The data set is provided without restrictions for research, educational or commercial purposes. The karyotype was evaluated as 46,XY with no apparent copy-number variation. 81% of all variants were found in two or three of the samples, whereas 19% were singletons. The raw number of single nucleotide variants were 3.3–4 million and the median variant read depth of GATK4-passed variants in three samples was 22, 18, and 10. Here, we provide a triplicate whole-genome paired-end sequencing data set, consisting of 1.38 billion raw sequencing reads derived from saliva DNA from a single anonymous male Caucasian donor, with the average sequencing depths aimed at 30x for two of the samples and 4x for a low-coverage sample. For LINSIGHT, the scores were downloaded. The rest of the columns are completely optional. In the case of CATO, the scores were extracted for the database version 1.0 using dbSNP 138 (Sherry et al., 2001). Raw download clone embed report print text 1.94 KB Known datasets: GATK bundle for human b37 reference wget -c. Publicly available data sets constitute a part of this strategy. Includes the UCSC-style hg18 reference along with all lifted over VCF files. However, the rapid and robust development of practical bioinformatics pipelines partly depends on convenient access to data for the testing of algorithms. Overall, we show that transcriptomic and epigenomic profiling can be used to place human pluripotent cultures along a developmental continuum and may inform their utility for clinical and research applications.Next-generation sequencing (NGS) of whole genomes has become more accessible to biomedical researchers as the sequencing price continues to drop, and more laboratories have NGS facilities or have access to a core facility. Although early NHSM cultures displayed naive characteristics, including greater proliferation and clonogenic potential compared with primed cultures, they drifted toward a more primed-like substate over time, including accumulation of genetic abnormalities. Through phenotypic, transcriptomic, and methylation profiling, we identified changes that arose during the transition to a primed substate. We derived four hESC lines in naive human stem cell medium (NHSM) and generated isogenic pairs of NHSM and primed cultures. Genetic instability and risk of tumorigenicity of primed hPSCs are well documented, but a systematic isogenic comparison between substates has not been performed. A detailed understanding of the developmental substates of human pluripotent stem cells (hPSCs) is needed to optimize their use in cell therapy and for modeling early development.
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