CK3 - SRA - NCBI

SRX318064: CK3
4 ILLUMINA (Illumina HiSeq 2000) runs: 13.2M spots, 2.4G bases, 1.4Gb downloads

Design: Given P1 strain important ecological role in the degrade of PAHs and with the availability of its full genome sequence, Cycloclasticus may now serve as a model organism to understand bacterial PAHs metabolism. Much more work is needed to understand the pathways that Cycloclasticus uses to catabolize PAH compounds. In addition to determining the metabolic and enzymatic capabilities, a number of specific questions intrinsically linked to PAHs utilization by this important group of PAH degraders, for example how PAHs enter the cell and which transport systems may be involved, how the cells physically interact with the hydrophobic substrate, whether and how they attach to it, and which molecular mechanisms allow the cells chemotactic to PAHs, how these bacteria regulate the pathways that carry out PAH degradation especially when high-molecular weight PAH compounds, etc. To obtain a still more comprehensive picture of PAHs utilization, and in particular to be able to look more closely into some of the aforementioned issues, we have now used RNA-seq technology to compare the transcriptional profile of P1 grown on naphthalene, phenathrene , pyrene, respectively, as a model PAH, as compared with pyruvate, one of the few non PAH substrates Cycloclasticus sp. P1 is able to use.

Submitted by: THIRD INSTITUTE OF OCEANOGRAPHY, SOA

Study: Cycloclasticus sp. P1 strain:P1 Transcriptome or Gene expression

PRJNA210343 • SRP026545 • All experiments • All runs

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Given P1 strain important ecological role in the degrade of PAHs and with the availability of its full genome sequence, Cycloclasticus may now serve as a model organism to understand bacterial PAHs metabolism. In addition to determining the metabolic and enzymatic capabilities, a number of specific questions intrinsically linked to PAHs utilization by this important group of PAH degraders, for example how PAHs enter the cell and which transport systems may be involved, how the cells physically interact with the hydrophobic substrate, whether and how they attach to it, and which molecular mechanisms allow the cells chemotactic to PAHs, how different pathways of different PAHs are regulated.

Sample: General Sample for Cycloclasticus sp. P1

SAMN02225187 • SRS455042 • All experiments • All runs

Organism: Cycloclasticus sp. P1

Library:

Name: CK3

Instrument: Illumina HiSeq 2000

Strategy: WGS

Source: TRANSCRIPTOMIC

Selection: RANDOM

Layout: PAIRED

Spot descriptor:

1 forward91 reverse

Runs: 4 runs, 13.2M spots, 2.4G bases, 1.4Gb

Run	# of Spots	# of Bases	Size	Published
SRR926181	3,403,278	612.6M	387.3Mb	2015-07-22
SRR926183	3,394,220	611M	386.7Mb	2015-07-22
SRR926186	3,235,320	582.4M	356Mb	2015-07-22
SRR926223	3,206,436	577.2M	352.6Mb	2015-07-22

ID:: 443599

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