (H9) cells into human Primordial germ cell-like cells (PGCLCs), profiled at different time-points of differentiation - Day 0 (H9), D0.5, D3.5 (sorted) and D3.5 unsorted population and a negative control of hPSCs differentiated into definitive endoderm (DE) (using the protocol described in (Loh et al., 2014, Cell Stem Cell 14, 237-252)). The data comprises of 5 single-cell RNA-sequencing libraries (H9, D0.5, D3.5S, D3.5U and DE) generated using 10xChromium Single cell RNA-expression platform and 10xGenomics Chromium version 2 chemistry with a targeted capture of ~6000 cells each. Single cell libraries were sequenced on Illumina HiSeq4000 platform as paired-end 150bp reads. Bulk RNA seq libraries were sequnced as paired-end reads.
2023-08-09 | GSE210711 | GEO