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Title: Morphological differentiation and secondary metabolism responses of Streptomyces coelicolor A3(2) to simulated microgravity based on comparative transcriptomics      
dateReleased:
02-01-2014
description:
In order to gain a better understanding of the effects of Streptomyces coelicolor A3(2) wild type strain exposed to simulated microgravity condition by clinorotation, we constructed a whole genome microarray to screen simulated microgravity sensitive genes using the Agilent eArray 5.0 program. The genechip was custom designed according to the manufacturer’s recommendations (Agilent, 8*15K). The genome sequences were downloaded from: =genome&Cmd = Search&Term = NC_003888, NC_003903.1, NC_003904.1. Each gene was represented by one 60-nt oligonucleotide probe, and 680 genes associated with morphological differentiation and secondary metabolism out of the total 8116 genes were replicated 9 times each. Cells of Streptomyces coelicolor A3(2) wild type strain were harvested from the colonies grown in JCM42 agar medium at 28°C for 96h (4d) under simulated microgravity and 1g control conditions. Total RNA was extracted to conduct the microarray hybridization experiments. Three independent experiments were performed in which ASM_1A, ASM_2A, ASM_3A were the test group samples and ANG_1A, ANG_2A, ANG_3A were the control group samples. Differentially expressed genes were selected with P<0.05, FC≥2.0 by T-test methods using the independent three sets data.
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-GEOD-53748
refinement:
raw
alternateIdentifiers:
53748
keywords:
functional genomics
dateModified:
06-03-2014
availability:
available
types:
gene expression
name:
Streptomyces coelicolor A3(2)
ID:
A-GEOD-18103
name:
Agilent-031115 Streptomyces coelicolor A3(2) 8X15K Microarray (Probe Name version)
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-53748/E-GEOD-53748.raw.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-53748/E-GEOD-53748.processed.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE53748
storedIn:
Gene Expression Omnibus
qualifier:
not compressed
format:
HTML
accessType:
landing page
primary:
true
authentication:
none
authorization:
none
abbreviation:
EBI
homePage: http://www.ebi.ac.uk/
ID:
SCR:004727
name:
European Bioinformatics Institute
homePage: https://www.ebi.ac.uk/arrayexpress/
ID:
SCR:002964
name:
ArrayExpress

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