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DRX103878: Ion Torrent PGM sequencing of SAMD00098740
1 ION_TORRENT (Ion Torrent PGM) run: 2.7M spots, 389.9M bases, 252.6Mb downloads

Submitted by: KYOTO_SC
Study: Controlling nonlinear biological system based on network structure
show Abstracthide Abstract
We have developed a mathematical theory named Linkage Logic, by which key nodes both for observing and controlling dynamics are identified from network structures alone as feedback vertex sets. We applied our theory to a gene regulatory network for cell fate specification of seven tissues in ascidian embryo, and examined whether dynamics of this system is controllable by manipulating activities of key nodes.
Sample: RNA-sequencing sample of notochord_partial embryos_2
SAMD00098740 • DRS062854 • All experiments • All runs
Library:
Instrument: Ion Torrent PGM
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: RT-PCR
Layout: SINGLE
Construction protocol: All the protocols were followed as per manufacturer's instructions. Poly(A) RNA was prepared from the embryos using Dynabeads mRNA DIRECT Micro Kit (Thermo Fisher Scientific, USA), then mRNA was enriched from the poly(A) RNA using Low input RiboMinus Eukaryote System v2 (Thermo Fisher Scientific, USA). Quality control of purified RNA was then performed using the Agilent RNA 6000 Pico Kit with the Agilent 2100 Bioanalyzer instrument (Agilent Technologies, USA). Preparation of a whole-transcriptome cDNA library from purified mRNA was then performed using an Ion Total RNA-Seq Kit v2 (Thermo Fisher Scientific, USA). Quality control of the cDNA libraries was then performed using the Agilent High Sensitivity DNA Kit with the Agilent 2100 Bioanalyzer instrument (Agilent Technologies, USA).
Spot descriptor:
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Runs: 1 run, 2.7M spots, 389.9M bases, 252.6Mb
Run# of Spots# of BasesSizePublished
DRR1107892,732,273389.9M252.6Mb2018-05-27

ID:
5615622

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