Similar Datasets
Project description:We introduce FACIL (http://www.cmbi.ru.nl/FACIL), a fast, reliable tool to evaluate nucleic acid sequences for non-standard codes that detects alternative genetic codes even in species distantly related to known organisms. Results are visualized in a Genetic Code Logo. To illustrate the use of our method, we analysed several contigs derived from the mitochondrial genome of the foraminifer Globobulimina pseudospinescens. These are particularly challenging data, as the genome is highly fragmented and incomplete. Approximately 10,000 single-cell Globobulimina pseudospinescens organisms were isolated by hand from Gullmar Fjord Sweden sediment. After washing, total DNA was extracted and sequenced by Illumina sequencing. The reads were assembled using Edena. To illustrate the use of our method, we analysed several contigs derived from the mitochondrial genome of the foraminifer Globobulimina pseudospinescens, an organism without any sequenced relatives in the databases. These are particularly challenging data, as the genome is highly fragmented and incomplete. DNA isolated from approximately 10,000 single-cell Globobulimina pseudospinescens organisms
2011-06-20 | E-GEOD-26664 | biostudies-arrayexpress
Project description:DNA are packaged into nucleosomes and chromatin. We performed incomplete MNase digestion of chromatin to identify nucleosome-free regions that may indicate active promoters and regulatory regions. Additionally, HpaII digestion was performed which cleaves CCGG sites when the internal C remains unmodified. The hypomethylation state and nuclease sensitivity of the chromatin are indicators of transcription regulatory regions.
2015-02-25 | E-MTAB-1958 | biostudies-arrayexpress
Project description:MyoD is known to transdifferentiate fibroblasts into muscle-like cells. Despite phenotypic resemblance and expression of myogenic marker genes in transdifferentiated cells, our global gene expression data suggests that ~100 genes, many involved in muscle development and function, remain non-reprogrammed. To understand this incomplete reprogramming, we characterized genome-wide chromatin accessibility and MyoD binding in human primary myoblasts and in MyoD-induced skin fibroblast cells. Our analyses revealed thousands of sites with incomplete chromatin reprogramming.Combined analyses of gene expression and epigenetic profiles revealed that many myogenic genes not upregulated during the transdifferentiation process have undergone MyoD-dependent chromatin remodeling, but to a significantly lower extent than reprogrammed genes. Our findings suggest that incomplete MyoD-induced transdifferentiation is due to chromatin-remodeling deficiencies, and that additional factors are required to transdifferentiate cells into a state more similar to myoblasts.
2017-01-07 | GSE93257 | GEO
Project description:MyoD is known to transdifferentiate fibroblasts into muscle-like cells. Despite phenotypic resemblance and expression of myogenic marker genes in transdifferentiated cells, our global gene expression data suggests that ~100 genes, many involved in muscle development and function, remain non-reprogrammed. To understand this incomplete reprogramming, we characterized genome-wide chromatin accessibility and MyoD binding in human primary myoblasts and in MyoD-induced skin fibroblast cells. Our analyses revealed thousands of sites with incomplete chromatin reprogramming.Combined analyses of gene expression and epigenetic profiles revealed that many myogenic genes not upregulated during the transdifferentiation process have undergone MyoD-dependent chromatin remodeling, but to a significantly lower extent than reprogrammed genes. Our findings suggest that incomplete MyoD-induced transdifferentiation is due to chromatin-remodeling deficiencies, and that additional factors are required to transdifferentiate cells into a state more similar to myoblasts.
2017-01-07 | GSE93258 | GEO
Project description:We performed WGBS analyses on 6 human fetal samples at 53-137 days of development, 4 female and 2 male. We show that methylation reprogramming in the human germline is global yet incomplete with exons, 3’UTRs and human-specific transposons remaining methylated. Whole Genome Bisulfite-Seq of cKIT+ cells analyzed from 4 biological samples for fetal ovaries from 57-113 days of development and 2 samples for fetal testes at 59 and 137 days of development.
2015-05-28 | E-GEOD-63393 | biostudies-arrayexpress
Project description:Target sequencing of incomplete TRB DD and DJ rearrangements
| PRJNA952099 | ENA
Project description:Following European guidelines patients undergoing colonoscopy in one of Odense University Hospitals units will now be offered a colon capsule endoscopy (CCE) in case of incomplete examinations. Patients formerly referred to colonoscopy in general anesthesia or patients who decline colonoscopy after having completed bowel preparation will also be offered a CCE. In our department we have conducted a comparison study documenting that the sensitivity of CCE is superior to CT colonography in both polyps >9 mm and polyps >5 mm, which is also supported by an Italian study. The safety and completion rate of CCE following incomplete colonoscopy is confirmed by several studies including one multicenter study and the completion rate is not significantly lower compared to other patient groups. In an incomplete colonoscopy it is always the most oral part of the colon which is not visualized, whereas in CCE, an incomplete investigation will most often have visualized the oral part. By combining incomplete colonoscopy results and incomplete CCE results we can identify patients who have had a complete colon investigation although both investigations were incomplete.
Aim: to investigate the quality of CCE and the completion rate in patients who have undergone an incomplete colonoscopy, have completed bowel preparation but declines colonoscopy or have been referred to colonoscopy in general anesthesia.
| 2333052 | ecrin-mdr-crc