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Multi-Targeted Priming For Genome-Wide Gene Expression Assays

ABSTRACT: This SuperSeries is composed of the following subset Series: GSE22658: Neurospora crassa early sexual development with MTP priming GSE22936: Saccharomyces cerevisiae grown in nitrogen depletion with MTP priming GSE22972: Neurospora crassa early sexual development with oligod(T) priming GSE22992: Saccharomyces cerevisiae grown in nitrogen depletion with oligodT priming Refer to individual Series

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Francesc Lopez

PROVIDER: E-GEOD-23003 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Multi-targeted priming for genome-wide gene expression assays.

Adomas Aleksandra B AB Lopez-Giraldez Francesc F Clark Travis A TA Wang Zheng Z Townsend Jeffrey P JP

BMC genomics 20100817

<h4>Background</h4>Complementary approaches to assaying global gene expression are needed to assess gene expression in regions that are poorly assayed by current methodologies. A key component of nearly all gene expression assays is the reverse transcription of transcribed sequences that has traditionally been performed by priming the poly-A tails on many of the transcribed genes in eukaryotes with oligo-dT, or by priming RNA indiscriminately with random hexamers. We designed an algorithm to fin ...[more]

PMID: 20716356

Similar Datasets

Saccharomyces cerevisiae grown in nitrogen depletion with oligodT priming

Project description:Multi-targeting priming (MTP) for genome-wide gene expression assays provides selective targeting of multiple sequences and counter-selection against undesirable sequences. We demonstrated superior performance of two MTPs compared to oligo-dT microarray profling and RNA tag sequencing the response of Saccharomyces cerevisiae to nitrogen deficiency and profiling Neurospora crassa early sexual development. Priming with MTPs in addition to oligo-dT resulted in higher sensitivity, a greater number of well-measured genes, more genes significantly differentially expressed, and a greater power to detect meager differences. Saccharomyces cerevisiae S288c was grown on two different media and two different primers were used for reverse transcription: oligo(dT) and Multi-Targeted Primer [MTP] protoperithecia oligo(dT)+ MTP (PP2) perithecia oligo(dT)+ MTP (PT2). Two biological replicates and dye swapping

2010-07-20 | E-GEOD-22992 | biostudies-arrayexpress

Neurospora crassa early sexual development with MTP priming

Project description:Multi-targeting priming (MTP) for genome-wide gene expression assays provides selective targeting of multiple sequences and counter-selection against undesirable sequences. We demonstrated superior performance of two MTPs compared to oligo-dT microarray profling and RNA tag sequencing the response of Saccharomyces cerevisiae to nitrogen deficiency and profiling Neurospora crassa early sexual development. Priming with MTPs in addition to oligo-dT resulted in higher sensitivity, a greater number of well-measured genes, more genes significantly differentially expressed, and a greater power to detect meager differences. Neurospora crassa mat A FGSC#2489 Three developmental stages and two different primers used for reverse transcription: mycelium oligo(dT) M1 protoperithecia oligo(dT) PP1 perithecia oligo(dT) PT1 mycelium oligo(dT)+ Multi-Targeted Primer [MTP] (M2) protoperithecia oligo(dT)+ MTP (PP2) perithecia oligo(dT)+ MTP (PT2)

2010-07-03 | E-GEOD-22658 | biostudies-arrayexpress

Neurospora crassa early sexual development with oligod(T) priming

Project description:Multi-targeting priming (MTP) for genome-wide gene expression assays provides selective targeting of multiple sequences and counter-selection against undesirable sequences. We demonstrated superior performance of two MTPs compared to oligo-dT microarray profling and RNA tag sequencing the response of Saccharomyces cerevisiae to nitrogen deficiency and profiling Neurospora crassa early sexual development. Priming with MTPs in addition to oligo-dT resulted in higher sensitivity, a greater number of well-measured genes, more genes significantly differentially expressed, and a greater power to detect meager differences. Neurospora crassa mat A FGSC#2489 2 developmental stages and oligo(dT) primers.

2010-07-17 | E-GEOD-22972 | biostudies-arrayexpress

Saccharomyces cerevisiae grown in nitrogen depletion with MTP priming

2010-07-17 | E-GEOD-22936 | biostudies-arrayexpress

Transcriptional profiling of Neurospora crassaM-NM-^T mak-2reveals that mitogenactivated protein kinase MAK-2 participates in the phosphate signaling pathway

Project description:Transcriptional profiling of Neurospora crassa M-bM-^HM-^Fmak-2 strain grown under phosphate-shortage were compared the transcription profile of the control strain grown in both low- and high-Pi cultures. The filamentous fungus Neurospora crassa provides an excellent model system for the study of molecular responses to ambient signaling in eukaryotic microorganisms. Inorganic phosphate is an essential growth-limiting nutrient in nature and is crucial in genetic information. Numerous ambient signals activate the recruitment of mitogen-activated protein kinase (MAPK) cascades. Thus, in an attempt to identify genes involved in metabolic responses to exogenous phosphate sensing and in the functioning of a mitogen-activated protein kinase coding gene (mak-2) in N. crassa, we performed microarray experiments with the strain carrying the mak-2 gene knockout (M-NM-^Tmak-2) grown under phosphate-shortage by comparing the transcription profile to that of the control strain grown in both low- and high-phosphate cultures. Here we provide evidence that the mak-2 gene is an element of the adaptive response to extracellular Pi changes revealing novel aspects of phosphorus-sensing network in N. crassa. Neurospora crassa wild type strain St.L.74-OR23-1VA (FGSC #2489) cultivated in low and high Pi cultures and M-bM-^HM-^Fmak-2 (FGSC #11482) mutant strain cultivated in low Pi cultures.

2013-07-31 | E-GEOD-41806 | biostudies-arrayexpress

Saccharomyces cerevisiae grown in nitrogen depletion with oligodT priming

2010-07-20 | GSE22992 | GEO

Neurospora crassa early sexual development with MTP priming

2010-07-03 | GSE22658 | GEO

Neurospora crassa early sexual development with oligod(T) priming

2010-07-17 | GSE22972 | GEO

Saccharomyces cerevisiae grown in nitrogen depletion with MTP priming

2010-07-17 | GSE22936 | GEO

Gene expression in a wild type strain (FGSC 2489) versus an Dime-2 strain (FGSC 17937) in Neurospora crassa during nitrogen starvation

Project description:The protein kinase Ime2 is known to have an important role in meiosis in the yeast Saccharomyces cerevisiae. However, the Neurospora crassa IME2 homolog functions in self/nonself recognition as well as in the development of fungal sexual structures called protoperithecia. In N. crassa, protoperithecia are induced upon nitrogen starvation. We were interested in gene expression differences between an ime-2 deletion strain and a wild type strain, and due to the role of ime-2 during sexual development, carried out these arrays on media that was lacking in nitrogen. There is one condition and three samples in this experiment (wild type and Dime-2 strains grown on minimal media lacking nitrogen), and dye swaps were performed

2012-02-18 | E-GEOD-35905 | biostudies-arrayexpress

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