Sanger
Ontology highlight
ABSTRACT:
PROVIDER: EGAO00000001086 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:Organisation EGAO00000000080
| EGAO00000000080 | EGA
Project description:Abstract Summary In the era of next generation sequencing and beyond, the Sanger technique is still widely used for variant verification of inconclusive or ambiguous high-throughput sequencing results or as a low-cost molecular genetical analysis tool for single targets in many fields of study. Many analysis steps need time-consuming manual intervention. Therefore, we present here a pipeline-capable high-throughput solution with an optional Shiny web interface, that provides a binary mutation decision of hotspots together with plotted chromatograms including annotations via flat files. Availability and implementation SangeR is freely available at https://github.com/Neuropathology-Giessen/SangeR and https://hub.docker.com/repository/docker/kaischmid/sange_r Contact Kai.Schmid@patho.med.uni-giessen.de or Daniel.Amsel@patho.med.uni-giessen.de Supplementary information Supplementary data are available at Bioinformatics online.
| S-EPMC9710597 | biostudies-literature
Project description:Aselloidea isopods Sanger sequencing
| PRJEB30668 | ENA
Project description:Reprogramming of the gamete into a developmentally competent embryo identity is a fundamental aspect of preimplantation development. One of the most important processes of this reprogramming is the transcriptional awakening during embryonic genome activation (EGA), which robustly occurs in fertilized embryos but is defective in most somatic cell nuclear transfer (SCNT) embryos. However, little is known about the genome-wide underlying chromatin landscape during EGA in SCNT embryos and how it differs from a fertilized embryo. By profiling open chromatin genome-wide in both types of bovine embryos, we find that SCNT embryos fail to reprogram a subset of the EGA gene targets that are normally activated in fertilized embryos. Importantly, a small number of transcription factor (TF) motifs explain most chromatin regions that fail to open in SCNT embryos suggesting that over-expression of a limited number of TFs may provide more robust reprogramming. One such TF, the zygotically-expressed bovine gene DUXC which is a homologue of EGA factors DUX/DUX4 in mouse/human, is alone capable of activating ~84% of all EGA transcripts that fail to activate normally in SCNT embryos. Additionally, single-cell chromatin profiling revealed low intra-embryo heterogeneity but high inter-embryo heterogeneity in SCNT embryos and an uncoupling of cell division and open chromatin reprogramming during EGA. Surprisingly, our data also indicate that transcriptional defects may arise downstream of promoter chromatin opening in SCNT embryos, suggesting additional mechanistic insights into how and why transcription at EGA is dysregulated. We anticipate that our work will lead to altered SCNT protocols to increase the developmental competency of bovine SCNT embryos.
2025-06-01 | GSE236608 | GEO
Project description:Reprogramming of the gamete into a developmentally competent embryo identity is a fundamental aspect of preimplantation development. One of the most important processes of this reprogramming is the transcriptional awakening during embryonic genome activation (EGA), which robustly occurs in fertilized embryos but is defective in most somatic cell nuclear transfer (SCNT) embryos. However, little is known about the genome-wide underlying chromatin landscape during EGA in SCNT embryos and how it differs from a fertilized embryo. By profiling open chromatin genome-wide in both types of bovine embryos, we find that SCNT embryos fail to reprogram a subset of the EGA gene targets that are normally activated in fertilized embryos. Importantly, a small number of transcription factor (TF) motifs explain most chromatin regions that fail to open in SCNT embryos suggesting that over-expression of a limited number of TFs may provide more robust reprogramming. One such TF, the zygotically-expressed bovine gene DUXC which is a homologue of EGA factors DUX/DUX4 in mouse/human, is alone capable of activating ~84% of all EGA transcripts that fail to activate normally in SCNT embryos. Additionally, single-cell chromatin profiling revealed low intra-embryo heterogeneity but high inter-embryo heterogeneity in SCNT embryos and an uncoupling of cell division and open chromatin reprogramming during EGA. Surprisingly, our data also indicate that transcriptional defects may arise downstream of promoter chromatin opening in SCNT embryos, suggesting additional mechanistic insights into how and why transcription at EGA is dysregulated. We anticipate that our work will lead to altered SCNT protocols to increase the developmental competency of bovine SCNT embryos.
2025-06-01 | GSE236607 | GEO
Project description:Reprogramming of the gamete into a developmentally competent embryo identity is a fundamental aspect of preimplantation development. One of the most important processes of this reprogramming is the transcriptional awakening during embryonic genome activation (EGA), which robustly occurs in fertilized embryos but is defective in most somatic cell nuclear transfer (SCNT) embryos. However, little is known about the genome-wide underlying chromatin landscape during EGA in SCNT embryos and how it differs from a fertilized embryo. By profiling open chromatin genome-wide in both types of bovine embryos, we find that SCNT embryos fail to reprogram a subset of the EGA gene targets that are normally activated in fertilized embryos. Importantly, a small number of transcription factor (TF) motifs explain most chromatin regions that fail to open in SCNT embryos suggesting that over-expression of a limited number of TFs may provide more robust reprogramming. One such TF, the zygotically-expressed bovine gene DUXC which is a homologue of EGA factors DUX/DUX4 in mouse/human, is alone capable of activating ~84% of all EGA transcripts that fail to activate normally in SCNT embryos. Additionally, single-cell chromatin profiling revealed low intra-embryo heterogeneity but high inter-embryo heterogeneity in SCNT embryos and an uncoupling of cell division and open chromatin reprogramming during EGA. Surprisingly, our data also indicate that transcriptional defects may arise downstream of promoter chromatin opening in SCNT embryos, suggesting additional mechanistic insights into how and why transcription at EGA is dysregulated. We anticipate that our work will lead to altered SCNT protocols to increase the developmental competency of bovine SCNT embryos.
2025-06-01 | GSE236605 | GEO