Ontology highlight
ABSTRACT:
PROVIDER: PRJNA507762 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Total of 675 porcine miRNA candidates datasets revealed by 100% aligment homologs and review literatures publication. Probe-sets were screened, analysed for differential expression between different breeds (german landrace and pietrain) at different stages of development (63, 91 dpc and adult stage)
2013-01-19 | GSE34213 | GEO
Project description:see publication
| PRJEB20259 | ENA
Project description:This study focuses on epigenetic reprogramming in the mouse germ line: DNA methylation marks, including those of imprinted genes, are thought to be erased between E11.5 and E13.5 in primordial germ cells (PGCs), which are the direct progenitors of sperm or oocyte. DNA methylation patterns are then re-established during the de novo methylation phase in the male germ line several days later (around E15.5) and in the female germ line after birth during adult life. Epigenetic reprogramming in PGCs is poorly understood mainly because of the technical challenges that arise from very low cell numbers in the embryo. The aim of this study is to create genome-wide maps of DNA methylation patterns of male and female PGCs at crucial time points during epigenetic reprogramming and to investigate the changes in those profiles on a single-gene level. We have already successfully prepared and sequenced the first set of BS-Seq libraries of PGCs with Illumina's GAIIx platform. From this, we gained significant insight into the global DNA methylation levels and methylation patterns over multy-copy-loci such as repeat elements. In order further enhance our analysis and finish this project for publication, it is crucial to increase the genomic coverage of our datasets. This will also allow us to link the BS-Seq data with other MeDIP-Seq and RNA-Seq datasets that have already been created in this study.Protocol: Input DNA was sonicated using a Bioruptor UCD-200 (Diagenode) to a final size distribution of 300bp 1000bp. End-repair and A-tailing were performed with the NEBNext DNA Sample Prep Master Mix Set 1. Illuminas Early Access Methylation Adaptor Oligo Kit was used for the adapter ligation. The adapter-ligated DNA was treated with sodium-bisulfite using the Imprint DNA Modification Kit from Sigma-Aldrich according to the manufacturers instructions for the two-step protocol. After the clean up, the bisulfite-treated DNA was amplified using PfuTurbo Cx Hotstart DNA Polymerase from Agilent with 18 cycles of amplification. The entire PCR reaction was run on a 1.5% agarose TBE gel and size selection was performed for DNA fragments between 200bp 250bp. DNA from the excised gel piece was purified with the Qiagen Gel Extraction Kit.This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
2013-01-07 | E-ERAD-48 | biostudies-arrayexpress
Project description:human induced Pluripotent Stem cells (hiPSc) and their differentiated progeny have great potential for modelling disease. To realise this potential, robust protocols need to be developed for deriving authentic differentiated cell lineages and these lineages need to be rigorously characterised. We have generated hiPSc using retrovirus-mediated delivery of reprogramming factors, and have used them for assessing the efficiency of a defined protocol for differentiation to monocytes and macrophages. hiPSc lines have been screened using SNP array to assess chromosomal stability, and validation of the pluripotency of the hiPSc lines is provided by Pluritest assessment of transcriptome datasets. van Wilgenburg B, Browne C and Cowley SA, submitted for publication
2013-03-26 | GSE45471 | GEO
Project description:Total of 675 porcine miRNA candidates datasets revealed by 100% aligment homologs and review literatures publication. Probe-sets were screened, analysed for differential expression between different breeds (german landrace and pietrain) at different stages of development (63, 91 dpc and adult stage) microRNAs of skeletal muscle from german landrace and pietrain at 63, 91 dpc and adult stages were hybridized to Affymetrix GeneChip miRNA arrays.
2013-01-19 | E-GEOD-34213 | biostudies-arrayexpress
Project description:We have generated human induced Pluripotent Stem cells (hiPSc) from Parkinson's Disease patients, using retrovirus-mediated delivery of reprogramming factors. hiPSc lines have been screened using SNP array to assess chromosomal stability (alongside the fibroblast lines from which they derived), and validation of the pluripotency of the hiPSc lines is provided by Pluritest assessment of transcriptome datasets, prior to differentiation to dopaminergic neuronal clutures and downstream functional assays. Fernandes H.J.R., Hartfield E.M., Badger J., Christian H. C., Emmanoulidou E., Vowles J., Evetts S., Vekrellis K., Talbot K., Hu M.T., James W., Cowley S.A., and Wade-Martins, R. Heterozygous glucocerebrosidase mutations in Parkinson's increase autophagic demand, but decrease capacity, in induced pluripotent stem cell-derived dopaminergic neuronal cultures. submitted for publication
2013-12-18 | GSE53425 | GEO