Nematostella Embryonic Transcriptome
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RNA-Seq was performed on Nematostella Embryos at 5 timepoints during early development: 0hrs, 6hrs, 12hrs, 18hrs, 24hrs after fertilization. Embryos were harvested, lysed and mRNAs were selected using Dynabeads. Directional sequencing libraries were constructed using the ScriptSeq kit from Epicentre. A control RNA set from the National Institute of Standards and Technology (NIST) were spiked-into the library preparation. Libraries were sequenced using the Illumina HiSeq 1000, version 3 chemistry, 100bp paired-end reads and produced over 200million reads. The reads were quality controlled filtered and assembled using the Trinity Assembler. This database contains the raw read files and the assembled Transcriptome.
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A quantitative reference transcriptome for Nematostella vectensis early embryonic development : a pipeline for de novo assembly in emerging model systems Tulin, Sarah; Aguiar, Derek; Istrail, Sorin; Smith, Joel (BioMed Central, 2013-06-03)The de novo assembly of transcriptomes from short shotgun sequences raises challenges due to random and non-random sequencing biases and inherent transcript complexity. We sought to define a pipeline for de novo transcriptome ...
Morphometric analysis of human embryonic stem cell-derived ventricular cardiomyocytes : determining the maturation state of a population by quantifying parameters in individual cells Chan, Harvey Y. S.; Keung, Wendy; Li, Ronald A.; Miller, Andrew L.; Webb, Sarah E. (Hindawi Publishing Corp, 2015-07)Quantitative methods were established to determine the level of maturation of human embryonic stem cell-derived ventricular cardiomyocytes (hESC-vCMs) that were treated with different metabolic stimulants (i.e., isoproterenol ...
Expression and reconstitution of the bioluminescent Ca2+ reporter aequorin in human embryonic stem cells, and exploration of the presence of functional IP3 and ryanodine receptors during the early stages of their differentiation into cardiomyocytes Chan, Harvey Y. S.; Cheung, Man Chun; Gao, Yi; Miller, Andrew L.; Webb, Sarah E. (Springer, 2016-07-19)In order to develop a novel method of visualizing possible Ca2+ signaling during the early differentiation of hESCs into cardiomyocytes and avoid some of the inherent problems associated with using fluorescent reporters, ...