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Comparison of the transcriptome of the conditional afpig-a mutant and the wild-type

ABSTRACT: In order to gain a better understanding of the mechanism of increased cell death triggered by deficient GPI anchoring, we constructed a whole genome microarray using the Agilent eArray 5.0 program.The chip specification is 8×15K. The genome sequences were downloaded from the following site:http://www.ncbi.nlm.nih.gov/genome?Db=genome&Cmd=Search&Term=txid330879[orgn]. Each gene was represented by one 60-nt oligonucleotide probe, and 358 genes out of the 9630 total were replicated 14 times.Using this microarray,we got 3274 genes which were induced or reduced at least 1.5 fold in the afpig-a mutant comparing to the wild-type.

ORGANISM(S): Aspergillus fumigatus

PROVIDER: GSE42499 | GEO | 2013/07/22

SECONDARY ACCESSION(S): PRJNA182158

REPOSITORIES: GEO

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Morphological differentiation and secondary metabolism responses of Streptomyces coelicolor A3(2) to Shenzhou-8 spaceflight based on comparative transcriptomics.

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comparison of the transcriptome of the conditional afpig-a mutant and the wild-type

Project description:In order to gain a better understanding of the mechanism of increased cell death triggered by deficient GPI anchoring, we constructed a whole genome microarray using the Agilent eArray 5.0 program.The chip specification is 8M-CM-^W15K. The genome sequences were downloaded from the following site:http://www.ncbi.nlm.nih.gov/genome?Db=genome&Cmd=Search&Term=txid330879[orgn]. Each gene was represented by one 60-nt oligonucleotide probe, and 358 genes out of the 9630 total were replicated 14 times.Using this microarray,we got 3274 genes which were induced or reduced at least 1.5 fold in the afpig-a mutant comparing to the wild-type. Mycelia of the afpig-a mutant and the wild-type were harvested from strains grown in liquid CM at 37M-BM-0C for 36h with shaking at 200 rpm and ground by hand.Total RNA was extracted to do the hybridization.cRNAs were labled with Cy3 NHS ester.afpig-a_37 was sample, afpig_37_1a,afpig_37_2a,afpig_37_3a and afpig_37_4a were biological repeats. w_37 was control,w_37_1a,w_37_2a,w_37_3a and w_37_4a were biological repeats.Four independent experiments were performed. Each time we got a set of differentilly expressed genes.Differentially expressed genes were selected with PM-bM-^IM-$0.05, FCM-bM-^IM-%1.5 by T-test methods using the independent four sets data.

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Project 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: http://www.ncbi.nlm.nih.gov/genome?Db =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 144h (6d) under simulated microgravity (by a rotating clinostat) and 1g control conditions respectively. Total RNA was extracted to conduct the microarray hybridization experiments for two color (Cy3/Cy5).

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